From 30a0735ad38a6fce25a49bb1c5992e11e3ecd065 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 22 Oct 2026 09:46:11 +0200
Subject: [PATCH 1/7] Add `references` to the per-problem metadata

Add a required `references` list to `ProblemMetadata`: the publications
a problem is based on, each with its `doi` and a `bibtex` entry. The
first entry is the main publication, its BibTeX key is the problem ID
(checked by `bmp-check-metadata`). `get_bibtex()` aggregates the main
publications' entries; the site build writes them to `references.bib`.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 .github/pull_request_template.md              |  2 +-
 CONTRIBUTING.md                               | 21 +++--
 src/python/benchmark_models_petab/__init__.py |  2 +-
 .../benchmark_models_petab/_site/build.py     |  9 ++-
 .../_site/templates/index.html.j2             |  2 +
 .../benchmark_models_petab/check_metadata.py  |  9 ++-
 src/python/benchmark_models_petab/metadata.py | 71 +++++++++++++++-
 src/python/benchmark_models_petab/overview.py |  9 ++-
 .../schemas/metadata.schema.json              | 37 ++++++++-
 src/python/test/test_metadata.py              | 80 +++++++++++++++----
 src/python/test/test_overview.py              |  1 +
 11 files changed, 205 insertions(+), 38 deletions(-)

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index e5a511c..ac26c2d 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -21,7 +21,7 @@
   - [ ] A visualization table is included, that can be used with the simulated data to reproduce figures from the original publication
   - [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`)
   - [ ] Labels (e.g. `parameterName` in the parameter table or `xLabel` in the visualization table) encode special characters with tex-style strings instead of unicode, e.g. use `H$_2$O` for water.
-- [ ] `problems/<ProblemID>/metadata.yaml` contains a single-sentence `short_description` of the problem and passes `bmp-check-metadata`
+- [ ] `problems/<ProblemID>/metadata.yaml` contains a single-sentence `short_description` of the problem and the `references` (DOI and BibTeX entry, key = problem ID) of the original publication(s), and passes `bmp-check-metadata`
 - [ ] The PEtab problem author(s) are assigned to the GitHub issue
 - [ ] The README has been updated with `bmp-create-overview  --update` (requires `pip install -e src/python` from the repository root)
   - [ ] The new PEtab problem row in the generated table has the correct reference (and other entries)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 594c32f..6f8b79d 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -7,17 +7,16 @@ Each problem lives under `problems/<ProblemID>/`, with at least one of `v1/`/`v2
   `conditions.tsv`, `measurements.tsv`, `observables.tsv`, `parameters.tsv`, and optionally
   `simulations.tsv` and `visualizations.tsv`.
 - `v2/` holds the same problem in PEtab v2 format.
-- `metadata.yaml` contains version-independent metadata. Currently, this is a single-sentence
-  `short_description` of the problem, stating the type of model (e.g., biochemical reaction network,
-  compartmental epidemiological model), the biological system, and, where informative, the data.
-  For example:
-  ```yaml
-  short_description: Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data.
-  ```
-  The file is validated against the `ProblemMetadata` model in
-  [`metadata.py`](src/python/benchmark_models_petab/metadata.py)
-  (check with `bmp-check-metadata`); the corresponding JSON schema is
-  [`metadata.schema.json`](src/python/benchmark_models_petab/schemas/metadata.schema.json).
+- `metadata.yaml` contains version-independent metadata:
+  - `short_description`: a single sentence stating the type of model (e.g., biochemical reaction
+    network, compartmental epidemiological model), the biological system, and, where informative,
+    the data.
+  - `references`: the publications the problem is based on, each with its `doi` and a `bibtex`
+    entry (one field per line, including a matching `doi` field). The first entry is the main
+    publication; its BibTeX key is the problem ID.
+
+  See [`problems/Boehm_JProteomeRes2014/metadata.yaml`](problems/Boehm_JProteomeRes2014/metadata.yaml)
+  for an example.
 - `resources/` (optional) holds anything else related to the problem that isn't part of the
   PEtab files themselves (e.g. raw data, scripts, notebooks, figures). There's no prescribed
   structure — organize it however fits your problem.
diff --git a/src/python/benchmark_models_petab/__init__.py b/src/python/benchmark_models_petab/__init__.py
index c901db2..d4faeea 100644
--- a/src/python/benchmark_models_petab/__init__.py
+++ b/src/python/benchmark_models_petab/__init__.py
@@ -7,7 +7,7 @@
 from . import v1, v2
 from .v1 import get_problem, get_problem_yaml_path, get_simulation_df
 from .C import MODEL_DIRS, MODELS, MODELS_DIR
-from .metadata import ProblemMetadata, get_metadata
+from .metadata import ProblemMetadata, get_bibtex, get_metadata
 from .overview import get_overview_df
 from importlib.metadata import PackageNotFoundError, version
 
diff --git a/src/python/benchmark_models_petab/_site/build.py b/src/python/benchmark_models_petab/_site/build.py
index 07f8dc0..2b41b50 100644
--- a/src/python/benchmark_models_petab/_site/build.py
+++ b/src/python/benchmark_models_petab/_site/build.py
@@ -14,7 +14,7 @@
     V1_DIRNAME,
     V2_DIRNAME,
 )
-from ..metadata import get_metadata
+from ..metadata import get_bibtex, get_metadata
 
 REPO_URL = f"https://github.com/{GITHUB_REPO}"
 LOGO_URL = (
@@ -22,6 +22,8 @@
     f"/{GITHUB_DEFAULT_BRANCH}/gfx/logo.svg"
 )
 CONTRIBUTING_URL = f"{REPO_URL}/blob/{GITHUB_DEFAULT_BRANCH}/CONTRIBUTING.md"
+#: File name of the BibTeX entries of all problems, next to the page.
+BIBTEX_FILENAME = "references.bib"
 
 #: Rendering of the columns that are not plain text, by column name.
 #:  Other columns of integer dtype are rendered as numbers.
@@ -170,6 +172,9 @@ def get_summary_tiles(v1_df: pd.DataFrame, v2_df: pd.DataFrame) -> list:
 def create_overview_page(dest: Path) -> None:
     """Create the HTML page with the v1 and v2 overview tables.
 
+    The BibTeX entries of all problems' main publications are written to
+    `BIBTEX_FILENAME` in the same directory, linked from the page.
+
     :param dest: Path to the output HTML file.
     """
     from jinja2 import Environment, PackageLoader, select_autoescape
@@ -184,6 +189,7 @@ def create_overview_page(dest: Path) -> None:
         repo_url=REPO_URL,
         logo_url=LOGO_URL,
         contributing_url=CONTRIBUTING_URL,
+        bibtex_url=BIBTEX_FILENAME,
         summary_tiles=get_summary_tiles(v1_df, v2_df),
         tables={
             "v2": get_table(
@@ -202,3 +208,4 @@ def create_overview_page(dest: Path) -> None:
     )
     dest.parent.mkdir(parents=True, exist_ok=True)
     dest.write_text(html, encoding="utf-8")
+    (dest.parent / BIBTEX_FILENAME).write_text(get_bibtex(), encoding="utf-8")
diff --git a/src/python/benchmark_models_petab/_site/templates/index.html.j2 b/src/python/benchmark_models_petab/_site/templates/index.html.j2
index 278ddd8..9c5a6be 100644
--- a/src/python/benchmark_models_petab/_site/templates/index.html.j2
+++ b/src/python/benchmark_models_petab/_site/templates/index.html.j2
@@ -361,6 +361,8 @@ footer {
   <code>&gt;10</code>, <code>&lt;=5</code>, or <code>10-100</code>.
   Click a table and press <kbd>Ctrl</kbd>+<kbd>C</kbd> to copy its visible
   rows, including the column headers.
+  BibTeX entries of the publications the problems are based on:
+  <a href="{{ bibtex_url }}" download>{{ bibtex_url }}</a>.
 </p>
 <nav>
   <a href="#v2">PEtab v2</a>
diff --git a/src/python/benchmark_models_petab/check_metadata.py b/src/python/benchmark_models_petab/check_metadata.py
index 7d0ba68..7a6407d 100644
--- a/src/python/benchmark_models_petab/check_metadata.py
+++ b/src/python/benchmark_models_petab/check_metadata.py
@@ -21,7 +21,7 @@ def check_metadata_file(path: Path) -> list[str]:
         return [f"Missing metadata file `{path.name}`."]
 
     try:
-        ProblemMetadata.from_yaml(path)
+        metadata = ProblemMetadata.from_yaml(path)
     except yaml.YAMLError as e:
         return [f"Invalid YAML: {e}"]
     except pydantic.ValidationError as e:
@@ -30,6 +30,13 @@ def check_metadata_file(path: Path) -> list[str]:
             for error in e.errors()
         ]
 
+    problem_id = path.parent.name
+    if (key := metadata.references[0].bibtex_key) != problem_id:
+        return [
+            f"references/0/bibtex: BibTeX key `{key}` does not match the "
+            f"problem ID `{problem_id}`."
+        ]
+
     return []
 
 
diff --git a/src/python/benchmark_models_petab/metadata.py b/src/python/benchmark_models_petab/metadata.py
index f85e540..c378fe4 100644
--- a/src/python/benchmark_models_petab/metadata.py
+++ b/src/python/benchmark_models_petab/metadata.py
@@ -1,17 +1,58 @@
 """Version-independent per-problem metadata."""
 
 import json
+import re
 from importlib.resources import files
 from pathlib import Path
 from typing import Any
 
 import yaml
-from pydantic import BaseModel, ConfigDict, Field
+from pydantic import BaseModel, ConfigDict, Field, model_validator
 
-from .C import METADATA_FILENAME, MODELS_DIR
+from .C import METADATA_FILENAME, MODELS, MODELS_DIR
 
 METADATA_SCHEMA_FILENAME = "metadata.schema.json"
 
+_BIBTEX_ENTRY_RE = re.compile(r"\A@[a-zA-Z]+\{([^\s,{}]+),\n.*\n\}\n?\Z", re.S)
+_BIBTEX_DOI_RE = re.compile(r"^\s*doi\s*=\s*\{([^{}]*)\},?$", re.M | re.I)
+
+
+class Reference(BaseModel):
+    """A publication a benchmark problem is based on."""
+
+    model_config = ConfigDict(extra="forbid")
+
+    doi: str = Field(
+        pattern=r"^10\.\d{4,9}/\S+$",
+        description="DOI of the publication, without URL prefix.",
+    )
+    bibtex: str = Field(
+        description=(
+            "BibTeX entry of the publication, one field per line, "
+            "including a `doi` field matching `doi`."
+        ),
+    )
+
+    @model_validator(mode="after")
+    def _check_bibtex(self) -> "Reference":
+        if not _BIBTEX_ENTRY_RE.match(self.bibtex):
+            raise ValueError(
+                "`bibtex` must be a single BibTeX entry, "
+                "starting with `@<type>{<key>,` and ending with `}`."
+            )
+        dois = _BIBTEX_DOI_RE.findall(self.bibtex)
+        if [doi.lower() for doi in dois] != [self.doi.lower()]:
+            raise ValueError(
+                f"`bibtex` must contain a single `doi` field matching "
+                f"`{self.doi}`, found {dois}."
+            )
+        return self
+
+    @property
+    def bibtex_key(self) -> str:
+        """The citation key of the BibTeX entry."""
+        return _BIBTEX_ENTRY_RE.match(self.bibtex).group(1)
+
 
 class ProblemMetadata(BaseModel):
     """Version-independent metadata of a benchmark problem."""
@@ -37,6 +78,14 @@ class ProblemMetadata(BaseModel):
         ),
     )
 
+    references: list[Reference] = Field(
+        min_length=1,
+        description=(
+            "Publications the problem is based on. The first entry is the "
+            "main publication; its BibTeX key is the problem ID."
+        ),
+    )
+
     @classmethod
     def from_yaml(cls, path: str | Path) -> "ProblemMetadata":
         """Load and validate a metadata file.
@@ -88,6 +137,24 @@ def get_metadata(id_: str) -> ProblemMetadata:
     return ProblemMetadata.from_yaml(path)
 
 
+def get_bibtex(ids: list[str] | None = None) -> str:
+    """Get the BibTeX entries of the main publications of the given problems.
+
+    Parameters
+    ----------
+    ids: Problem names, as in `benchmark_models_petab.MODELS`.
+        Defaults to all problems.
+
+    Returns
+    -------
+    The BibTeX entries, separated by blank lines.
+    """
+    return "\n".join(
+        get_metadata(id_).references[0].bibtex.rstrip("\n") + "\n"
+        for id_ in (MODELS if ids is None else ids)
+    )
+
+
 def write_metadata_schema(path: str | Path | None = None) -> None:
     """Write the JSON schema for the metadata files.
 
diff --git a/src/python/benchmark_models_petab/overview.py b/src/python/benchmark_models_petab/overview.py
index f1fb4d6..6316857 100644
--- a/src/python/benchmark_models_petab/overview.py
+++ b/src/python/benchmark_models_petab/overview.py
@@ -348,8 +348,8 @@ def get_overview_df() -> pd.DataFrame:
 def get_readme_table() -> str:
     """Get the version-independent overview table for the README.
 
