{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2026/10/17/peer-reviewed-articles-about-biological-processes.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/2qh9a-37895", "url": "https://chem-bla-ics.linkedchemistry.info/2026/10/17/peer-reviewed-articles-about-biological-processes.html", "title": "Peer reviewed articles about biological processes in WikiPathways", "content_html": "

Earlier this year I blogged about a few\ncollaborations where WikiPathways content has been created and/or curated. I mentioned that\nthere are pathways in WikiPathways supported by a full paper, but I will leave that for a later moment.

\n\n

Well, it has been a busy year, but that moment has arrived.

\n\n

Almost every year since the start of WikiPathways a paper was published described mostly one and sometimes a few pathways. Here\nis an overview:

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2010-2020

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2021-2022

\n\n\n\n

2023-

\n\n\n\n

That list turned out to be quite a bit longer than I expected. I only knew of a handful of articles describing newly created/curated\npathways. This is positive. If peer review works well, then these pathways, as part of these articles have been peer reviewed well too.\nIt is reasonable assume that peer review will not be ideal (it is not), but I even found an example of an article describing a WikiPathways\nthat was retracted, and so has been the WikiPathways itself.

\n\n

Did I miss an article? Let me know, and I will add it to this list!

\n\n

References

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Chatterjee, O., Gopalakrishnan, L., Pullimamidi, D., Raj, C., Yelamanchi, S., Gangadharappa, B. S., Nair, B., Mahadevan, A., Raju, R., & Keshava Prasad, T. S. (2022). A molecular network map of orexin-orexin receptor signaling system. Journal of Cell Communication and Signaling, 17(1), 217–227. https://doi.org/10.1007/s12079-022-00700-3 CrossRef Scholia
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Daemen, S., Kutmon, M., & Evelo, C. T. (2013). A pathway approach to investigate the function and regulation of SREBPs. Genes & Nutrition, 8(3), 289–300. https://doi.org/10.1007/s12263-013-0342-x CrossRef Scholia
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Dagamajalu, S., Rex, D. A. B., Philem, P. D., Rainey, J. K., & Keshava Prasad, T. S. (2021). A network map of apelin-mediated signaling. Journal of Cell Communication and Signaling, 16(1), 137–143. https://doi.org/10.1007/s12079-021-00614-6 CrossRef Scholia
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Dagamajalu, S., Rex, D. A. B., Suchitha, G. P., Rai, A. B., Kumar, S., Joshi, S., Raju, R., & Prasad, T. S. K. (2022). A network map of discoidin domain receptor 1(DDR1)-mediated signaling in pathological conditions. Journal of Cell Communication and Signaling, 17(3), 1081–1088. https://doi.org/10.1007/s12079-022-00714-x CrossRef Scholia
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Dagamajalu, S., Rex, D. A. B., Suchitha, G. P., Rai, A. B., Rainey, J. K., & Prasad, T. S. K. (2021). The network map of Elabela signaling pathway in physiological and pathological conditions. Journal of Cell Communication and Signaling, 16(1), 145–154. https://doi.org/10.1007/s12079-021-00640-4 CrossRef Scholia
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Ehrhart, F., Coort, S. L. M., Cirillo, E., Smeets, E., Evelo, C. T., & Curfs, L. M. G. (2016). Rett syndrome – biological pathways leading from MECP2 to disorder phenotypes. Orphanet Journal of Rare Diseases, 11(1). https://doi.org/10.1186/s13023-016-0545-5 CrossRef Scholia
