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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton … See abstract for full author list ➔ Zhou N, et al. Among authors: lee aj. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure.
Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, McGowan LD, Guebila MB, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Sun Y, Mai D, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T; COVID-19 Review Consortium; Gitter A, Greene CS. Rando HM, et al. Among authors: lee aj. ArXiv [Preprint]. 2021 Feb 1:arXiv:2102.01521v4. ArXiv. 2021. PMID: 33594340 Free PMC article. Updated. Preprint.
Identification and Development of Therapeutics for COVID-19.
Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Lordan R, Qi Y, Sun Y, Brueffer C, Field JM, Guebila MB, Jadavji NM, Skelly AN, Ramsundar B, Wang J, Goel RR, Park Y; COVID-19 Review Consortium; Boca SM, Gitter A, Greene CS. Rando HM, et al. Among authors: lee aj. ArXiv [Preprint]. 2021 Mar 3:arXiv:2103.02723v3. ArXiv. 2021. PMID: 33688554 Free PMC article. Updated. Preprint.
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure.
Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D'Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T; COVID-19 Review Consortium Vikas Bansal, John P. Barton, Simina M. Boca, Joel D. Boerckel, Christian Brueffer, James Brian Byrd, Stephen Capone, Shikta Das, Anna Ada Dattoli, John J. Dziak, Jeffrey M. Field, Soumita Ghosh, Anthony Gitter, Rishi Raj Goel, Casey S. Greene, Marouen Ben Guebila, Daniel S. Himmelstein, Fengling Hu, Nafisa M. Jadavji, Jeremy P. Kamil, Sergey Knyazev, Likhitha Kolla, Alexandra J. Lee, Ronan Lordan, Tiago Lubiana, Temitayo Lukan, Adam L. MacLean, David Mai, Serghei Mangul, David Manheim, Lucy D’Agostino McGowan, Amruta Naik, YoSon Park, Dimitri Perrin, Yanjun Qi, Diane N. Rafizadeh, Bharath Ramsundar, Halie M. Rando, Sandipan Ray, Michael P. Robson, Vincent Rubinetti, Elizabeth Sell, Lamonica Shinholster, Ashwin N. Skelly, Yuchen Sun, Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen,; Gitter A, Greene CS. Rando HM, et al. Among authors: lee aj. mSystems. 2021 Oct 26;6(5):e0009521. doi: 10.1128/mSystems.00095-21. Epub 2021 Oct 26. mSystems. 2021. PMID: 34698547 Free PMC article.
Identification and Development of Therapeutics for COVID-19.
Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Lordan R, Qi Y, Sun Y, Brueffer C, Field JM, Ben Guebila M, Jadavji NM, Skelly AN, Ramsundar B, Wang J, Goel RR, Park Y; COVID-19 Review Consortium Vikas Bansal, John P. Barton, Simina M. Boca, Joel D. Boerckel, Christian Brueffer, James Brian Byrd, Stephen Capone, Shikta Das, Anna Ada Dattoli, John J. Dziak, Jeffrey M. Field, Soumita Ghosh, Anthony Gitter, Rishi Raj Goel, Casey S. Greene, Marouen Ben Guebila, Daniel S. Himmelstein, Fengling Hu, Nafisa M. Jadavji, Jeremy P. Kamil, Sergey Knyazev, Likhitha Kolla, Alexandra J. Lee, Ronan Lordan, Tiago Lubiana, Temitayo Lukan, Adam L. MacLean, David Mai, Serghei Mangul, David Manheim, Lucy D’Agostino McGowan, Amruta Naik, YoSon Park, Dimitri Perrin, Yanjun Qi, Diane N. Rafizadeh, Bharath Ramsundar, Halie M. Rando, Sandipan Ray, Michael P. Robson, Vincent Rubinetti, Elizabeth Sell, Lamonica Shinholster, Ashwin N. Skelly, Yuchen Sun, Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen; Boca SM, Gitter A, Greene CS. Rando HM, et al. Among authors: lee aj. mSystems. 2021 Dec 21;6(6):e0023321. doi: 10.1128/mSystems.00233-21. Epub 2021 Nov 2. mSystems. 2021. PMID: 34726496 Free PMC article.
Correction for Rando et al., "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure".
Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D'Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T; COVID-19 Review Consortium; Gitter A, Greene CS. Rando HM, et al. Among authors: lee aj. mSystems. 2022 Feb 22;7(1):e0144721. doi: 10.1128/msystems.01447-21. Epub 2022 Jan 25. mSystems. 2022. PMID: 35076276 Free PMC article. No abstract available.
Ten simple rules for large-scale data processing.
Fungtammasan A, Lee A, Taroni J, Wheeler K, Chin CS, Davis S, Greene C. Fungtammasan A, et al. PLoS Comput Biol. 2022 Feb 10;18(2):e1009757. doi: 10.1371/journal.pcbi.1009757. eCollection 2022 Feb. PLoS Comput Biol. 2022. PMID: 35143491 Free PMC article. No abstract available.
1,186 results