-    Lists each problem's short description and links to its PEtab v1 and
-    v2 encodings, where available.
+    Lists each problem's short description, links to its PEtab v1 and
+    v2 encodings, where available, and the DOI of its main publication.
     """
     rows = []
     for petab_problem_id in MODELS:
@@ -364,7 +364,10 @@ def get_readme_table() -> str:
                 if petab_problem_id in version.MODELS
                 else ""
             )
-        row["Description"] = get_metadata(petab_problem_id).short_description
+        metadata = get_metadata(petab_problem_id)
+        doi = metadata.references[0].doi
+        row["Reference"] = f"[{doi}](https://doi.org/{doi})"
+        row["Description"] = metadata.short_description
         rows.append(row)
     return pd.DataFrame(rows).to_markdown(index=False)
 
diff --git a/src/python/benchmark_models_petab/schemas/metadata.schema.json b/src/python/benchmark_models_petab/schemas/metadata.schema.json
index 95d89fd..4c11ca2 100644
--- a/src/python/benchmark_models_petab/schemas/metadata.schema.json
+++ b/src/python/benchmark_models_petab/schemas/metadata.schema.json
@@ -1,4 +1,29 @@
 {
+  "$defs": {
+    "Reference": {
+      "additionalProperties": false,
+      "description": "A publication a benchmark problem is based on.",
+      "properties": {
+        "doi": {
+          "description": "DOI of the publication, without URL prefix.",
+          "pattern": "^10\\.\\d{4,9}/\\S+$",
+          "title": "Doi",
+          "type": "string"
+        },
+        "bibtex": {
+          "description": "BibTeX entry of the publication, one field per line, including a `doi` field matching `doi`.",
+          "title": "Bibtex",
+          "type": "string"
+        }
+      },
+      "required": [
+        "doi",
+        "bibtex"
+      ],
+      "title": "Reference",
+      "type": "object"
+    }
+  },
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "additionalProperties": false,
   "description": "Version-independent metadata of a benchmark problem.",
@@ -10,10 +35,20 @@
       "pattern": "^[A-Z][\\x20-\\x7E]*\\.$",
       "title": "Short Description",
       "type": "string"
+    },
+    "references": {
+      "description": "Publications the problem is based on. The first entry is the main publication; its BibTeX key is the problem ID.",
+      "items": {
+        "$ref": "#/$defs/Reference"
+      },
+      "minItems": 1,
+      "title": "References",
+      "type": "array"
     }
   },
   "required": [
-    "short_description"
+    "short_description",
+    "references"
   ],
   "title": "Benchmark problem metadata",
   "type": "object"
diff --git a/src/python/test/test_metadata.py b/src/python/test/test_metadata.py
index b5e5cc1..7386cb2 100644
--- a/src/python/test/test_metadata.py
+++ b/src/python/test/test_metadata.py
@@ -5,6 +5,7 @@
 
 import pydantic
 import pytest
+import yaml
 
 import benchmark_models_petab as models
 from benchmark_models_petab.check_metadata import check_metadata_file
@@ -15,6 +16,22 @@
     get_metadata_schema,
 )
 
+DESCRIPTION = "Reaction network model of something."
+BIBTEX = """\
+@article{Doe_Journal2000,
+  author = {Doe, Jane},
+  title = {Something},
+  doi = {10.1234/ABC.5},
+}
+"""
+REFERENCE = {"doi": "10.1234/abc.5", "bibtex": BIBTEX}
+VALID = {"short_description": DESCRIPTION, "references": [REFERENCE]}
+
+
+def with_reference(**kwargs):
+    """`VALID` with the given fields of the first reference replaced."""
+    return VALID | {"references": [REFERENCE | kwargs]}
+
 
 def test_packaged_schema_is_up_to_date():
     """The packaged JSON schema matches `ProblemMetadata`."""
@@ -32,11 +49,22 @@ def test_get_metadata():
     metadata = models.get_metadata("Boehm_JProteomeRes2014")
     assert isinstance(metadata, ProblemMetadata)
     assert "STAT5" in metadata.short_description
+    assert metadata.references[0].doi == "10.1021/pr5006923"
+    assert metadata.references[0].bibtex_key == "Boehm_JProteomeRes2014"
 
     with pytest.raises(ValueError):
         models.get_metadata("not a problem name")
 
 
+def test_get_bibtex():
+    bibtex = models.get_bibtex(["Boehm_JProteomeRes2014", "Bachmann_MSB2011"])
+    assert bibtex.startswith("@article{Boehm_JProteomeRes2014,\n")
+    assert "}\n\n@article{Bachmann_MSB2011,\n" in bibtex
+    assert bibtex.endswith("}\n")
+
+    assert models.get_bibtex().count("\n@") == len(models.MODELS) - 1
+
+
 @pytest.mark.parametrize("problem_id", models.MODELS)
 def test_all_problems_have_valid_metadata(problem_id):
     assert check_metadata_file(get_metadata_path(problem_id)) == []
@@ -45,7 +73,8 @@ def test_all_problems_have_valid_metadata(problem_id):
 @pytest.mark.parametrize(
     "metadata",
     [
-        {"short_description": "Reaction network model of something."},
+        VALID,
+        VALID | {"references": [REFERENCE, REFERENCE]},
     ],
 )
 def test_valid_metadata(metadata):
@@ -56,19 +85,31 @@ def test_valid_metadata(metadata):
     "metadata",
     [
         {},
-        {"short_description": None},
-        {"short_description": "Too short."},
-        {"short_description": "Reaction network model of something"},
-        {"short_description": "reaction network model of something."},
-        {"short_description": "Reaction network model\nof something."},
-        {"short_description": "Reaction network model of Ca²⁺ signaling."},
-        {"short_description": "Reaction network model of " + 200 * "x" + "."},
-        {"description": "Reaction network model of something."},
-        {
-            "short_description": "Reaction network model of something.",
-            "unknown": 1,
+        {"short_description": DESCRIPTION},
+        VALID | {"short_description": None},
+        VALID | {"short_description": "Too short."},
+        VALID | {"short_description": "Reaction network model of something"},
+        VALID | {"short_description": "reaction network model of something."},
+        VALID | {"short_description": "Reaction network model\nof something."},
+        VALID
+        | {"short_description": "Reaction network model of Ca²⁺ signaling."},
+        VALID
+        | {
+            "short_description": "Reaction network model of " + 200 * "x" + "."
         },
+        {"description": DESCRIPTION, "references": [REFERENCE]},
+        VALID | {"unknown": 1},
         ["short_description"],
+        VALID | {"references": []},
+        VALID | {"references": [{"doi": "10.1234/abc.5"}]},
+        with_reference(unknown=1),
+        with_reference(doi="doi:10.1234/abc.5"),
+        with_reference(doi="10.1234/other"),
+        with_reference(
+            bibtex=BIBTEX.replace("  doi = {10.1234/ABC.5},\n", "")
+        ),
+        with_reference(bibtex=BIBTEX + BIBTEX),
+        with_reference(bibtex="doi = {10.1234/abc.5}"),
     ],
 )
 def test_invalid_metadata(metadata):
@@ -77,7 +118,8 @@ def test_invalid_metadata(metadata):
 
 
 def test_check_metadata_file(tmp_path):
-    path = tmp_path / "metadata.yaml"
+    path = tmp_path / "Doe_Journal2000" / "metadata.yaml"
+    path.parent.mkdir()
     assert check_metadata_file(path) == [
         "Missing metadata file `metadata.yaml`."
     ]
@@ -85,11 +127,15 @@ def test_check_metadata_file(tmp_path):
     path.write_text("short_description: [unclosed\n")
     assert check_metadata_file(path)[0].startswith("Invalid YAML")
 
-    path.write_text("short_description: Too short.\n")
+    path.write_text(
+        yaml.safe_dump(VALID | {"short_description": "Too short."})
+    )
     (error,) = check_metadata_file(path)
     assert error.startswith("short_description: ")
 
-    path.write_text(
-        "short_description: Reaction network model of something.\n"
-    )
+    path.write_text(yaml.safe_dump(VALID))
     assert check_metadata_file(path) == []
+
+    path = path.rename(tmp_path / "metadata.yaml")
+    (error,) = check_metadata_file(path)
+    assert "does not match the problem ID" in error
diff --git a/src/python/test/test_overview.py b/src/python/test/test_overview.py
index 1269427..2a6c148 100644
--- a/src/python/test/test_overview.py
+++ b/src/python/test/test_overview.py
@@ -12,6 +12,7 @@ def test_get_readme_table():
     assert models.get_metadata(PROBLEM_ID).short_description in row
     assert f"[v1](problems/{PROBLEM_ID}/v1/)" in row
     assert f"[v2](problems/{PROBLEM_ID}/v2/)" in row
+    assert "[10.1021/pr5006923](https://doi.org/10.1021/pr5006923)" in row
     # a problem without a v2 encoding
     no_v2 = next(id_ for id_ in models.MODELS if id_ not in models.v2.MODELS)
     (row,) = [line for line in table.splitlines() if f"[{no_v2}]" in line]

From ebc1d32b7dc50b6fb2af6a07a2be782fe034587a Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 22 Oct 2026 09:46:12 +0200
Subject: [PATCH 2/7] Add references from Crossref

DOIs are taken from the SBML model annotations (for
`Giordano_Nature2020` and `Zhao_QuantBiol2020`, which only have PubMed
IDs, via NCBI E-utilities). The BibTeX entries were generated from the
Crossref API records (fetched 2026-10-22) without manual edits; only
HTML entities were decoded, non-breaking spaces replaced, `&` escaped,
and page ranges written with `--`. Article numbers are used as `pages`
where there are no pages.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 problems/Alkan_SciSignal2018/metadata.yaml          | 13 +++++++++++++
 problems/Armistead_CellDeathDis2024/metadata.yaml   | 13 +++++++++++++
 problems/Bachmann_MSB2011/metadata.yaml             | 13 +++++++++++++
 problems/Beer_MolBioSystems2014/metadata.yaml       | 13 +++++++++++++
 problems/Bertozzi_PNAS2020/metadata.yaml            | 13 +++++++++++++
 problems/Blasi_CellSystems2016/metadata.yaml        | 13 +++++++++++++
 problems/Boehm_JProteomeRes2014/metadata.yaml       | 13 +++++++++++++
 problems/Borghans_BiophysChem1997/metadata.yaml     | 13 +++++++++++++
 problems/Brannmark_JBC2010/metadata.yaml            | 13 +++++++++++++
 problems/Bruno_JExpBot2016/metadata.yaml            | 13 +++++++++++++
 problems/Chen_MSB2009/metadata.yaml                 | 13 +++++++++++++
 problems/Crauste_CellSystems2017/metadata.yaml      | 13 +++++++++++++
 problems/Elowitz_Nature2000/metadata.yaml           | 13 +++++++++++++
 problems/Fiedler_BMCSystBiol2016/metadata.yaml      | 13 +++++++++++++
 problems/Froehlich_CellSystems2018/metadata.yaml    | 13 +++++++++++++
 problems/Fujita_SciSignal2010/metadata.yaml         | 12 ++++++++++++
 problems/Giordano_Nature2020/metadata.yaml          | 13 +++++++++++++
 problems/Isensee_JCB2018/metadata.yaml              | 13 +++++++++++++
 problems/Lang_PLOSComputBiol2024/metadata.yaml      | 13 +++++++++++++
 problems/Laske_PLOSComputBiol2019/metadata.yaml     | 13 +++++++++++++
 problems/Liu_IFACPapersOnLine2025/metadata.yaml     | 13 +++++++++++++
 problems/Lucarelli_CellSystems2018/metadata.yaml    | 13 +++++++++++++
 .../metadata.yaml                                   | 12 ++++++++++++
 problems/Oliveira_NatCommun2021/metadata.yaml       | 13 +++++++++++++
 problems/Perelson_Science1996/metadata.yaml         | 13 +++++++++++++
 problems/Rahman_MBS2016/metadata.yaml               | 12 ++++++++++++
 problems/Raia_CancerResearch2011/metadata.yaml      | 13 +++++++++++++
 problems/Raimundez_PCB2020/metadata.yaml            | 13 +++++++++++++
 problems/SalazarCavazos_MBoC2020/metadata.yaml      | 13 +++++++++++++
 problems/Schwen_PONE2014/metadata.yaml              | 13 +++++++++++++
 problems/Smith_BMCSystBiol2013/metadata.yaml        | 13 +++++++++++++
 problems/Sneyd_PNAS2002/metadata.yaml               | 13 +++++++++++++
 problems/Weber_BMC2015/metadata.yaml                | 13 +++++++++++++
 problems/Zhao_QuantBiol2020/metadata.yaml           | 13 +++++++++++++
 problems/Zheng_PNAS2012/metadata.yaml               | 13 +++++++++++++
 35 files changed, 452 insertions(+)