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Ehrhart, F., Janssen, K. J. M., Coort, S. L., Evelo, C. T., & Curfs, L. M. G. (2018). Prader-Willi syndrome and Angelman syndrome: Visualisation of the molecular pathways for two chromosomal disorders. The World Journal of Biological Psychiatry, 20(9), 670–682. https://doi.org/10.1080/15622975.2018.1439594 CrossRef Scholia
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Ehrhart, F., Martens, H., Rosenblum, N. D., Schedl, A., Schlesinger, T. A., Gjerstad, A. C., Haffner, D., Ho, J., Evelo, C. T., Woolf, A. S., Weber, R. G., & Schaefer, F. (2026). Molecular pathways of kidney development and their applications to clinical research. Kidney International, 109(2), 287–296. https://doi.org/10.1016/j.kint.2025.09.032 CrossRef Scholia
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Ehrhart, F., Silva, A., Amelsvoort, T. van, von Scheibler, E., Evelo, C., & Linden, D. E. J. (2024). Copy number variant risk loci for schizophrenia converge on the BDNF pathway. The World Journal of Biological Psychiatry, 25(4), 222–232. https://doi.org/10.1080/15622975.2024.2327027 CrossRef Scholia
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Fijten, R. R. R., Jennen, D. G. J., & Delft, J. H. M. (2013). Pathways for Ligand Activated Nuclear Receptors to Unravel the Genomic Responses Induced by Hepatotoxicants. Current Drug Metabolism, 14(10), 1022–1028. https://doi.org/10.2174/1389200214666131118234138 CrossRef Scholia
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Goel, R., & Raju, R. (2011). A Signaling Network of Thyroid-Stimulating Hormone. Journal of Proteomics & Bioinformatics, 04(10). https://doi.org/10.4172/jpb.1000195 CrossRef Scholia
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Gopalakrishnan, L., Chatterjee, O., Raj, C., Pullimamidi, D., Advani, J., Mahadevan, A., & Keshava Prasad, T. S. (2020). An assembly of galanin–galanin receptor signaling network. Journal of Cell Communication and Signaling, 15(2), 269–275. https://doi.org/10.1007/s12079-020-00590-3 CrossRef Scholia
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Jennen, D. G. J., Gaj, S., Giesbertz, P. J., van Delft, J. H. M., Evelo, C. T., & Kleinjans, J. C. S. (2010). Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes. Drug Discovery Today, 15(19–20), 851–858. https://doi.org/10.1016/j.drudis.2010.08.002 CrossRef Scholia
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Koole, L., Martinez-Martinez, P., Amelsvoort, T. van, Evelo, C. T., & Ehrhart, F. (2023). Interactive neuroinflammation pathways and transcriptomics-based identification of drugs and chemical compounds for schizophrenia. The World Journal of Biological Psychiatry, 25(2), 116–129. https://doi.org/10.1080/15622975.2023.2281514 CrossRef Scholia
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Martens, M., Kreidl, F., Ehrhart, F., Jean, D., Mei, M., Mortensen, H. M., Nash, A., Nymark, P., Evelo, C. T., & Cerciello, F. (2022). A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. Frontiers in Oncology, 12. https://doi.org/10.3389/fonc.2022.849640 CrossRef Scholia
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Mol, P., Balaya, R. D. A., Dagamajalu, S., Babu, S., Chandrasekaran, P., Raghavan, R., Suresh, S., Ravishankara, N., Raju, A. H., Nair, B., Modi, P. K., Mahadevan, A., Prasad, T. S. K., & Raju, R. (2023). A network map of GDNF/RET signaling pathway in physiological and pathological conditions. Journal of Cell Communication and Signaling, 17(3), 1089–1095. https://doi.org/10.1007/s12079-023-00726-1 CrossRef Scholia
