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Analyzing single cell transcriptome data from severe COVID-19 patients.
Nassir N, Tambi R, Bankapur A, Karuvantevida N, Khansaheb HH, Zehra B, Begum G, Hameid RA, Ahmed A, Deesi Z, Alkhajeh A, Uddin KMF, Akter H, Safizadeh Shabestari SA, Gaudet M, Hachim MY, Alsheikh-Ali A, Berdiev BK, Al Heialy S, Uddin M. Nassir N, et al. Among authors: bankapur a. STAR Protoc. 2022 Apr 21;3(2):101379. doi: 10.1016/j.xpro.2022.101379. eCollection 2022 Jun 17. STAR Protoc. 2022. PMID: 35582459 Free PMC article.
Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19.
Nassir N, Tambi R, Bankapur A, Al Heialy S, Karuvantevida N, Khansaheb HH, Zehra B, Begum G, Hameid RA, Ahmed A, Deesi Z, Alkhajeh A, Uddin KMF, Akter H, Safizadeh Shabestari SA, Almidani O, Islam A, Gaudet M, Kandasamy RK, Loney T, Tayoun AA, Nowotny N, Woodbury-Smith M, Rahman P, Kuebler WM, Yaseen Hachim M, Casanova JL, Berdiev BK, Alsheikh-Ali A, Uddin M. Nassir N, et al. Among authors: bankapur a. iScience. 2021 Sep 24;24(9):103030. doi: 10.1016/j.isci.2021.103030. Epub 2021 Aug 25. iScience. 2021. PMID: 34458692 Free PMC article.
Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome.
Begum G, Albanna A, Bankapur A, Nassir N, Tambi R, Berdiev BK, Akter H, Karuvantevida N, Kellam B, Alhashmi D, Sung WWL, Thiruvahindrapuram B, Alsheikh-Ali A, Scherer SW, Uddin M. Begum G, et al. Among authors: bankapur a. Int J Mol Sci. 2021 Feb 19;22(4):2060. doi: 10.3390/ijms22042060. Int J Mol Sci. 2021. PMID: 33669700 Free PMC article.
Single-cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss-of-function variants regulating glial cells.
Nassir N, Bankapur A, Samara B, Ali A, Ahmed A, Inuwa IM, Zarrei M, Safizadeh Shabestari SA, AlBanna A, Howe JL, Berdiev BK, Scherer SW, Woodbury-Smith M, Uddin M. Nassir N, et al. Among authors: bankapur a. Hum Genomics. 2021 Nov 21;15(1):68. doi: 10.1186/s40246-021-00368-7. Hum Genomics. 2021. PMID: 34802461 Free PMC article.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A… See abstract for full author list ➔ Jiang Y, et al. Among authors: bankapur ar. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.