diff --git a/problems/Alkan_SciSignal2018/metadata.yaml b/problems/Alkan_SciSignal2018/metadata.yaml
index abdb326..4a68cec 100644
--- a/problems/Alkan_SciSignal2018/metadata.yaml
+++ b/problems/Alkan_SciSignal2018/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of the DNA damage response and cell fate in cancer cells treated with chemotherapeutics, fitted to signaling and cell count data.
+references:
+  - doi: 10.1126/scisignal.aat0229
+    bibtex: |
+      @article{Alkan_SciSignal2018,
+        author = {Alkan, Ozan and Schoeberl, Birgit and Shah, Millie and Koshkaryev, Alexander and Heinemann, Tim and Drummond, Daryl C. and Yaffe, Michael B. and Raue, Andreas},
+        title = {Modeling chemotherapy-induced stress to identify rational combination therapies in the DNA damage response pathway},
+        journal = {Science Signaling},
+        year = {2018},
+        volume = {11},
+        number = {540},
+        pages = {eaat0229},
+        doi = {10.1126/scisignal.aat0229},
+      }
diff --git a/problems/Armistead_CellDeathDis2024/metadata.yaml b/problems/Armistead_CellDeathDis2024/metadata.yaml
index 2631044..14c6028 100644
--- a/problems/Armistead_CellDeathDis2024/metadata.yaml
+++ b/problems/Armistead_CellDeathDis2024/metadata.yaml
@@ -1 +1,14 @@
 short_description: Small reaction network model of sphingolipid metabolism with ceramide feedback, fitted to lipidomics data of wild-type and mutant zebrafish embryos.
+references:
+  - doi: 10.1038/s41419-024-07134-2
+    bibtex: |
+      @article{Armistead_CellDeathDis2024,
+        author = {Armistead, Joy and Höpfl, Sebastian and Goldhausen, Pierre and Müller-Hartmann, Andrea and Fahle, Evelin and Hatzold, Julia and Franzen, Rainer and Brodesser, Susanne and Radde, Nicole E. and Hammerschmidt, Matthias},
+        title = {A sphingolipid rheostat controls apoptosis versus apical cell extrusion as alternative tumour-suppressive mechanisms},
+        journal = {Cell Death \& Disease},
+        year = {2024},
+        volume = {15},
+        number = {10},
+        pages = {746},
+        doi = {10.1038/s41419-024-07134-2},
+      }
diff --git a/problems/Bachmann_MSB2011/metadata.yaml b/problems/Bachmann_MSB2011/metadata.yaml
index 8d62e9e..11c703d 100644
--- a/problems/Bachmann_MSB2011/metadata.yaml
+++ b/problems/Bachmann_MSB2011/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of Epo-induced JAK2/STAT5 signaling with two negative feedback regulators (SOCS3, CIS) in murine erythroid progenitor cells.
+references:
+  - doi: 10.1038/msb.2011.50
+    bibtex: |
+      @article{Bachmann_MSB2011,
+        author = {Bachmann, Julie and Raue, Andreas and Schilling, Marcel and Böhm, Martin E and Kreutz, Clemens and Kaschek, Daniel and Busch, Hauke and Gretz, Norbert and Lehmann, Wolf D and Timmer, Jens and Klingmüller, Ursula},
+        title = {Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range},
+        journal = {Molecular Systems Biology},
+        year = {2011},
+        volume = {7},
+        number = {1},
+        pages = {MSB201150},
+        doi = {10.1038/msb.2011.50},
+      }
diff --git a/problems/Beer_MolBioSystems2014/metadata.yaml b/problems/Beer_MolBioSystems2014/metadata.yaml
index c8ba170..b4ea961 100644
--- a/problems/Beer_MolBioSystems2014/metadata.yaml
+++ b/problems/Beer_MolBioSystems2014/metadata.yaml
@@ -1 +1,14 @@
 short_description: Small kinetic model of bacterial growth and production of the blue pigment indigoidine by engineered variants of a non-ribosomal peptide synthetase.
+references:
+  - doi: 10.1039/c3mb70594c
+    bibtex: |
+      @article{Beer_MolBioSystems2014,
+        author = {Beer, Ralf and Herbst, Konrad and Ignatiadis, Nikolaos and Kats, Ilia and Adlung, Lorenz and Meyer, Hannah and Niopek, Dominik and Christiansen, Tania and Georgi, Fanny and Kurzawa, Nils and Meichsner, Johanna and Rabe, Sophie and Riedel, Anja and Sachs, Joshua and Schessner, Julia and Schmidt, Florian and Walch, Philipp and Niopek, Katharina and Heinemann, Tim and Eils, Roland and Di Ventura, Barbara},
+        title = {Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange},
+        journal = {Molecular BioSystems},
+        year = {2014},
+        volume = {10},
+        number = {7},
+        pages = {1709--1718},
+        doi = {10.1039/c3mb70594c},
+      }
diff --git a/problems/Bertozzi_PNAS2020/metadata.yaml b/problems/Bertozzi_PNAS2020/metadata.yaml
index 846f7d4..1b111a9 100644
--- a/problems/Bertozzi_PNAS2020/metadata.yaml
+++ b/problems/Bertozzi_PNAS2020/metadata.yaml
@@ -1 +1,14 @@
 short_description: SIR compartmental epidemiological model of the early COVID-19 outbreak in New York and California.
+references:
+  - doi: 10.1073/pnas.2006520117
+    bibtex: |
+      @article{Bertozzi_PNAS2020,
+        author = {Bertozzi, Andrea L. and Franco, Elisa and Mohler, George and Short, Martin B. and Sledge, Daniel},
+        title = {The challenges of modeling and forecasting the spread of COVID-19},
+        journal = {Proceedings of the National Academy of Sciences},
+        year = {2020},
+        volume = {117},
+        number = {29},
+        pages = {16732--16738},
+        doi = {10.1073/pnas.2006520117},
+      }
diff --git a/problems/Blasi_CellSystems2016/metadata.yaml b/problems/Blasi_CellSystems2016/metadata.yaml
index 18d5f69..2cbae89 100644
--- a/problems/Blasi_CellSystems2016/metadata.yaml
+++ b/problems/Blasi_CellSystems2016/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of combinatorial histone H4 acetylation states generated by motif-specific acetylation reactions.
+references:
+  - doi: 10.1016/j.cels.2016.01.002
+    bibtex: |
+      @article{Blasi_CellSystems2016,
+        author = {Blasi, Thomas and Feller, Christian and Feigelman, Justin and Hasenauer, Jan and Imhof, Axel and Theis, Fabian J. and Becker, Peter B. and Marr, Carsten},
+        title = {Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions},
+        journal = {Cell Systems},
+        year = {2016},
+        volume = {2},
+        number = {1},
+        pages = {49--58},
+        doi = {10.1016/j.cels.2016.01.002},
+      }
diff --git a/problems/Boehm_JProteomeRes2014/metadata.yaml b/problems/Boehm_JProteomeRes2014/metadata.yaml
index 6242d33..53a44bf 100644
--- a/problems/Boehm_JProteomeRes2014/metadata.yaml
+++ b/problems/Boehm_JProteomeRes2014/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data.
+references:
+  - doi: 10.1021/pr5006923
+    bibtex: |
+      @article{Boehm_JProteomeRes2014,
+        author = {Boehm, Martin E. and Adlung, Lorenz and Schilling, Marcel and Roth, Susanne and Klingmüller, Ursula and Lehmann, Wolf D.},
+        title = {Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent STAT5 Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling},
+        journal = {Journal of Proteome Research},
+        year = {2014},
+        volume = {13},
+        number = {12},
+        pages = {5685--5694},
+        doi = {10.1021/pr5006923},
+      }
diff --git a/problems/Borghans_BiophysChem1997/metadata.yaml b/problems/Borghans_BiophysChem1997/metadata.yaml
index 5bad55b..cb55539 100644
--- a/problems/Borghans_BiophysChem1997/metadata.yaml
+++ b/problems/Borghans_BiophysChem1997/metadata.yaml
@@ -1 +1,14 @@
 short_description: Three-variable ODE model of complex calcium oscillations with Ca2+-activated IP3 degradation, fitted to measured calcium bursting in a single hepatocyte.
+references:
+  - doi: 10.1016/s0301-4622(97)00010-0
+    bibtex: |
+      @article{Borghans_BiophysChem1997,
+        author = {Borghans, JoséA.M. and Dupont, Geneviève and Goldbeter, Albert},
+        title = {Complex intracellular calcium oscillations A theoretical exploration of possible mechanisms},
+        journal = {Biophysical Chemistry},
+        year = {1997},
+        volume = {66},
+        number = {1},
+        pages = {25--41},
+        doi = {10.1016/s0301-4622(97)00010-0},
+      }
diff --git a/problems/Brannmark_JBC2010/metadata.yaml b/problems/Brannmark_JBC2010/metadata.yaml
index c6acdef..177c70b 100644
--- a/problems/Brannmark_JBC2010/metadata.yaml
+++ b/problems/Brannmark_JBC2010/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of insulin receptor and IRS1 phosphorylation with receptor endocytosis and feedback in primary human adipocytes.
+references:
+  - doi: 10.1074/jbc.M110.106849
+    bibtex: |
+      @article{Brannmark_JBC2010,
+        author = {Brännmark, Cecilia and Palmér, Robert and Glad, S. Torkel and Cedersund, Gunnar and Strålfors, Peter},
+        title = {Mass and Information Feedbacks through Receptor Endocytosis Govern Insulin Signaling as Revealed Using a Parameter-free Modeling Framework},
+        journal = {Journal of Biological Chemistry},
+        year = {2010},
+        volume = {285},
+        number = {26},
+        pages = {20171--20179},
+        doi = {10.1074/jbc.M110.106849},
+      }
diff --git a/problems/Bruno_JExpBot2016/metadata.yaml b/problems/Bruno_JExpBot2016/metadata.yaml
index 71343bf..e3828f5 100644
--- a/problems/Bruno_JExpBot2016/metadata.yaml
+++ b/problems/Bruno_JExpBot2016/metadata.yaml
@@ -1 +1,14 @@
 short_description: Enzyme kinetic model of the in vitro cleavage of carotenoids and apocarotenoids by Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4).
+references:
+  - doi: 10.1093/jxb/erw356
+    bibtex: |
+      @article{Bruno_JExpBot2016,
+        author = {Bruno, Mark and Koschmieder, Julian and Wuest, Florian and Schaub, Patrick and Fehling-Kaschek, Mirjam and Timmer, Jens and Beyer, Peter and Al-Babili, Salim},
+        title = {Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites},
+        journal = {Journal of Experimental Botany},
+        year = {2016},
+        volume = {67},
+        number = {21},
+        pages = {5993--6005},
+        doi = {10.1093/jxb/erw356},
+      }
diff --git a/problems/Chen_MSB2009/metadata.yaml b/problems/Chen_MSB2009/metadata.yaml
index 9f773fd..5fb36db 100644
--- a/problems/Chen_MSB2009/metadata.yaml
+++ b/problems/Chen_MSB2009/metadata.yaml
@@ -1 +1,14 @@
 short_description: Large mass-action reaction network model of ErbB receptor signaling to ERK and AKT in response to EGF and heregulin.
+references:
+  - doi: 10.1038/msb.2008.74
+    bibtex: |
+      @article{Chen_MSB2009,
+        author = {Chen, William W and Schoeberl, Birgit and Jasper, Paul J and Niepel, Mario and Nielsen, Ulrik B and Lauffenburger, Douglas A and Sorger, Peter K},
+        title = {Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data},
+        journal = {Molecular Systems Biology},
+        year = {2009},
+        volume = {5},
+        number = {1},
+        pages = {MSB200874},
+        doi = {10.1038/msb.2008.74},
+      }
diff --git a/problems/Crauste_CellSystems2017/metadata.yaml b/problems/Crauste_CellSystems2017/metadata.yaml
index 7dddb22..4fb05d3 100644
--- a/problems/Crauste_CellSystems2017/metadata.yaml
+++ b/problems/Crauste_CellSystems2017/metadata.yaml
@@ -1 +1,14 @@
 short_description: Cell population model of CD8 T cell differentiation (naive, early/late effector, memory), fitted to cell counts in mice after vaccinia virus infection.
+references:
+  - doi: 10.1016/j.cels.2017.01.014
+    bibtex: |
+      @article{Crauste_CellSystems2017,
+        author = {Crauste, Fabien and Mafille, Julien and Boucinha, Lilia and Djebali, Sophia and Gandrillon, Olivier and Marvel, Jacqueline and Arpin, Christophe},
+        title = {Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny},
+        journal = {Cell Systems},
+        year = {2017},
+        volume = {4},
+        number = {3},
+        pages = {306--317.e4},
+        doi = {10.1016/j.cels.2017.01.014},
+      }
diff --git a/problems/Elowitz_Nature2000/metadata.yaml b/problems/Elowitz_Nature2000/metadata.yaml
index 7141a5a..fbc1d84 100644
--- a/problems/Elowitz_Nature2000/metadata.yaml
+++ b/problems/Elowitz_Nature2000/metadata.yaml
@@ -1 +1,14 @@
 short_description: Gene regulatory network model of the repressilator, a synthetic three-gene transcriptional oscillator in E. coli, fitted to a fluorescence time course.
+references:
+  - doi: 10.1038/35002125
+    bibtex: |
+      @article{Elowitz_Nature2000,
+        author = {Elowitz, Michael B. and Leibler, Stanislas},
+        title = {A synthetic oscillatory network of transcriptional regulators},
+        journal = {Nature},
+        year = {2000},
+        volume = {403},
+        number = {6767},
+        pages = {335--338},
+        doi = {10.1038/35002125},
+      }
diff --git a/problems/Fiedler_BMCSystBiol2016/metadata.yaml b/problems/Fiedler_BMCSystBiol2016/metadata.yaml
index a3bf4ce..49d574b 100644
--- a/problems/Fiedler_BMCSystBiol2016/metadata.yaml
+++ b/problems/Fiedler_BMCSystBiol2016/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of RAF/MEK/ERK signaling with ERK feedback in HeLa cells, fitted to phospho-MEK/ERK data without and with RAF or MEK inhibitors.
+references:
+  - doi: 10.1186/s12918-016-0319-7
+    bibtex: |
+      @article{Fiedler_BMCSystBiol2016,
+        author = {Fiedler, Anna and Raeth, Sebastian and Theis, Fabian J. and Hausser, Angelika and Hasenauer, Jan},
+        title = {Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints},
+        journal = {BMC Systems Biology},
+        year = {2016},
+        volume = {10},
+        number = {1},
+        pages = {80},
+        doi = {10.1186/s12918-016-0319-7},
+      }
diff --git a/problems/Froehlich_CellSystems2018/metadata.yaml b/problems/Froehlich_CellSystems2018/metadata.yaml
index 09997e1..f551038 100644
--- a/problems/Froehlich_CellSystems2018/metadata.yaml
+++ b/problems/Froehlich_CellSystems2018/metadata.yaml
@@ -1 +1,14 @@
 short_description: Large-scale reaction network model of cancer signaling pathways, parameterized by cell-line-specific gene expression and fitted to drug response viability data.
+references:
+  - doi: 10.1016/j.cels.2018.10.013
+    bibtex: |
+      @article{Froehlich_CellSystems2018,
+        author = {Fröhlich, Fabian and Kessler, Thomas and Weindl, Daniel and Shadrin, Alexey and Schmiester, Leonard and Hache, Hendrik and Muradyan, Artur and Schütte, Moritz and Lim, Ji-Hyun and Heinig, Matthias and Theis, Fabian J. and Lehrach, Hans and Wierling, Christoph and Lange, Bodo and Hasenauer, Jan},
+        title = {Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model},
+        journal = {Cell Systems},
+        year = {2018},
+        volume = {7},
+        number = {6},
+        pages = {567--579.e6},
+        doi = {10.1016/j.cels.2018.10.013},
+      }
diff --git a/problems/Fujita_SciSignal2010/metadata.yaml b/problems/Fujita_SciSignal2010/metadata.yaml
index df8148f..e10adff 100644
--- a/problems/Fujita_SciSignal2010/metadata.yaml
+++ b/problems/Fujita_SciSignal2010/metadata.yaml
@@ -1 +1,13 @@
 short_description: Reaction network model of EGF-induced EGFR, Akt and S6 phosphorylation in PC12 cells under different EGF stimulation profiles.
+references:
+  - doi: 10.1126/scisignal.2000810
+    bibtex: |
+      @article{Fujita_SciSignal2010,
+        author = {Fujita, Kazuhiro A. and Toyoshima, Yu and Uda, Shinsuke and Ozaki, Yu-ichi and Kubota, Hiroyuki and Kuroda, Shinya},
+        title = {Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics},
+        journal = {Science Signaling},
+        year = {2010},
+        volume = {3},
+        number = {132},
+        doi = {10.1126/scisignal.2000810},
+      }
diff --git a/problems/Giordano_Nature2020/metadata.yaml b/problems/Giordano_Nature2020/metadata.yaml
index 193160f..63a3716 100644
--- a/problems/Giordano_Nature2020/metadata.yaml
+++ b/problems/Giordano_Nature2020/metadata.yaml
@@ -1 +1,14 @@
 short_description: Compartmental epidemiological model (SIDARTHE, distinguishing detected/undetected and symptom severity) of the COVID-19 epidemic in Italy.
+references:
+  - doi: 10.1038/s41591-020-0883-7
+    bibtex: |
+      @article{Giordano_Nature2020,
+        author = {Giordano, Giulia and Blanchini, Franco and Bruno, Raffaele and Colaneri, Patrizio and Di Filippo, Alessandro and Di Matteo, Angela and Colaneri, Marta},
+        title = {Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy},
+        journal = {Nature Medicine},
+        year = {2020},
+        volume = {26},
+        number = {6},
+        pages = {855--860},
+        doi = {10.1038/s41591-020-0883-7},
+      }
diff --git a/problems/Isensee_JCB2018/metadata.yaml b/problems/Isensee_JCB2018/metadata.yaml
index d030491..3ffc4bb 100644
--- a/problems/Isensee_JCB2018/metadata.yaml
+++ b/problems/Isensee_JCB2018/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of cAMP-induced PKA activation and phosphorylation of its regulatory subunit in rat sensory neurons under pharmacological perturbations.
+references:
+  - doi: 10.1083/jcb.201708053
+    bibtex: |
+      @article{Isensee_JCB2018,
+        author = {Isensee, Jörg and Kaufholz, Melanie and Knape, Matthias J. and Hasenauer, Jan and Hammerich, Hanna and Gonczarowska-Jorge, Humberto and Zahedi, René P. and Schwede, Frank and Herberg, Friedrich W. and Hucho, Tim},
+        title = {PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination},
+        journal = {Journal of Cell Biology},
+        year = {2018},
+        volume = {217},
+        number = {6},
+        pages = {2167--2184},
+        doi = {10.1083/jcb.201708053},
+      }
diff --git a/problems/Lang_PLOSComputBiol2024/metadata.yaml b/problems/Lang_PLOSComputBiol2024/metadata.yaml
index 50ec321..debc670 100644
--- a/problems/Lang_PLOSComputBiol2024/metadata.yaml
+++ b/problems/Lang_PLOSComputBiol2024/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of the human cell cycle, generated from a rule-based model and fitted to compartment-resolved single-cell imaging data of RPE-1 cells.
+references:
+  - doi: 10.1371/journal.pcbi.1011151
+    bibtex: |
+      @article{Lang_PLOSComputBiol2024,
+        author = {Lang, Paul F. and Penas, David R. and Banga, Julio R. and Weindl, Daniel and Novak, Bela},
+        title = {Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells},
+        journal = {PLOS Computational Biology},
+        year = {2024},
+        volume = {20},
+        number = {1},
+        pages = {e1011151},
+        doi = {10.1371/journal.pcbi.1011151},
+      }
diff --git a/problems/Laske_PLOSComputBiol2019/metadata.yaml b/problems/Laske_PLOSComputBiol2019/metadata.yaml
index 60a5792..62292d0 100644
--- a/problems/Laske_PLOSComputBiol2019/metadata.yaml
+++ b/problems/Laske_PLOSComputBiol2019/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of intracellular influenza A virus replication, fitted to viral RNA, genome import and virus release data in human A549 cells.
+references:
+  - doi: 10.1371/journal.pcbi.1006944
+    bibtex: |
+      @article{Laske_PLOSComputBiol2019,
+        author = {Laske, Tanja and Bachmann, Mandy and Dostert, Melanie and Karlas, Alexander and Wirth, Dagmar and Frensing, Timo and Meyer, Thomas F. and Hauser, Hansjörg and Reichl, Udo},
+        title = {Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth},
+        journal = {PLOS Computational Biology},
+        year = {2019},
+        volume = {15},
+        number = {4},
+        pages = {e1006944},
+        doi = {10.1371/journal.pcbi.1006944},
+      }
diff --git a/problems/Liu_IFACPapersOnLine2025/metadata.yaml b/problems/Liu_IFACPapersOnLine2025/metadata.yaml
index 6d7e1ec..a52c202 100644
--- a/problems/Liu_IFACPapersOnLine2025/metadata.yaml
+++ b/problems/Liu_IFACPapersOnLine2025/metadata.yaml
@@ -1 +1,14 @@
 short_description: Population model of oncolytic virus therapy with uninfected and infected tumor cells and virus, fitted to tumor size data in zebrafish.
+references:
+  - doi: 10.1016/j.ifacol.2025.07.160
+    bibtex: |
+      @article{Liu_IFACPapersOnLine2025,
+        author = {Liu, Yuhong and Pathirana, Dilan and Hasenauer, Jan},
+        title = {Parameter Estimation and Model Selection for the Quantitative Analysis of Oncolytic Virus Therapy in Zebrafish},
+        journal = {IFAC-PapersOnLine},
+        year = {2025},
+        volume = {59},
+        number = {6},
+        pages = {289--294},
+        doi = {10.1016/j.ifacol.2025.07.160},
+      }
diff --git a/problems/Lucarelli_CellSystems2018/metadata.yaml b/problems/Lucarelli_CellSystems2018/metadata.yaml
index c36659d..fe49374 100644
--- a/problems/Lucarelli_CellSystems2018/metadata.yaml
+++ b/problems/Lucarelli_CellSystems2018/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of TGF-beta-induced SMAD complex formation and target gene expression.
+references:
+  - doi: 10.1016/j.cels.2017.11.010
+    bibtex: |
+      @article{Lucarelli_CellSystems2018,
+        author = {Lucarelli, Philippe and Schilling, Marcel and Kreutz, Clemens and Vlasov, Artyom and Boehm, Martin E. and Iwamoto, Nao and Steiert, Bernhard and Lattermann, Susen and Wäsch, Marvin and Stepath, Markus and Matter, Matthias S. and Heikenwälder, Mathias and Hoffmann, Katrin and Deharde, Daniela and Damm, Georg and Seehofer, Daniel and Muciek, Maria and Gretz, Norbert and Lehmann, Wolf D. and Timmer, Jens and Klingmüller, Ursula},
+        title = {Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression},
+        journal = {Cell Systems},
+        year = {2018},
+        volume = {6},
+        number = {1},
+        pages = {75--89.e11},
+        doi = {10.1016/j.cels.2017.11.010},
+      }
diff --git a/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml b/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml
index ff043e6..b690867 100644
--- a/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml
+++ b/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml
@@ -1 +1,13 @@
 short_description: Compartmental epidemiological model of COVID-19 in Lagos, Nigeria, including asymptomatic and detected infections.
+references:
+  - doi: 10.1016/j.chaos.2020.110032
+    bibtex: |
+      @article{Okuonghae_ChaosSolitonsFractals2020,
+        author = {Okuonghae, D. and Omame, A.},
+        title = {Analysis of a mathematical model for COVID-19 population dynamics in Lagos, Nigeria},
+        journal = {Chaos, Solitons \& Fractals},
+        year = {2020},
+        volume = {139},
+        pages = {110032},
+        doi = {10.1016/j.chaos.2020.110032},
+      }
diff --git a/problems/Oliveira_NatCommun2021/metadata.yaml b/problems/Oliveira_NatCommun2021/metadata.yaml
index 6c16909..2d78a44 100644
--- a/problems/Oliveira_NatCommun2021/metadata.yaml
+++ b/problems/Oliveira_NatCommun2021/metadata.yaml
@@ -1 +1,14 @@
 short_description: Compartmental epidemiological model of COVID-19 in Bahia, Brazil (state excluding the capital Salvador), with non-detected cases, hospitalization and deaths.
+references:
+  - doi: 10.1038/s41467-020-19798-3
+    bibtex: |
+      @article{Oliveira_NatCommun2021,
+        author = {Oliveira, Juliane F. and Jorge, Daniel C. P. and Veiga, Rafael V. and Rodrigues, Moreno S. and Torquato, Matheus F. and da Silva, Nivea B. and Fiaccone, Rosemeire L. and Cardim, Luciana L. and Pereira, Felipe A. C. and de Castro, Caio P. and Paiva, Aureliano S. S. and Amad, Alan A. S. and Lima, Ernesto A. B. F. and Souza, Diego S. and Pinho, Suani T. R. and Ramos, Pablo Ivan P. and Andrade, Roberto F. S.},
+        title = {Mathematical modeling of COVID-19 in 14.8 million individuals in Bahia, Brazil},
+        journal = {Nature Communications},
+        year = {2021},
+        volume = {12},
+        number = {1},
+        pages = {333},
+        doi = {10.1038/s41467-020-19798-3},
+      }
diff --git a/problems/Perelson_Science1996/metadata.yaml b/problems/Perelson_Science1996/metadata.yaml
index 41fa767..235f5ce 100644
--- a/problems/Perelson_Science1996/metadata.yaml
+++ b/problems/Perelson_Science1996/metadata.yaml
@@ -1 +1,14 @@
 short_description: Within-host model of HIV-1 viral dynamics, fitted to plasma HIV-1 RNA levels after treatment with the protease inhibitor ritonavir.
+references:
+  - doi: 10.1126/science.271.5255.1582
+    bibtex: |
+      @article{Perelson_Science1996,
+        author = {Perelson, Alan S. and Neumann, Avidan U. and Markowitz, Martin and Leonard, John M. and Ho, David D.},
+        title = {HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time},
+        journal = {Science},
+        year = {1996},
+        volume = {271},
+        number = {5255},
+        pages = {1582--1586},
+        doi = {10.1126/science.271.5255.1582},
+      }
diff --git a/problems/Rahman_MBS2016/metadata.yaml b/problems/Rahman_MBS2016/metadata.yaml
index e65e1b1..93fa637 100644
--- a/problems/Rahman_MBS2016/metadata.yaml
+++ b/problems/Rahman_MBS2016/metadata.yaml
@@ -1 +1,13 @@
 short_description: Compartmental epidemiological model of HIV transmission with CD4+ T cell count-based infection stages and treatment, fitted to HIV prevalence in South Africa.
+references:
+  - doi: 10.1016/j.mbs.2016.07.009
+    bibtex: |
+      @article{Rahman_MBS2016,
+        author = {Rahman, S.M. Ashrafur and Vaidya, Naveen K. and Zou, Xingfu},
+        title = {Impact of early treatment programs on HIV epidemics: An immunity-based mathematical model},
+        journal = {Mathematical Biosciences},
+        year = {2016},
+        volume = {280},
+        pages = {38--49},
+        doi = {10.1016/j.mbs.2016.07.009},
+      }
diff --git a/problems/Raia_CancerResearch2011/metadata.yaml b/problems/Raia_CancerResearch2011/metadata.yaml
index 6c2f454..08c99ca 100644
--- a/problems/Raia_CancerResearch2011/metadata.yaml
+++ b/problems/Raia_CancerResearch2011/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of IL-13-induced JAK2/STAT5 signaling in the primary mediastinal B-cell lymphoma cell line MedB-1.
+references:
+  - doi: 10.1158/0008-5472.CAN-10-2987
+    bibtex: |
+      @article{Raia_CancerResearch2011,
+        author = {Raia, Valentina and Schilling, Marcel and Böhm, Martin and Hahn, Bettina and Kowarsch, Andreas and Raue, Andreas and Sticht, Carsten and Bohl, Sebastian and Saile, Maria and Möller, Peter and Gretz, Norbert and Timmer, Jens and Theis, Fabian and Lehmann, Wolf-Dieter and Lichter, Peter and Klingmüller, Ursula},
+        title = {Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets},
+        journal = {Cancer Research},
+        year = {2011},
+        volume = {71},
+        number = {3},
+        pages = {693--704},
+        doi = {10.1158/0008-5472.CAN-10-2987},
+      }
diff --git a/problems/Raimundez_PCB2020/metadata.yaml b/problems/Raimundez_PCB2020/metadata.yaml
index 6525abc..a661b32 100644
--- a/problems/Raimundez_PCB2020/metadata.yaml
+++ b/problems/Raimundez_PCB2020/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of EGFR and MET signaling to ERK and AKT in two gastric cancer cell lines in response to EGF and the anti-EGFR antibody cetuximab.
+references:
+  - doi: 10.1371/journal.pcbi.1007147
+    bibtex: |
+      @article{Raimundez_PCB2020,
+        author = {Raimúndez, Elba and Keller, Simone and Zwingenberger, Gwen and Ebert, Karolin and Hug, Sabine and Theis, Fabian J. and Maier, Dieter and Luber, Birgit and Hasenauer, Jan},
+        title = {Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines},
+        journal = {PLOS Computational Biology},
+        year = {2020},
+        volume = {16},
+        number = {3},
+        pages = {e1007147},
+        doi = {10.1371/journal.pcbi.1007147},
+      }
diff --git a/problems/SalazarCavazos_MBoC2020/metadata.yaml b/problems/SalazarCavazos_MBoC2020/metadata.yaml
index 9b8d8f1..8a74869 100644
--- a/problems/SalazarCavazos_MBoC2020/metadata.yaml
+++ b/problems/SalazarCavazos_MBoC2020/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of EGFR dimerization, multisite phosphorylation and binding of the adaptor proteins GRB2 and SHC1, generated from a rule-based model.
+references:
+  - doi: 10.1091/mbc.E19-09-0548
+    bibtex: |
+      @article{SalazarCavazos_MBoC2020,
+        author = {Salazar-Cavazos, Emanuel and Nitta, Carolina Franco and Mitra, Eshan D. and Wilson, Bridget S. and Lidke, Keith A. and Hlavacek, William S. and Lidke, Diane S.},
+        title = {Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes},
+        journal = {Molecular Biology of the Cell},
+        year = {2020},
+        volume = {31},
+        number = {7},
+        pages = {695--708},
+        doi = {10.1091/mbc.E19-09-0548},
+      }
diff --git a/problems/Schwen_PONE2014/metadata.yaml b/problems/Schwen_PONE2014/metadata.yaml
index 1a9a5ea..1507a73 100644
--- a/problems/Schwen_PONE2014/metadata.yaml
+++ b/problems/Schwen_PONE2014/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding.
+references:
+  - doi: 10.1371/journal.pone.0133653
+    bibtex: |
+      @article{Schwen_PONE2014,
+        author = {Schwen, Lars Ole and Schenk, Arne and Kreutz, Clemens and Timmer, Jens and Bartolomé Rodríguez, María Matilde and Kuepfer, Lars and Preusser, Tobias},
+        title = {Representative Sinusoids for Hepatic Four-Scale Pharmacokinetics Simulations},
+        journal = {PLOS ONE},
+        year = {2015},
+        volume = {10},
+        number = {7},
+        pages = {e0133653},
+        doi = {10.1371/journal.pone.0133653},
+      }
diff --git a/problems/Smith_BMCSystBiol2013/metadata.yaml b/problems/Smith_BMCSystBiol2013/metadata.yaml
index ff36c4d..57ca51f 100644
--- a/problems/Smith_BMCSystBiol2013/metadata.yaml
+++ b/problems/Smith_BMCSystBiol2013/metadata.yaml
@@ -1 +1,14 @@
 short_description: Large reaction network model of insulin signaling in rodent adipocytes and its regulation by oxidative stress.
+references:
+  - doi: 10.1186/1752-0509-7-41
+    bibtex: |
+      @article{Smith_BMCSystBiol2013,
+        author = {Smith, Graham R and Shanley, Daryl P},
+        title = {Computational modelling of the regulation of Insulin signalling by oxidative stress},
+        journal = {BMC Systems Biology},
+        year = {2013},
+        volume = {7},
+        number = {1},
+        pages = {41},
+        doi = {10.1186/1752-0509-7-41},
+      }
diff --git a/problems/Sneyd_PNAS2002/metadata.yaml b/problems/Sneyd_PNAS2002/metadata.yaml
index fe97b22..dab381d 100644
--- a/problems/Sneyd_PNAS2002/metadata.yaml
+++ b/problems/Sneyd_PNAS2002/metadata.yaml
@@ -1 +1,14 @@
 short_description: Kinetic model of the type-2 IP3 receptor, fitted to time courses of calcium release from liver microsomes at varying IP3 and calcium concentrations.
+references:
+  - doi: 10.1073/pnas.032281999
+    bibtex: |
+      @article{Sneyd_PNAS2002,
+        author = {Sneyd, James and Dufour, Jean-François},
+        title = {A dynamic model of the type-2 inositol trisphosphate receptor},
+        journal = {Proceedings of the National Academy of Sciences},
+        year = {2002},
+        volume = {99},
+        number = {4},
+        pages = {2398--2403},
+        doi = {10.1073/pnas.032281999},
+      }
diff --git a/problems/Weber_BMC2015/metadata.yaml b/problems/Weber_BMC2015/metadata.yaml
index a7ab06f..fa86b77 100644
--- a/problems/Weber_BMC2015/metadata.yaml
+++ b/problems/Weber_BMC2015/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of interactions of protein kinase D, a lipid kinase (PI4KIIIbeta) and a ceramide transfer protein (CERT) at the trans-Golgi network.
+references:
+  - doi: 10.1186/s12918-015-0147-1
+    bibtex: |
+      @article{Weber_BMC2015,
+        author = {Weber, Patrick and Hornjik, Mariana and Olayioye, Monilola A and Hausser, Angelika and Radde, Nicole E},
+        title = {A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells},
+        journal = {BMC Systems Biology},
+        year = {2015},
+        volume = {9},
+        number = {1},
+        pages = {9},
+        doi = {10.1186/s12918-015-0147-1},
+      }
diff --git a/problems/Zhao_QuantBiol2020/metadata.yaml b/problems/Zhao_QuantBiol2020/metadata.yaml
index a580bb1..a284672 100644
--- a/problems/Zhao_QuantBiol2020/metadata.yaml
+++ b/problems/Zhao_QuantBiol2020/metadata.yaml
@@ -1 +1,14 @@
 short_description: Compartmental epidemiological model of COVID-19 in Wuhan, Hubei and the rest of China, with quarantined and unquarantined infected individuals.
+references:
+  - doi: 10.1007/s40484-020-0199-0
+    bibtex: |
+      @article{Zhao_QuantBiol2020,
+        author = {Zhao, Shilei and Chen, Hua},
+        title = {Modeling the epidemic dynamics and control of COVID‐19 outbreak in China},
+        journal = {Quantitative Biology},
+        year = {2020},
+        volume = {8},
+        number = {1},
+        pages = {11--19},
+        doi = {10.1007/s40484-020-0199-0},
+      }
diff --git a/problems/Zheng_PNAS2012/metadata.yaml b/problems/Zheng_PNAS2012/metadata.yaml
index ee3dece..ebd5753 100644
--- a/problems/Zheng_PNAS2012/metadata.yaml
+++ b/problems/Zheng_PNAS2012/metadata.yaml
@@ -1 +1,14 @@
 short_description: Reaction network model of the combinatorial methylation of lysines 27 and 36 on histone H3.
+references:
+  - doi: 10.1073/pnas.1205707109
+    bibtex: |
+      @article{Zheng_PNAS2012,
+        author = {Zheng, Yupeng and Sweet, Steve M. M. and Popovic, Relja and Martinez-Garcia, Eva and Tipton, Jeremiah D. and Thomas, Paul M. and Licht, Jonathan D. and Kelleher, Neil L.},
+        title = {Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3},
+        journal = {Proceedings of the National Academy of Sciences},
+        year = {2012},
+        volume = {109},
+        number = {34},
+        pages = {13549--13554},
+        doi = {10.1073/pnas.1205707109},
+      }

