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Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.
Sonrel A, Luetge A, Soneson C, Mallona I, Germain PL, Knyazev S, Gilis J, Gerber R, Seurinck R, Paul D, Sonder E, Crowell HL, Fanaswala I, Al-Ajami A, Heidari E, Schmeing S, Milosavljevic S, Saeys Y, Mangul S, Robinson MD. Sonrel A, et al. Among authors: germain pl. Genome Biol. 2023 May 17;24(1):119. doi: 10.1186/s13059-023-02962-5. Genome Biol. 2023. PMID: 37198712 Free PMC article.
The vascular gene Apold1 is dispensable for normal development but controls angiogenesis under pathological conditions.
Fan Z, Ardicoglu R, Batavia AA, Rust R, von Ziegler L, Waag R, Zhang J, Desgeorges T, Sturman O, Dang H, Weber R, Roszkowski M, Moor AE, Schwab ME, Germain PL, Bohacek J, De Bock K. Fan Z, et al. Among authors: germain pl. Angiogenesis. 2023 Aug;26(3):385-407. doi: 10.1007/s10456-023-09870-z. Epub 2023 Mar 18. Angiogenesis. 2023. PMID: 36933174 Free PMC article.
Reuniting philosophy and science to advance cancer research.
Pradeu T, Daignan-Fornier B, Ewald A, Germain PL, Okasha S, Plutynski A, Benzekry S, Bertolaso M, Bissell M, Brown JS, Chin-Yee B, Chin-Yee I, Clevers H, Cognet L, Darrason M, Farge E, Feunteun J, Galon J, Giroux E, Green S, Gross F, Jaulin F, Knight R, Laconi E, Larmonier N, Maley C, Mantovani A, Moreau V, Nassoy P, Rondeau E, Santamaria D, Sawai CM, Seluanov A, Sepich-Poore GD, Sisirak V, Solary E, Yvonnet S, Laplane L. Pradeu T, et al. Among authors: germain pl. Biol Rev Camb Philos Soc. 2023 Oct;98(5):1668-1686. doi: 10.1111/brv.12971. Epub 2023 May 8. Biol Rev Camb Philos Soc. 2023. PMID: 37157910 Free PMC article.
Multiscale modeling uncovers 7q11.23 copy number variation-dependent changes in ribosomal biogenesis and neuronal maturation and excitability.
Mihailovich M, Germain PL, Shyti R, Pozzi D, Noberini R, Liu Y, Aprile D, Tenderini E, Troglio F, Trattaro S, Fabris S, Ciptasari U, Rigoli MT, Caporale N, D'Agostino G, Mirabella F, Vitriolo A, Capocefalo D, Skaros A, Franchini AV, Ricciardi S, Biunno I, Neri A, Nadif Kasri N, Bonaldi T, Aebersold R, Matteoli M, Testa G. Mihailovich M, et al. Among authors: germain pl. J Clin Invest. 2024 Jul 15;134(14):e168982. doi: 10.1172/JCI168982. J Clin Invest. 2024. PMID: 39007270 Free PMC article.
Ten simple rules for computational biologists collaborating with wet lab researchers.
Robinson MD, Cai P, Emons M, Gerber R, Germain PL, Gunz S, Luo S, Moro G, Sonder E, Sonrel A, Wang J, Wissel D, Mallona I. Robinson MD, et al. Among authors: germain pl. PLoS Comput Biol. 2024 Jun 20;20(6):e1012174. doi: 10.1371/journal.pcbi.1012174. eCollection 2024 Jun. PLoS Comput Biol. 2024. PMID: 38900718 Free PMC article.
On the identification of differentially-active transcription factors from ATAC-seq data.
Gerbaldo FE, Sonder E, Fischer V, Frei S, Wang J, Gapp K, Robinson MD, Germain PL. Gerbaldo FE, et al. Among authors: germain pl. bioRxiv [Preprint]. 2024 Aug 20:2024.03.06.583825. doi: 10.1101/2024.03.06.583825. bioRxiv. 2024. Update in: PLoS Comput Biol. 2024 Oct 23;20(10):e1011971. doi: 10.1371/journal.pcbi.1011971 PMID: 38496482 Free PMC article. Updated. Preprint.
46 results