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Nymark, P., Rieswijk, L., Ehrhart, F., Jeliazkova, N., Tsiliki, G., Sarimveis, H., Evelo, C. T., Hongisto, V., Kohonen, P., Willighagen, E., & Grafström, R. C. (2017). A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicological Sciences, 162(1), 264–275. https://doi.org/10.1093/toxsci/kfx252 CrossRef Scholia
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Rex, D. A. B., Agarwal, N., Prasad, T. S. K., Kandasamy, R. K., Subbannayya, Y., & Pinto, S. M. (2019). A comprehensive pathway map of IL-18-mediated signalling. Journal of Cell Communication and Signaling, 14(2), 257–266. https://doi.org/10.1007/s12079-019-00544-4 CrossRef Scholia
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Rex, D. A. B., Dagamajalu, S., Kandasamy, R. K., Raju, R., & Prasad, T. S. K. (2021). SARS-CoV-2 signaling pathway map: A functional landscape of molecular mechanisms in COVID-19. Journal of Cell Communication and Signaling, 15(4), 601–608. https://doi.org/10.1007/s12079-021-00632-4 CrossRef Scholia
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Rex, D. A. B., Deepak, K., Vaid, N., Dagamajalu, S., Kandasamy, R. K., Flo, T. H., & Keshava Prasad, T. S. (2021). A modular map of Bradykinin-mediated inflammatory signaling network. Journal of Cell Communication and Signaling, 16(2), 301–310. https://doi.org/10.1007/s12079-021-00652-0 CrossRef Scholia
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Rex, D. A. B., Suchitha, G. P., Palollathil, A., Kanichery, A., Prasad, T. S. K., & Dagamajalu, S. (2022). The network map of urotensin-II mediated signaling pathway in physiological and pathological conditions. Journal of Cell Communication and Signaling, 16(4), 601–608. https://doi.org/10.1007/s12079-022-00672-4 CrossRef Scholia
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Salomonis, N. (2014). Systems-level perspective of sudden infant death syndrome. Pediatric Research, 76(3), 220–229. https://doi.org/10.1038/pr.2014.90 CrossRef Scholia
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Sanjeev, D., Dagamajalu, S., Shaji, V., George, M., Subbannayya, Y., Prasad, T. S. K., Raju, R., & Devasahayam Arokia Balaya, R. (2023). A network map of macrophage-stimulating protein (MSP) signaling. Journal of Cell Communication and Signaling, 17(3), 1113–1120. https://doi.org/10.1007/s12079-023-00755-w CrossRef Scholia
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Siddiqa, A., Cirillo, E., Tareen, S. H. K., Ali, A., Kutmon, M., Eijssen, L. M. T., Ahmad, J., Evelo, C. T., & Coort, S. L. (2017). Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways. Genomics, 109(5–6), 408–418. https://doi.org/10.1016/j.ygeno.2017.06.006 CrossRef Scholia
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Stobbe, M. D., Houten, S. M., van Kampen, A. H. C., Wanders, R. J. A., & Moerland, P. D. (2012). Improving the description of metabolic networks: the TCA cycle as example. The FASEB Journal, 26(9), 3625–3636. https://doi.org/10.1096/fj.11-203091 CrossRef Scholia
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Upadhyay, S. S., Devasahayam Arokia Balaya, R., Parate, S. S., Dagamajalu, S., Keshava Prasad, T. S., Shetty, R., & Raju, R. (2023). An assembly of TROP2-mediated signaling events. Journal of Cell Communication and Signaling, 17(3), 1105–1111. https://doi.org/10.1007/s12079-023-00742-1 CrossRef Scholia
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Valenbreder, I. M. E., Balăn, S., Breuer, M., & Adriaens, M. E. (2023). Mapping out the gut microbiota-dependent trimethylamine N-oxide super pathway for systems biology applications. Frontiers in Systems Biology, 3. https://doi.org/10.3389/fsysb.2023.1074749 CrossRef Scholia