From 90a02938cbefa74df58dedb117bd0351bbd978ae Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 22 Oct 2026 09:46:12 +0200
Subject: [PATCH 3/7] Add main publication DOI to the README overview table

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 README.md | 74 +++++++++++++++++++++++++++----------------------------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/README.md b/README.md
index 85729fd..5e9ea71 100644
--- a/README.md
+++ b/README.md
@@ -18,43 +18,43 @@ available encodings in PEtab v1 and v2.
 The PEtab files are available in the respective subdirectories.
 
 <!-- START OVERVIEW TABLE -->
-| ID                                                                                   | PEtab v1                                               | PEtab v2                                  | Description                                                                                                                                                      |
-|:-------------------------------------------------------------------------------------|:-------------------------------------------------------|:------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| [Alkan_SciSignal2018](problems/Alkan_SciSignal2018/)                                 | [v1](problems/Alkan_SciSignal2018/v1/)                 |                                           | Reaction network model of the DNA damage response and cell fate in cancer cells treated with chemotherapeutics, fitted to signaling and cell count data.         |
-| [Armistead_CellDeathDis2024](problems/Armistead_CellDeathDis2024/)                   | [v1](problems/Armistead_CellDeathDis2024/v1/)          |                                           | Small reaction network model of sphingolipid metabolism with ceramide feedback, fitted to lipidomics data of wild-type and mutant zebrafish embryos.             |
-| [Bachmann_MSB2011](problems/Bachmann_MSB2011/)                                       | [v1](problems/Bachmann_MSB2011/v1/)                    |                                           | Reaction network model of Epo-induced JAK2/STAT5 signaling with two negative feedback regulators (SOCS3, CIS) in murine erythroid progenitor cells.              |
-| [Beer_MolBioSystems2014](problems/Beer_MolBioSystems2014/)                           | [v1](problems/Beer_MolBioSystems2014/v1/)              |                                           | Small kinetic model of bacterial growth and production of the blue pigment indigoidine by engineered variants of a non-ribosomal peptide synthetase.             |
-| [Bertozzi_PNAS2020](problems/Bertozzi_PNAS2020/)                                     | [v1](problems/Bertozzi_PNAS2020/v1/)                   |                                           | SIR compartmental epidemiological model of the early COVID-19 outbreak in New York and California.                                                               |
-| [Blasi_CellSystems2016](problems/Blasi_CellSystems2016/)                             | [v1](problems/Blasi_CellSystems2016/v1/)               |                                           | Reaction network model of combinatorial histone H4 acetylation states generated by motif-specific acetylation reactions.                                         |
-| [Boehm_JProteomeRes2014](problems/Boehm_JProteomeRes2014/)                           | [v1](problems/Boehm_JProteomeRes2014/v1/)              | [v2](problems/Boehm_JProteomeRes2014/v2/) | Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data.             |
-| [Borghans_BiophysChem1997](problems/Borghans_BiophysChem1997/)                       | [v1](problems/Borghans_BiophysChem1997/v1/)            |                                           | Three-variable ODE model of complex calcium oscillations with Ca2+-activated IP3 degradation, fitted to measured calcium bursting in a single hepatocyte.        |
-| [Brannmark_JBC2010](problems/Brannmark_JBC2010/)                                     | [v1](problems/Brannmark_JBC2010/v1/)                   |                                           | Reaction network model of insulin receptor and IRS1 phosphorylation with receptor endocytosis and feedback in primary human adipocytes.                          |
-| [Bruno_JExpBot2016](problems/Bruno_JExpBot2016/)                                     | [v1](problems/Bruno_JExpBot2016/v1/)                   |                                           | Enzyme kinetic model of the in vitro cleavage of carotenoids and apocarotenoids by Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4).                         |
-| [Chen_MSB2009](problems/Chen_MSB2009/)                                               | [v1](problems/Chen_MSB2009/v1/)                        |                                           | Large mass-action reaction network model of ErbB receptor signaling to ERK and AKT in response to EGF and heregulin.                                             |
-| [Crauste_CellSystems2017](problems/Crauste_CellSystems2017/)                         | [v1](problems/Crauste_CellSystems2017/v1/)             |                                           | Cell population model of CD8 T cell differentiation (naive, early/late effector, memory), fitted to cell counts in mice after vaccinia virus infection.          |
-| [Elowitz_Nature2000](problems/Elowitz_Nature2000/)                                   | [v1](problems/Elowitz_Nature2000/v1/)                  |                                           | Gene regulatory network model of the repressilator, a synthetic three-gene transcriptional oscillator in E. coli, fitted to a fluorescence time course.          |
-| [Fiedler_BMCSystBiol2016](problems/Fiedler_BMCSystBiol2016/)                         | [v1](problems/Fiedler_BMCSystBiol2016/v1/)             |                                           | Reaction network model of RAF/MEK/ERK signaling with ERK feedback in HeLa cells, fitted to phospho-MEK/ERK data without and with RAF or MEK inhibitors.          |
-| [Froehlich_CellSystems2018](problems/Froehlich_CellSystems2018/)                     | [v1](problems/Froehlich_CellSystems2018/v1/)           |                                           | Large-scale reaction network model of cancer signaling pathways, parameterized by cell-line-specific gene expression and fitted to drug response viability data. |
-| [Fujita_SciSignal2010](problems/Fujita_SciSignal2010/)                               | [v1](problems/Fujita_SciSignal2010/v1/)                |                                           | Reaction network model of EGF-induced EGFR, Akt and S6 phosphorylation in PC12 cells under different EGF stimulation profiles.                                   |
-| [Giordano_Nature2020](problems/Giordano_Nature2020/)                                 | [v1](problems/Giordano_Nature2020/v1/)                 |                                           | Compartmental epidemiological model (SIDARTHE, distinguishing detected/undetected and symptom severity) of the COVID-19 epidemic in Italy.                       |
-| [Isensee_JCB2018](problems/Isensee_JCB2018/)                                         | [v1](problems/Isensee_JCB2018/v1/)                     |                                           | Reaction network model of cAMP-induced PKA activation and phosphorylation of its regulatory subunit in rat sensory neurons under pharmacological perturbations.  |
-| [Lang_PLOSComputBiol2024](problems/Lang_PLOSComputBiol2024/)                         | [v1](problems/Lang_PLOSComputBiol2024/v1/)             |                                           | Reaction network model of the human cell cycle, generated from a rule-based model and fitted to compartment-resolved single-cell imaging data of RPE-1 cells.    |
-| [Laske_PLOSComputBiol2019](problems/Laske_PLOSComputBiol2019/)                       | [v1](problems/Laske_PLOSComputBiol2019/v1/)            |                                           | Reaction network model of intracellular influenza A virus replication, fitted to viral RNA, genome import and virus release data in human A549 cells.            |
-| [Liu_IFACPapersOnLine2025](problems/Liu_IFACPapersOnLine2025/)                       | [v1](problems/Liu_IFACPapersOnLine2025/v1/)            |                                           | Population model of oncolytic virus therapy with uninfected and infected tumor cells and virus, fitted to tumor size data in zebrafish.                          |
-| [Lucarelli_CellSystems2018](problems/Lucarelli_CellSystems2018/)                     | [v1](problems/Lucarelli_CellSystems2018/v1/)           |                                           | Reaction network model of TGF-beta-induced SMAD complex formation and target gene expression.                                                                    |
-| [Okuonghae_ChaosSolitonsFractals2020](problems/Okuonghae_ChaosSolitonsFractals2020/) | [v1](problems/Okuonghae_ChaosSolitonsFractals2020/v1/) |                                           | Compartmental epidemiological model of COVID-19 in Lagos, Nigeria, including asymptomatic and detected infections.                                               |
-| [Oliveira_NatCommun2021](problems/Oliveira_NatCommun2021/)                           | [v1](problems/Oliveira_NatCommun2021/v1/)              |                                           | Compartmental epidemiological model of COVID-19 in Bahia, Brazil (state excluding the capital Salvador), with non-detected cases, hospitalization and deaths.    |
-| [Perelson_Science1996](problems/Perelson_Science1996/)                               | [v1](problems/Perelson_Science1996/v1/)                |                                           | Within-host model of HIV-1 viral dynamics, fitted to plasma HIV-1 RNA levels after treatment with the protease inhibitor ritonavir.                              |
-| [Rahman_MBS2016](problems/Rahman_MBS2016/)                                           | [v1](problems/Rahman_MBS2016/v1/)                      |                                           | Compartmental epidemiological model of HIV transmission with CD4+ T cell count-based infection stages and treatment, fitted to HIV prevalence in South Africa.   |
-| [Raia_CancerResearch2011](problems/Raia_CancerResearch2011/)                         | [v1](problems/Raia_CancerResearch2011/v1/)             |                                           | Reaction network model of IL-13-induced JAK2/STAT5 signaling in the primary mediastinal B-cell lymphoma cell line MedB-1.                                        |
-| [Raimundez_PCB2020](problems/Raimundez_PCB2020/)                                     | [v1](problems/Raimundez_PCB2020/v1/)                   |                                           | Reaction network model of EGFR and MET signaling to ERK and AKT in two gastric cancer cell lines in response to EGF and the anti-EGFR antibody cetuximab.        |
-| [SalazarCavazos_MBoC2020](problems/SalazarCavazos_MBoC2020/)                         | [v1](problems/SalazarCavazos_MBoC2020/v1/)             |                                           | Reaction network model of EGFR dimerization, multisite phosphorylation and binding of the adaptor proteins GRB2 and SHC1, generated from a rule-based model.     |
-| [Schwen_PONE2014](problems/Schwen_PONE2014/)                                         | [v1](problems/Schwen_PONE2014/v1/)                     | [v2](problems/Schwen_PONE2014/v2/)        | Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding.      |
-| [Smith_BMCSystBiol2013](problems/Smith_BMCSystBiol2013/)                             | [v1](problems/Smith_BMCSystBiol2013/v1/)               |                                           | Large reaction network model of insulin signaling in rodent adipocytes and its regulation by oxidative stress.                                                   |
-| [Sneyd_PNAS2002](problems/Sneyd_PNAS2002/)                                           | [v1](problems/Sneyd_PNAS2002/v1/)                      |                                           | Kinetic model of the type-2 IP3 receptor, fitted to time courses of calcium release from liver microsomes at varying IP3 and calcium concentrations.             |
-| [Weber_BMC2015](problems/Weber_BMC2015/)                                             | [v1](problems/Weber_BMC2015/v1/)                       |                                           | Reaction network model of interactions of protein kinase D, a lipid kinase (PI4KIIIbeta) and a ceramide transfer protein (CERT) at the trans-Golgi network.      |
-| [Zhao_QuantBiol2020](problems/Zhao_QuantBiol2020/)                                   | [v1](problems/Zhao_QuantBiol2020/v1/)                  |                                           | Compartmental epidemiological model of COVID-19 in Wuhan, Hubei and the rest of China, with quarantined and unquarantined infected individuals.                  |
-| [Zheng_PNAS2012](problems/Zheng_PNAS2012/)                                           | [v1](problems/Zheng_PNAS2012/v1/)                      |                                           | Reaction network model of the combinatorial methylation of lysines 27 and 36 on histone H3.                                                                      |
+| ID                                                                                   | PEtab v1                                               | PEtab v2                                  | Reference                                                                      | Description                                                                                                                                                      |
+|:-------------------------------------------------------------------------------------|:-------------------------------------------------------|:------------------------------------------|:-------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| [Alkan_SciSignal2018](problems/Alkan_SciSignal2018/)                                 | [v1](problems/Alkan_SciSignal2018/v1/)                 |                                           | [10.1126/scisignal.aat0229](https://doi.org/10.1126/scisignal.aat0229)         | Reaction network model of the DNA damage response and cell fate in cancer cells treated with chemotherapeutics, fitted to signaling and cell count data.         |
+| [Armistead_CellDeathDis2024](problems/Armistead_CellDeathDis2024/)                   | [v1](problems/Armistead_CellDeathDis2024/v1/)          |                                           | [10.1038/s41419-024-07134-2](https://doi.org/10.1038/s41419-024-07134-2)       | Small reaction network model of sphingolipid metabolism with ceramide feedback, fitted to lipidomics data of wild-type and mutant zebrafish embryos.             |
+| [Bachmann_MSB2011](problems/Bachmann_MSB2011/)                                       | [v1](problems/Bachmann_MSB2011/v1/)                    |                                           | [10.1038/msb.2011.50](https://doi.org/10.1038/msb.2011.50)                     | Reaction network model of Epo-induced JAK2/STAT5 signaling with two negative feedback regulators (SOCS3, CIS) in murine erythroid progenitor cells.              |
+| [Beer_MolBioSystems2014](problems/Beer_MolBioSystems2014/)                           | [v1](problems/Beer_MolBioSystems2014/v1/)              |                                           | [10.1039/c3mb70594c](https://doi.org/10.1039/c3mb70594c)                       | Small kinetic model of bacterial growth and production of the blue pigment indigoidine by engineered variants of a non-ribosomal peptide synthetase.             |
+| [Bertozzi_PNAS2020](problems/Bertozzi_PNAS2020/)                                     | [v1](problems/Bertozzi_PNAS2020/v1/)                   |                                           | [10.1073/pnas.2006520117](https://doi.org/10.1073/pnas.2006520117)             | SIR compartmental epidemiological model of the early COVID-19 outbreak in New York and California.                                                               |
+| [Blasi_CellSystems2016](problems/Blasi_CellSystems2016/)                             | [v1](problems/Blasi_CellSystems2016/v1/)               |                                           | [10.1016/j.cels.2016.01.002](https://doi.org/10.1016/j.cels.2016.01.002)       | Reaction network model of combinatorial histone H4 acetylation states generated by motif-specific acetylation reactions.                                         |
+| [Boehm_JProteomeRes2014](problems/Boehm_JProteomeRes2014/)                           | [v1](problems/Boehm_JProteomeRes2014/v1/)              | [v2](problems/Boehm_JProteomeRes2014/v2/) | [10.1021/pr5006923](https://doi.org/10.1021/pr5006923)                         | Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data.             |
+| [Borghans_BiophysChem1997](problems/Borghans_BiophysChem1997/)                       | [v1](problems/Borghans_BiophysChem1997/v1/)            |                                           | [10.1016/s0301-4622(97)00010-0](https://doi.org/10.1016/s0301-4622(97)00010-0) | Three-variable ODE model of complex calcium oscillations with Ca2+-activated IP3 degradation, fitted to measured calcium bursting in a single hepatocyte.        |
+| [Brannmark_JBC2010](problems/Brannmark_JBC2010/)                                     | [v1](problems/Brannmark_JBC2010/v1/)                   |                                           | [10.1074/jbc.M110.106849](https://doi.org/10.1074/jbc.M110.106849)             | Reaction network model of insulin receptor and IRS1 phosphorylation with receptor endocytosis and feedback in primary human adipocytes.                          |
+| [Bruno_JExpBot2016](problems/Bruno_JExpBot2016/)                                     | [v1](problems/Bruno_JExpBot2016/v1/)                   |                                           | [10.1093/jxb/erw356](https://doi.org/10.1093/jxb/erw356)                       | Enzyme kinetic model of the in vitro cleavage of carotenoids and apocarotenoids by Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4).                         |
+| [Chen_MSB2009](problems/Chen_MSB2009/)                                               | [v1](problems/Chen_MSB2009/v1/)                        |                                           | [10.1038/msb.2008.74](https://doi.org/10.1038/msb.2008.74)                     | Large mass-action reaction network model of ErbB receptor signaling to ERK and AKT in response to EGF and heregulin.                                             |
+| [Crauste_CellSystems2017](problems/Crauste_CellSystems2017/)                         | [v1](problems/Crauste_CellSystems2017/v1/)             |                                           | [10.1016/j.cels.2017.01.014](https://doi.org/10.1016/j.cels.2017.01.014)       | Cell population model of CD8 T cell differentiation (naive, early/late effector, memory), fitted to cell counts in mice after vaccinia virus infection.          |
+| [Elowitz_Nature2000](problems/Elowitz_Nature2000/)                                   | [v1](problems/Elowitz_Nature2000/v1/)                  |                                           | [10.1038/35002125](https://doi.org/10.1038/35002125)                           | Gene regulatory network model of the repressilator, a synthetic three-gene transcriptional oscillator in E. coli, fitted to a fluorescence time course.          |
+| [Fiedler_BMCSystBiol2016](problems/Fiedler_BMCSystBiol2016/)                         | [v1](problems/Fiedler_BMCSystBiol2016/v1/)             |                                           | [10.1186/s12918-016-0319-7](https://doi.org/10.1186/s12918-016-0319-7)         | Reaction network model of RAF/MEK/ERK signaling with ERK feedback in HeLa cells, fitted to phospho-MEK/ERK data without and with RAF or MEK inhibitors.          |
+| [Froehlich_CellSystems2018](problems/Froehlich_CellSystems2018/)                     | [v1](problems/Froehlich_CellSystems2018/v1/)           |                                           | [10.1016/j.cels.2018.10.013](https://doi.org/10.1016/j.cels.2018.10.013)       | Large-scale reaction network model of cancer signaling pathways, parameterized by cell-line-specific gene expression and fitted to drug response viability data. |
+| [Fujita_SciSignal2010](problems/Fujita_SciSignal2010/)                               | [v1](problems/Fujita_SciSignal2010/v1/)                |                                           | [10.1126/scisignal.2000810](https://doi.org/10.1126/scisignal.2000810)         | Reaction network model of EGF-induced EGFR, Akt and S6 phosphorylation in PC12 cells under different EGF stimulation profiles.                                   |
+| [Giordano_Nature2020](problems/Giordano_Nature2020/)                                 | [v1](problems/Giordano_Nature2020/v1/)                 |                                           | [10.1038/s41591-020-0883-7](https://doi.org/10.1038/s41591-020-0883-7)         | Compartmental epidemiological model (SIDARTHE, distinguishing detected/undetected and symptom severity) of the COVID-19 epidemic in Italy.                       |
+| [Isensee_JCB2018](problems/Isensee_JCB2018/)                                         | [v1](problems/Isensee_JCB2018/v1/)                     |                                           | [10.1083/jcb.201708053](https://doi.org/10.1083/jcb.201708053)                 | Reaction network model of cAMP-induced PKA activation and phosphorylation of its regulatory subunit in rat sensory neurons under pharmacological perturbations.  |
+| [Lang_PLOSComputBiol2024](problems/Lang_PLOSComputBiol2024/)                         | [v1](problems/Lang_PLOSComputBiol2024/v1/)             |                                           | [10.1371/journal.pcbi.1011151](https://doi.org/10.1371/journal.pcbi.1011151)   | Reaction network model of the human cell cycle, generated from a rule-based model and fitted to compartment-resolved single-cell imaging data of RPE-1 cells.    |
+| [Laske_PLOSComputBiol2019](problems/Laske_PLOSComputBiol2019/)                       | [v1](problems/Laske_PLOSComputBiol2019/v1/)            |                                           | [10.1371/journal.pcbi.1006944](https://doi.org/10.1371/journal.pcbi.1006944)   | Reaction network model of intracellular influenza A virus replication, fitted to viral RNA, genome import and virus release data in human A549 cells.            |
+| [Liu_IFACPapersOnLine2025](problems/Liu_IFACPapersOnLine2025/)                       | [v1](problems/Liu_IFACPapersOnLine2025/v1/)            |                                           | [10.1016/j.ifacol.2025.07.160](https://doi.org/10.1016/j.ifacol.2025.07.160)   | Population model of oncolytic virus therapy with uninfected and infected tumor cells and virus, fitted to tumor size data in zebrafish.                          |
+| [Lucarelli_CellSystems2018](problems/Lucarelli_CellSystems2018/)                     | [v1](problems/Lucarelli_CellSystems2018/v1/)           |                                           | [10.1016/j.cels.2017.11.010](https://doi.org/10.1016/j.cels.2017.11.010)       | Reaction network model of TGF-beta-induced SMAD complex formation and target gene expression.                                                                    |
+| [Okuonghae_ChaosSolitonsFractals2020](problems/Okuonghae_ChaosSolitonsFractals2020/) | [v1](problems/Okuonghae_ChaosSolitonsFractals2020/v1/) |                                           | [10.1016/j.chaos.2020.110032](https://doi.org/10.1016/j.chaos.2020.110032)     | Compartmental epidemiological model of COVID-19 in Lagos, Nigeria, including asymptomatic and detected infections.                                               |
+| [Oliveira_NatCommun2021](problems/Oliveira_NatCommun2021/)                           | [v1](problems/Oliveira_NatCommun2021/v1/)              |                                           | [10.1038/s41467-020-19798-3](https://doi.org/10.1038/s41467-020-19798-3)       | Compartmental epidemiological model of COVID-19 in Bahia, Brazil (state excluding the capital Salvador), with non-detected cases, hospitalization and deaths.    |
+| [Perelson_Science1996](problems/Perelson_Science1996/)                               | [v1](problems/Perelson_Science1996/v1/)                |                                           | [10.1126/science.271.5255.1582](https://doi.org/10.1126/science.271.5255.1582) | Within-host model of HIV-1 viral dynamics, fitted to plasma HIV-1 RNA levels after treatment with the protease inhibitor ritonavir.                              |
+| [Rahman_MBS2016](problems/Rahman_MBS2016/)                                           | [v1](problems/Rahman_MBS2016/v1/)                      |                                           | [10.1016/j.mbs.2016.07.009](https://doi.org/10.1016/j.mbs.2016.07.009)         | Compartmental epidemiological model of HIV transmission with CD4+ T cell count-based infection stages and treatment, fitted to HIV prevalence in South Africa.   |
+| [Raia_CancerResearch2011](problems/Raia_CancerResearch2011/)                         | [v1](problems/Raia_CancerResearch2011/v1/)             |                                           | [10.1158/0008-5472.CAN-10-2987](https://doi.org/10.1158/0008-5472.CAN-10-2987) | Reaction network model of IL-13-induced JAK2/STAT5 signaling in the primary mediastinal B-cell lymphoma cell line MedB-1.                                        |
+| [Raimundez_PCB2020](problems/Raimundez_PCB2020/)                                     | [v1](problems/Raimundez_PCB2020/v1/)                   |                                           | [10.1371/journal.pcbi.1007147](https://doi.org/10.1371/journal.pcbi.1007147)   | Reaction network model of EGFR and MET signaling to ERK and AKT in two gastric cancer cell lines in response to EGF and the anti-EGFR antibody cetuximab.        |
+| [SalazarCavazos_MBoC2020](problems/SalazarCavazos_MBoC2020/)                         | [v1](problems/SalazarCavazos_MBoC2020/v1/)             |                                           | [10.1091/mbc.E19-09-0548](https://doi.org/10.1091/mbc.E19-09-0548)             | Reaction network model of EGFR dimerization, multisite phosphorylation and binding of the adaptor proteins GRB2 and SHC1, generated from a rule-based model.     |
+| [Schwen_PONE2014](problems/Schwen_PONE2014/)                                         | [v1](problems/Schwen_PONE2014/v1/)                     | [v2](problems/Schwen_PONE2014/v2/)        | [10.1371/journal.pone.0133653](https://doi.org/10.1371/journal.pone.0133653)   | Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding.      |
+| [Smith_BMCSystBiol2013](problems/Smith_BMCSystBiol2013/)                             | [v1](problems/Smith_BMCSystBiol2013/v1/)               |                                           | [10.1186/1752-0509-7-41](https://doi.org/10.1186/1752-0509-7-41)               | Large reaction network model of insulin signaling in rodent adipocytes and its regulation by oxidative stress.                                                   |
+| [Sneyd_PNAS2002](problems/Sneyd_PNAS2002/)                                           | [v1](problems/Sneyd_PNAS2002/v1/)                      |                                           | [10.1073/pnas.032281999](https://doi.org/10.1073/pnas.032281999)               | Kinetic model of the type-2 IP3 receptor, fitted to time courses of calcium release from liver microsomes at varying IP3 and calcium concentrations.             |
+| [Weber_BMC2015](problems/Weber_BMC2015/)                                             | [v1](problems/Weber_BMC2015/v1/)                       |                                           | [10.1186/s12918-015-0147-1](https://doi.org/10.1186/s12918-015-0147-1)         | Reaction network model of interactions of protein kinase D, a lipid kinase (PI4KIIIbeta) and a ceramide transfer protein (CERT) at the trans-Golgi network.      |
+| [Zhao_QuantBiol2020](problems/Zhao_QuantBiol2020/)                                   | [v1](problems/Zhao_QuantBiol2020/v1/)                  |                                           | [10.1007/s40484-020-0199-0](https://doi.org/10.1007/s40484-020-0199-0)         | Compartmental epidemiological model of COVID-19 in Wuhan, Hubei and the rest of China, with quarantined and unquarantined infected individuals.                  |
+| [Zheng_PNAS2012](problems/Zheng_PNAS2012/)                                           | [v1](problems/Zheng_PNAS2012/v1/)                      |                                           | [10.1073/pnas.1205707109](https://doi.org/10.1073/pnas.1205707109)             | Reaction network model of the combinatorial methylation of lysines 27 and 36 on histone H3.                                                                      |
 <!-- END OVERVIEW TABLE -->
 
 ## License

From 7f10b8ca17292ff57f4ed276841b89483e4a1b5c Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 22 Oct 2026 10:37:40 +0200
Subject: [PATCH 4/7] Fix references imported from Crossref
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Corrections verified against the publications' full texts:

* `Bachmann_MSB2011`: `pages` `MSB201150` -> `516` ("Molecular Systems
  Biology 7; Article number 516")
* `Chen_MSB2009`: `pages` `MSB200874` -> `239` ("Molecular Systems
  Biology 5; Article number 239")
* `Fujita_SciSignal2010`: add missing `pages` `ra56` ("Volume 3 Issue
  132 ra56")
* `Borghans_BiophysChem1997`: author "JoséA.M." -> "José A.M." ("José
  A.M. Borghans"); title: add the missing separator between title and
  subtitle, which the paper sets on separate lines (". " as in PubMed,
  PMID 17029867)
* `Zhao_QuantBiol2020`: title: U+2010 hyphen -> "-" in "COVID-19"

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 problems/Bachmann_MSB2011/metadata.yaml         | 2 +-
 problems/Borghans_BiophysChem1997/metadata.yaml | 4 ++--
 problems/Chen_MSB2009/metadata.yaml             | 2 +-
 problems/Fujita_SciSignal2010/metadata.yaml     | 1 +
 problems/Zhao_QuantBiol2020/metadata.yaml       | 2 +-
 5 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/problems/Bachmann_MSB2011/metadata.yaml b/problems/Bachmann_MSB2011/metadata.yaml
index 11c703d..bb88868 100644
--- a/problems/Bachmann_MSB2011/metadata.yaml
+++ b/problems/Bachmann_MSB2011/metadata.yaml
@@ -9,6 +9,6 @@ references:
         year = {2011},
         volume = {7},
         number = {1},
-        pages = {MSB201150},
+        pages = {516},
         doi = {10.1038/msb.2011.50},
       }
diff --git a/problems/Borghans_BiophysChem1997/metadata.yaml b/problems/Borghans_BiophysChem1997/metadata.yaml
index cb55539..d80c68b 100644
--- a/problems/Borghans_BiophysChem1997/metadata.yaml
+++ b/problems/Borghans_BiophysChem1997/metadata.yaml
@@ -3,8 +3,8 @@ references:
   - doi: 10.1016/s0301-4622(97)00010-0
     bibtex: |
       @article{Borghans_BiophysChem1997,
-        author = {Borghans, JoséA.M. and Dupont, Geneviève and Goldbeter, Albert},
-        title = {Complex intracellular calcium oscillations A theoretical exploration of possible mechanisms},
+        author = {Borghans, José A.M. and Dupont, Geneviève and Goldbeter, Albert},
+        title = {Complex intracellular calcium oscillations. A theoretical exploration of possible mechanisms},
         journal = {Biophysical Chemistry},
         year = {1997},
         volume = {66},
diff --git a/problems/Chen_MSB2009/metadata.yaml b/problems/Chen_MSB2009/metadata.yaml
index 5fb36db..e9c60a4 100644
--- a/problems/Chen_MSB2009/metadata.yaml
+++ b/problems/Chen_MSB2009/metadata.yaml
@@ -9,6 +9,6 @@ references:
         year = {2009},
         volume = {5},
         number = {1},
-        pages = {MSB200874},
+        pages = {239},
         doi = {10.1038/msb.2008.74},
       }
diff --git a/problems/Fujita_SciSignal2010/metadata.yaml b/problems/Fujita_SciSignal2010/metadata.yaml
index e10adff..860e54c 100644
--- a/problems/Fujita_SciSignal2010/metadata.yaml
+++ b/problems/Fujita_SciSignal2010/metadata.yaml
@@ -9,5 +9,6 @@ references:
         year = {2010},
         volume = {3},
         number = {132},
+        pages = {ra56},
         doi = {10.1126/scisignal.2000810},
       }
diff --git a/problems/Zhao_QuantBiol2020/metadata.yaml b/problems/Zhao_QuantBiol2020/metadata.yaml
index a284672..082f8a4 100644
--- a/problems/Zhao_QuantBiol2020/metadata.yaml
+++ b/problems/Zhao_QuantBiol2020/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Zhao_QuantBiol2020,
         author = {Zhao, Shilei and Chen, Hua},
-        title = {Modeling the epidemic dynamics and control of COVID‐19 outbreak in China},
+        title = {Modeling the epidemic dynamics and control of COVID-19 outbreak in China},
         journal = {Quantitative Biology},
         year = {2020},
         volume = {8},

From fb1065901c78953a16b7bda35d01d45501e90924 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 22 Oct 2026 14:21:00 +0200
Subject: [PATCH 5/7] Separate merged initials in BibTeX author names

BibTeX treats "A.M." as a single name part, so abbreviating styles
(e.g. `abbrv`) drop the second initial ("J. A. Borghans" instead of
"J. A. M. Borghans"). Affects `Borghans_BiophysChem1997` and
`Rahman_MBS2016`.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 problems/Borghans_BiophysChem1997/metadata.yaml | 2 +-
 problems/Rahman_MBS2016/metadata.yaml           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/problems/Borghans_BiophysChem1997/metadata.yaml b/problems/Borghans_BiophysChem1997/metadata.yaml
index d80c68b..43ec255 100644
--- a/problems/Borghans_BiophysChem1997/metadata.yaml
+++ b/problems/Borghans_BiophysChem1997/metadata.yaml
@@ -3,7 +3,7 @@ references:
   - doi: 10.1016/s0301-4622(97)00010-0
     bibtex: |
       @article{Borghans_BiophysChem1997,
-        author = {Borghans, José A.M. and Dupont, Geneviève and Goldbeter, Albert},
+        author = {Borghans, José A. M. and Dupont, Geneviève and Goldbeter, Albert},
         title = {Complex intracellular calcium oscillations. A theoretical exploration of possible mechanisms},
         journal = {Biophysical Chemistry},
         year = {1997},
diff --git a/problems/Rahman_MBS2016/metadata.yaml b/problems/Rahman_MBS2016/metadata.yaml
index 93fa637..0228a8d 100644
--- a/problems/Rahman_MBS2016/metadata.yaml
+++ b/problems/Rahman_MBS2016/metadata.yaml
@@ -3,7 +3,7 @@ references:
   - doi: 10.1016/j.mbs.2016.07.009
     bibtex: |
       @article{Rahman_MBS2016,
-        author = {Rahman, S.M. Ashrafur and Vaidya, Naveen K. and Zou, Xingfu},
+        author = {Rahman, S. M. Ashrafur and Vaidya, Naveen K. and Zou, Xingfu},
         title = {Impact of early treatment programs on HIV epidemics: An immunity-based mathematical model},
         journal = {Mathematical Biosciences},
         year = {2016},

From 01e3e155ea47068170532c751cabeacd1f51d879 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 22 Oct 2026 14:25:50 +0200
Subject: [PATCH 6/7] Protect acronyms and proper nouns in BibTeX titles

Bibliography styles that convert titles to sentence case (e.g. `plain`,
or biblatex with `\MakeSentenceCase`) would otherwise lowercase them
("dna", "covid-19", "italy"). Only acronyms, gene/protein names, proper
nouns, and single capital letters are braced; other capitalized words
are left for the style to handle.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 problems/Alkan_SciSignal2018/metadata.yaml                 | 2 +-
 problems/Bachmann_MSB2011/metadata.yaml                    | 2 +-
 problems/Beer_MolBioSystems2014/metadata.yaml              | 2 +-
 problems/Bertozzi_PNAS2020/metadata.yaml                   | 2 +-
 problems/Boehm_JProteomeRes2014/metadata.yaml              | 2 +-
 problems/Borghans_BiophysChem1997/metadata.yaml            | 2 +-
 problems/Bruno_JExpBot2016/metadata.yaml                   | 2 +-
 problems/Chen_MSB2009/metadata.yaml                        | 2 +-
 problems/Crauste_CellSystems2017/metadata.yaml             | 2 +-
 problems/Fujita_SciSignal2010/metadata.yaml                | 2 +-
 problems/Giordano_Nature2020/metadata.yaml                 | 2 +-
 problems/Isensee_JCB2018/metadata.yaml                     | 2 +-
 problems/Lang_PLOSComputBiol2024/metadata.yaml             | 2 +-
 problems/Laske_PLOSComputBiol2019/metadata.yaml            | 2 +-
 problems/Lucarelli_CellSystems2018/metadata.yaml           | 2 +-
 problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml | 2 +-
 problems/Oliveira_NatCommun2021/metadata.yaml              | 2 +-
 problems/Perelson_Science1996/metadata.yaml                | 2 +-
 problems/Rahman_MBS2016/metadata.yaml                      | 2 +-
 problems/Raia_CancerResearch2011/metadata.yaml             | 2 +-
 problems/SalazarCavazos_MBoC2020/metadata.yaml             | 2 +-
 problems/Weber_BMC2015/metadata.yaml                       | 2 +-
 problems/Zhao_QuantBiol2020/metadata.yaml                  | 2 +-
 problems/Zheng_PNAS2012/metadata.yaml                      | 2 +-
 24 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/problems/Alkan_SciSignal2018/metadata.yaml b/problems/Alkan_SciSignal2018/metadata.yaml
index 4a68cec..8795ee6 100644
--- a/problems/Alkan_SciSignal2018/metadata.yaml
+++ b/problems/Alkan_SciSignal2018/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Alkan_SciSignal2018,
         author = {Alkan, Ozan and Schoeberl, Birgit and Shah, Millie and Koshkaryev, Alexander and Heinemann, Tim and Drummond, Daryl C. and Yaffe, Michael B. and Raue, Andreas},
-        title = {Modeling chemotherapy-induced stress to identify rational combination therapies in the DNA damage response pathway},
+        title = {Modeling chemotherapy-induced stress to identify rational combination therapies in the {DNA} damage response pathway},
         journal = {Science Signaling},
         year = {2018},
         volume = {11},
diff --git a/problems/Bachmann_MSB2011/metadata.yaml b/problems/Bachmann_MSB2011/metadata.yaml
index bb88868..0f90051 100644
--- a/problems/Bachmann_MSB2011/metadata.yaml
+++ b/problems/Bachmann_MSB2011/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Bachmann_MSB2011,
         author = {Bachmann, Julie and Raue, Andreas and Schilling, Marcel and Böhm, Martin E and Kreutz, Clemens and Kaschek, Daniel and Busch, Hauke and Gretz, Norbert and Lehmann, Wolf D and Timmer, Jens and Klingmüller, Ursula},
-        title = {Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range},
+        title = {Division of labor by dual feedback regulators controls {JAK2/STAT5} signaling over broad ligand range},
         journal = {Molecular Systems Biology},
         year = {2011},
         volume = {7},
diff --git a/problems/Beer_MolBioSystems2014/metadata.yaml b/problems/Beer_MolBioSystems2014/metadata.yaml
index b4ea961..f5e5cdd 100644
--- a/problems/Beer_MolBioSystems2014/metadata.yaml
+++ b/problems/Beer_MolBioSystems2014/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Beer_MolBioSystems2014,
         author = {Beer, Ralf and Herbst, Konrad and Ignatiadis, Nikolaos and Kats, Ilia and Adlung, Lorenz and Meyer, Hannah and Niopek, Dominik and Christiansen, Tania and Georgi, Fanny and Kurzawa, Nils and Meichsner, Johanna and Rabe, Sophie and Riedel, Anja and Sachs, Joshua and Schessner, Julia and Schmidt, Florian and Walch, Philipp and Niopek, Katharina and Heinemann, Tim and Eils, Roland and Di Ventura, Barbara},
-        title = {Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange},
+        title = {Creating functional engineered variants of the single-module non-ribosomal peptide synthetase {IndC} by {T} domain exchange},
         journal = {Molecular BioSystems},
         year = {2014},
         volume = {10},
diff --git a/problems/Bertozzi_PNAS2020/metadata.yaml b/problems/Bertozzi_PNAS2020/metadata.yaml
index 1b111a9..ad7000c 100644
--- a/problems/Bertozzi_PNAS2020/metadata.yaml
+++ b/problems/Bertozzi_PNAS2020/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Bertozzi_PNAS2020,
         author = {Bertozzi, Andrea L. and Franco, Elisa and Mohler, George and Short, Martin B. and Sledge, Daniel},
-        title = {The challenges of modeling and forecasting the spread of COVID-19},
+        title = {The challenges of modeling and forecasting the spread of {COVID-19}},
         journal = {Proceedings of the National Academy of Sciences},
         year = {2020},
         volume = {117},
diff --git a/problems/Boehm_JProteomeRes2014/metadata.yaml b/problems/Boehm_JProteomeRes2014/metadata.yaml
index 53a44bf..7d878f1 100644
--- a/problems/Boehm_JProteomeRes2014/metadata.yaml
+++ b/problems/Boehm_JProteomeRes2014/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Boehm_JProteomeRes2014,
         author = {Boehm, Martin E. and Adlung, Lorenz and Schilling, Marcel and Roth, Susanne and Klingmüller, Ursula and Lehmann, Wolf D.},
-        title = {Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent STAT5 Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling},
+        title = {Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent {STAT5} Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling},
         journal = {Journal of Proteome Research},
         year = {2014},
         volume = {13},
diff --git a/problems/Borghans_BiophysChem1997/metadata.yaml b/problems/Borghans_BiophysChem1997/metadata.yaml
index 43ec255..6e9734d 100644
--- a/problems/Borghans_BiophysChem1997/metadata.yaml
+++ b/problems/Borghans_BiophysChem1997/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Borghans_BiophysChem1997,
         author = {Borghans, José A. M. and Dupont, Geneviève and Goldbeter, Albert},
-        title = {Complex intracellular calcium oscillations. A theoretical exploration of possible mechanisms},
+        title = {Complex intracellular calcium oscillations. {A} theoretical exploration of possible mechanisms},
         journal = {Biophysical Chemistry},
         year = {1997},
         volume = {66},
diff --git a/problems/Bruno_JExpBot2016/metadata.yaml b/problems/Bruno_JExpBot2016/metadata.yaml
index e3828f5..4b1a343 100644
--- a/problems/Bruno_JExpBot2016/metadata.yaml
+++ b/problems/Bruno_JExpBot2016/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Bruno_JExpBot2016,
         author = {Bruno, Mark and Koschmieder, Julian and Wuest, Florian and Schaub, Patrick and Fehling-Kaschek, Mirjam and Timmer, Jens and Beyer, Peter and Al-Babili, Salim},
-        title = {Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites},
+        title = {Enzymatic study on {AtCCD4} and {AtCCD7} and their potential to form acyclic regulatory metabolites},
         journal = {Journal of Experimental Botany},
         year = {2016},
         volume = {67},
diff --git a/problems/Chen_MSB2009/metadata.yaml b/problems/Chen_MSB2009/metadata.yaml
index e9c60a4..c9eb334 100644
--- a/problems/Chen_MSB2009/metadata.yaml
+++ b/problems/Chen_MSB2009/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Chen_MSB2009,
         author = {Chen, William W and Schoeberl, Birgit and Jasper, Paul J and Niepel, Mario and Nielsen, Ulrik B and Lauffenburger, Douglas A and Sorger, Peter K},
-        title = {Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data},
+        title = {Input–output behavior of {ErbB} signaling pathways as revealed by a mass action model trained against dynamic data},
         journal = {Molecular Systems Biology},
         year = {2009},
         volume = {5},
diff --git a/problems/Crauste_CellSystems2017/metadata.yaml b/problems/Crauste_CellSystems2017/metadata.yaml
index 4fb05d3..acdf089 100644
--- a/problems/Crauste_CellSystems2017/metadata.yaml
+++ b/problems/Crauste_CellSystems2017/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Crauste_CellSystems2017,
         author = {Crauste, Fabien and Mafille, Julien and Boucinha, Lilia and Djebali, Sophia and Gandrillon, Olivier and Marvel, Jacqueline and Arpin, Christophe},
-        title = {Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny},
+        title = {Identification of Nascent Memory {CD8} {T} Cells and Modeling of Their Ontogeny},
         journal = {Cell Systems},
         year = {2017},
         volume = {4},
diff --git a/problems/Fujita_SciSignal2010/metadata.yaml b/problems/Fujita_SciSignal2010/metadata.yaml
index 860e54c..b9581c8 100644
--- a/problems/Fujita_SciSignal2010/metadata.yaml
+++ b/problems/Fujita_SciSignal2010/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Fujita_SciSignal2010,
         author = {Fujita, Kazuhiro A. and Toyoshima, Yu and Uda, Shinsuke and Ozaki, Yu-ichi and Kubota, Hiroyuki and Kuroda, Shinya},
-        title = {Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics},
+        title = {Decoupling of Receptor and Downstream Signals in the {Akt} Pathway by Its Low-Pass Filter Characteristics},
         journal = {Science Signaling},
         year = {2010},
         volume = {3},
diff --git a/problems/Giordano_Nature2020/metadata.yaml b/problems/Giordano_Nature2020/metadata.yaml
index 63a3716..4472327 100644
--- a/problems/Giordano_Nature2020/metadata.yaml
+++ b/problems/Giordano_Nature2020/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Giordano_Nature2020,
         author = {Giordano, Giulia and Blanchini, Franco and Bruno, Raffaele and Colaneri, Patrizio and Di Filippo, Alessandro and Di Matteo, Angela and Colaneri, Marta},
-        title = {Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy},
+        title = {Modelling the {COVID-19} epidemic and implementation of population-wide interventions in {Italy}},
         journal = {Nature Medicine},
         year = {2020},
         volume = {26},
diff --git a/problems/Isensee_JCB2018/metadata.yaml b/problems/Isensee_JCB2018/metadata.yaml
index 3ffc4bb..8269803 100644
--- a/problems/Isensee_JCB2018/metadata.yaml
+++ b/problems/Isensee_JCB2018/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Isensee_JCB2018,
         author = {Isensee, Jörg and Kaufholz, Melanie and Knape, Matthias J. and Hasenauer, Jan and Hammerich, Hanna and Gonczarowska-Jorge, Humberto and Zahedi, René P. and Schwede, Frank and Herberg, Friedrich W. and Hucho, Tim},
-        title = {PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination},
+        title = {{PKA-RII} subunit phosphorylation precedes activation by {cAMP} and regulates activity termination},
         journal = {Journal of Cell Biology},
         year = {2018},
         volume = {217},
diff --git a/problems/Lang_PLOSComputBiol2024/metadata.yaml b/problems/Lang_PLOSComputBiol2024/metadata.yaml
index debc670..412a28e 100644
--- a/problems/Lang_PLOSComputBiol2024/metadata.yaml
+++ b/problems/Lang_PLOSComputBiol2024/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Lang_PLOSComputBiol2024,
         author = {Lang, Paul F. and Penas, David R. and Banga, Julio R. and Weindl, Daniel and Novak, Bela},
-        title = {Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells},
+        title = {Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in {RPE-1} cells},
         journal = {PLOS Computational Biology},
         year = {2024},
         volume = {20},
diff --git a/problems/Laske_PLOSComputBiol2019/metadata.yaml b/problems/Laske_PLOSComputBiol2019/metadata.yaml
index 62292d0..7cee2a5 100644
--- a/problems/Laske_PLOSComputBiol2019/metadata.yaml
+++ b/problems/Laske_PLOSComputBiol2019/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Laske_PLOSComputBiol2019,
         author = {Laske, Tanja and Bachmann, Mandy and Dostert, Melanie and Karlas, Alexander and Wirth, Dagmar and Frensing, Timo and Meyer, Thomas F. and Hauser, Hansjörg and Reichl, Udo},
-        title = {Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth},
+        title = {Model-based analysis of influenza {A} virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth},
         journal = {PLOS Computational Biology},
         year = {2019},
         volume = {15},
diff --git a/problems/Lucarelli_CellSystems2018/metadata.yaml b/problems/Lucarelli_CellSystems2018/metadata.yaml
index fe49374..3892807 100644
--- a/problems/Lucarelli_CellSystems2018/metadata.yaml
+++ b/problems/Lucarelli_CellSystems2018/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Lucarelli_CellSystems2018,
         author = {Lucarelli, Philippe and Schilling, Marcel and Kreutz, Clemens and Vlasov, Artyom and Boehm, Martin E. and Iwamoto, Nao and Steiert, Bernhard and Lattermann, Susen and Wäsch, Marvin and Stepath, Markus and Matter, Matthias S. and Heikenwälder, Mathias and Hoffmann, Katrin and Deharde, Daniela and Damm, Georg and Seehofer, Daniel and Muciek, Maria and Gretz, Norbert and Lehmann, Wolf D. and Timmer, Jens and Klingmüller, Ursula},
-        title = {Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression},
+        title = {Resolving the Combinatorial Complexity of {Smad} Protein Complex Formation and Its Link to Gene Expression},
         journal = {Cell Systems},
         year = {2018},
         volume = {6},
diff --git a/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml b/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml
index b690867..10a8ff9 100644
--- a/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml
+++ b/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Okuonghae_ChaosSolitonsFractals2020,
         author = {Okuonghae, D. and Omame, A.},
-        title = {Analysis of a mathematical model for COVID-19 population dynamics in Lagos, Nigeria},
+        title = {Analysis of a mathematical model for {COVID-19} population dynamics in {Lagos}, {Nigeria}},
         journal = {Chaos, Solitons \& Fractals},
         year = {2020},
         volume = {139},
diff --git a/problems/Oliveira_NatCommun2021/metadata.yaml b/problems/Oliveira_NatCommun2021/metadata.yaml
index 2d78a44..d3d608e 100644
--- a/problems/Oliveira_NatCommun2021/metadata.yaml
+++ b/problems/Oliveira_NatCommun2021/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Oliveira_NatCommun2021,
         author = {Oliveira, Juliane F. and Jorge, Daniel C. P. and Veiga, Rafael V. and Rodrigues, Moreno S. and Torquato, Matheus F. and da Silva, Nivea B. and Fiaccone, Rosemeire L. and Cardim, Luciana L. and Pereira, Felipe A. C. and de Castro, Caio P. and Paiva, Aureliano S. S. and Amad, Alan A. S. and Lima, Ernesto A. B. F. and Souza, Diego S. and Pinho, Suani T. R. and Ramos, Pablo Ivan P. and Andrade, Roberto F. S.},
-        title = {Mathematical modeling of COVID-19 in 14.8 million individuals in Bahia, Brazil},
+        title = {Mathematical modeling of {COVID-19} in 14.8 million individuals in {Bahia}, {Brazil}},
         journal = {Nature Communications},
         year = {2021},
         volume = {12},
diff --git a/problems/Perelson_Science1996/metadata.yaml b/problems/Perelson_Science1996/metadata.yaml
index 235f5ce..a185ce7 100644
--- a/problems/Perelson_Science1996/metadata.yaml
+++ b/problems/Perelson_Science1996/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Perelson_Science1996,
         author = {Perelson, Alan S. and Neumann, Avidan U. and Markowitz, Martin and Leonard, John M. and Ho, David D.},
-        title = {HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time},
+        title = {{HIV-1} Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time},
         journal = {Science},
         year = {1996},
         volume = {271},
diff --git a/problems/Rahman_MBS2016/metadata.yaml b/problems/Rahman_MBS2016/metadata.yaml
index 0228a8d..7b6d045 100644
--- a/problems/Rahman_MBS2016/metadata.yaml
+++ b/problems/Rahman_MBS2016/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Rahman_MBS2016,
         author = {Rahman, S. M. Ashrafur and Vaidya, Naveen K. and Zou, Xingfu},
-        title = {Impact of early treatment programs on HIV epidemics: An immunity-based mathematical model},
+        title = {Impact of early treatment programs on {HIV} epidemics: An immunity-based mathematical model},
         journal = {Mathematical Biosciences},
         year = {2016},
         volume = {280},
diff --git a/problems/Raia_CancerResearch2011/metadata.yaml b/problems/Raia_CancerResearch2011/metadata.yaml
index 08c99ca..e9a5935 100644
--- a/problems/Raia_CancerResearch2011/metadata.yaml
+++ b/problems/Raia_CancerResearch2011/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Raia_CancerResearch2011,
         author = {Raia, Valentina and Schilling, Marcel and Böhm, Martin and Hahn, Bettina and Kowarsch, Andreas and Raue, Andreas and Sticht, Carsten and Bohl, Sebastian and Saile, Maria and Möller, Peter and Gretz, Norbert and Timmer, Jens and Theis, Fabian and Lehmann, Wolf-Dieter and Lichter, Peter and Klingmüller, Ursula},
-        title = {Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets},
+        title = {Dynamic Mathematical Modeling of {IL13}-Induced Signaling in {Hodgkin} and Primary Mediastinal {B}-Cell Lymphoma Allows Prediction of Therapeutic Targets},
         journal = {Cancer Research},
         year = {2011},
         volume = {71},
diff --git a/problems/SalazarCavazos_MBoC2020/metadata.yaml b/problems/SalazarCavazos_MBoC2020/metadata.yaml
index 8a74869..bbf707b 100644
--- a/problems/SalazarCavazos_MBoC2020/metadata.yaml
+++ b/problems/SalazarCavazos_MBoC2020/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{SalazarCavazos_MBoC2020,
         author = {Salazar-Cavazos, Emanuel and Nitta, Carolina Franco and Mitra, Eshan D. and Wilson, Bridget S. and Lidke, Keith A. and Hlavacek, William S. and Lidke, Diane S.},
-        title = {Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes},
+        title = {Multisite {EGFR} phosphorylation is regulated by adaptor protein abundances and dimer lifetimes},
         journal = {Molecular Biology of the Cell},
         year = {2020},
         volume = {31},
diff --git a/problems/Weber_BMC2015/metadata.yaml b/problems/Weber_BMC2015/metadata.yaml
index fa86b77..b7dbb53 100644
--- a/problems/Weber_BMC2015/metadata.yaml
+++ b/problems/Weber_BMC2015/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Weber_BMC2015,
         author = {Weber, Patrick and Hornjik, Mariana and Olayioye, Monilola A and Hausser, Angelika and Radde, Nicole E},
-        title = {A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells},
+        title = {A computational model of {PKD} and {CERT} interactions at the trans-{Golgi} network of mammalian cells},
         journal = {BMC Systems Biology},
         year = {2015},
         volume = {9},
diff --git a/problems/Zhao_QuantBiol2020/metadata.yaml b/problems/Zhao_QuantBiol2020/metadata.yaml
index 082f8a4..cf2b723 100644
--- a/problems/Zhao_QuantBiol2020/metadata.yaml
+++ b/problems/Zhao_QuantBiol2020/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Zhao_QuantBiol2020,
         author = {Zhao, Shilei and Chen, Hua},
-        title = {Modeling the epidemic dynamics and control of COVID-19 outbreak in China},
+        title = {Modeling the epidemic dynamics and control of {COVID-19} outbreak in {China}},
         journal = {Quantitative Biology},
         year = {2020},
         volume = {8},
diff --git a/problems/Zheng_PNAS2012/metadata.yaml b/problems/Zheng_PNAS2012/metadata.yaml
index ebd5753..f630836 100644
--- a/problems/Zheng_PNAS2012/metadata.yaml
+++ b/problems/Zheng_PNAS2012/metadata.yaml
@@ -4,7 +4,7 @@ references:
     bibtex: |
       @article{Zheng_PNAS2012,
         author = {Zheng, Yupeng and Sweet, Steve M. M. and Popovic, Relja and Martinez-Garcia, Eva and Tipton, Jeremiah D. and Thomas, Paul M. and Licht, Jonathan D. and Kelleher, Neil L.},
-        title = {Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3},
+        title = {Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone {H3}},
         journal = {Proceedings of the National Academy of Sciences},
         year = {2012},
         volume = {109},

From 0e23ee897e0e269f63883d58538190139f582d0b Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 22 Oct 2026 14:27:57 +0200
Subject: [PATCH 7/7] Add periods to initials in BibTeX author names
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Some journals print initials without periods ("Martin E Böhm"), and
Crossref has them that way. In BibTeX, initials should end with a
period; otherwise styles that print full given names show "Martin E
Böhm", and JabRef reports the names as not in standard BibTeX format.
Affects `Bachmann_MSB2011`, `Chen_MSB2009`, `Smith_BMCSystBiol2013`,
and `Weber_BMC2015`.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 problems/Bachmann_MSB2011/metadata.yaml      | 2 +-
 problems/Chen_MSB2009/metadata.yaml          | 2 +-
 problems/Smith_BMCSystBiol2013/metadata.yaml | 2 +-
 problems/Weber_BMC2015/metadata.yaml         | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/problems/Bachmann_MSB2011/metadata.yaml b/problems/Bachmann_MSB2011/metadata.yaml
index 0f90051..9677ef0 100644
--- a/problems/Bachmann_MSB2011/metadata.yaml
+++ b/problems/Bachmann_MSB2011/metadata.yaml
@@ -3,7 +3,7 @@ references:
   - doi: 10.1038/msb.2011.50
     bibtex: |
       @article{Bachmann_MSB2011,
-        author = {Bachmann, Julie and Raue, Andreas and Schilling, Marcel and Böhm, Martin E and Kreutz, Clemens and Kaschek, Daniel and Busch, Hauke and Gretz, Norbert and Lehmann, Wolf D and Timmer, Jens and Klingmüller, Ursula},
+        author = {Bachmann, Julie and Raue, Andreas and Schilling, Marcel and Böhm, Martin E. and Kreutz, Clemens and Kaschek, Daniel and Busch, Hauke and Gretz, Norbert and Lehmann, Wolf D. and Timmer, Jens and Klingmüller, Ursula},
         title = {Division of labor by dual feedback regulators controls {JAK2/STAT5} signaling over broad ligand range},
         journal = {Molecular Systems Biology},
         year = {2011},
diff --git a/problems/Chen_MSB2009/metadata.yaml b/problems/Chen_MSB2009/metadata.yaml
index c9eb334..d3a800a 100644
--- a/problems/Chen_MSB2009/metadata.yaml
+++ b/problems/Chen_MSB2009/metadata.yaml
@@ -3,7 +3,7 @@ references:
   - doi: 10.1038/msb.2008.74
     bibtex: |
       @article{Chen_MSB2009,
-        author = {Chen, William W and Schoeberl, Birgit and Jasper, Paul J and Niepel, Mario and Nielsen, Ulrik B and Lauffenburger, Douglas A and Sorger, Peter K},
+        author = {Chen, William W. and Schoeberl, Birgit and Jasper, Paul J. and Niepel, Mario and Nielsen, Ulrik B. and Lauffenburger, Douglas A. and Sorger, Peter K.},
         title = {Input–output behavior of {ErbB} signaling pathways as revealed by a mass action model trained against dynamic data},
         journal = {Molecular Systems Biology},
         year = {2009},
diff --git a/problems/Smith_BMCSystBiol2013/metadata.yaml b/problems/Smith_BMCSystBiol2013/metadata.yaml
index 57ca51f..96091b2 100644
--- a/problems/Smith_BMCSystBiol2013/metadata.yaml
+++ b/problems/Smith_BMCSystBiol2013/metadata.yaml
@@ -3,7 +3,7 @@ references:
   - doi: 10.1186/1752-0509-7-41
     bibtex: |
       @article{Smith_BMCSystBiol2013,
-        author = {Smith, Graham R and Shanley, Daryl P},
+        author = {Smith, Graham R. and Shanley, Daryl P.},
         title = {Computational modelling of the regulation of Insulin signalling by oxidative stress},
         journal = {BMC Systems Biology},
         year = {2013},
diff --git a/problems/Weber_BMC2015/metadata.yaml b/problems/Weber_BMC2015/metadata.yaml
index b7dbb53..39952d0 100644
--- a/problems/Weber_BMC2015/metadata.yaml
+++ b/problems/Weber_BMC2015/metadata.yaml
@@ -3,7 +3,7 @@ references:
   - doi: 10.1186/s12918-015-0147-1
     bibtex: |
       @article{Weber_BMC2015,
-        author = {Weber, Patrick and Hornjik, Mariana and Olayioye, Monilola A and Hausser, Angelika and Radde, Nicole E},
+        author = {Weber, Patrick and Hornjik, Mariana and Olayioye, Monilola A. and Hausser, Angelika and Radde, Nicole E.},
         title = {A computational model of {PKD} and {CERT} interactions at the trans-{Golgi} network of mammalian cells},
         journal = {BMC Systems Biology},
         year = {2015},