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Walter, A. S., Volkmer, E., Gauglitz, G., Böcker, W., & Saller, M. M. (2023). Systematic review of molecular pathways in burn wound healing. Burns, 49(7), 1525–1533. https://doi.org/10.1016/j.burns.2023.03.006 CrossRef Scholia
\n
", "summary": "Earlier this year I blogged about a few collaborations where WikiPathways content has been created and/or curated. I mentioned that there are pathways in WikiPathways supported by a full paper, but I will leave that for a later moment.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/jcellcommsignal.png", "date_published": "2026-10-17T00:00:00+00:00", "date_modified": "2026-10-17T00:00:00+00:00", "tags": ["wikipathways","publishing"], "_references": [ { "url": "https://doi.org/10.1016/j.drudis.2010.08.002", "doi": "10.1016/j.drudis.2010.08.002" } , { "url": "https://doi.org/10.1007/s12263-013-0342-x", "doi": "10.1007/s12263-013-0342-x" } , { "url": "https://doi.org/10.4172/jpb.1000195", "doi": "10.4172/jpb.1000195" } , { "url": "https://doi.org/10.2174/1389200214666131118234138", "doi": "10.2174/1389200214666131118234138" } , { "url": "https://doi.org/10.1038/pr.2014.90", "doi": "10.1038/pr.2014.90" } , { "url": "https://doi.org/10.1007/s12079-019-00544-4", "doi": "10.1007/s12079-019-00544-4" } , { "url": "https://doi.org/10.1186/s13023-016-0545-5", "doi": "10.1186/s13023-016-0545-5" } , { "url": "https://doi.org/10.1016/j.ygeno.2017.06.006", "doi": "10.1016/j.ygeno.2017.06.006" } , { "url": "https://doi.org/10.1093/toxsci/kfx252", "doi": "10.1093/toxsci/kfx252" } , { "url": "https://doi.org/10.1080/15622975.2018.1439594", "doi": "10.1080/15622975.2018.1439594" } , { "url": "https://doi.org/10.1016/j.kint.2025.09.032", "doi": "10.1016/j.kint.2025.09.032" } , { "url": "https://doi.org/10.3389/fonc.2022.849640", "doi": "10.3389/fonc.2022.849640" } , { "url": "https://doi.org/10.1007/s12079-021-00632-4", "doi": "10.1007/s12079-021-00632-4" } , { "url": "https://doi.org/10.1007/s12079-020-00590-3", "doi": "10.1007/s12079-020-00590-3" } , { "url": "https://doi.org/10.1096/fj.11-203091", "doi": "10.1096/fj.11-203091" } , { "url": "https://doi.org/10.1080/15622975.2024.2327027", "doi": "10.1080/15622975.2024.2327027" } , { "url": "https://doi.org/10.1080/15622975.2023.2281514", "doi": "10.1080/15622975.2023.2281514" } , { "url": "https://doi.org/10.1007/s12079-023-00742-1", "doi": "10.1007/s12079-023-00742-1" } , { "url": "https://doi.org/10.1016/j.burns.2023.03.006", "doi": "10.1016/j.burns.2023.03.006" } , { "url": "https://doi.org/10.1007/s12079-023-00755-w", "doi": "10.1007/s12079-023-00755-w" } , { "url": "https://doi.org/10.1007/s12079-023-00726-1", "doi": "10.1007/s12079-023-00726-1" } , { "url": "https://doi.org/10.3389/fsysb.2023.1074749", "doi": "10.3389/fsysb.2023.1074749" } , { "url": "https://doi.org/10.1007/s12079-022-00714-x", "doi": "10.1007/s12079-022-00714-x" } , { "url": "https://doi.org/10.1007/s12079-022-00700-3", "doi": "10.1007/s12079-022-00700-3" } , { "url": "https://doi.org/10.1007/s12079-022-00672-4", "doi": "10.1007/s12079-022-00672-4" } , { "url": "https://doi.org/10.1007/s12079-021-00640-4", "doi": "10.1007/s12079-021-00640-4" } , { "url": "https://doi.org/10.1007/s12079-021-00614-6", "doi": "10.1007/s12079-021-00614-6" } , { "url": "https://doi.org/10.1007/s12079-021-00652-0", "doi": "10.1007/s12079-021-00652-0" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }