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Page 1
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
A global metagenomic map of urban microbiomes and antimicrobial resistance.
Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE; International MetaSUB Consortium. Danko D, et al. Cell. 2021 Jun 24;184(13):3376-3393.e17. doi: 10.1016/j.cell.2021.05.002. Epub 2021 May 26. Cell. 2021. PMID: 34043940 Free PMC article.
A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium; Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. 1000 Genomes Project Consortium, et al. Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Nature. 2010. PMID: 20981092 Free PMC article.
A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study.
Barnes J, Brendel M, Gao VR, Rajendran S, Kim J, Li Q, Malmsten JE, Sierra JT, Zisimopoulos P, Sigaras A, Khosravi P, Meseguer M, Zhan Q, Rosenwaks Z, Elemento O, Zaninovic N, Hajirasouliha I. Barnes J, et al. Lancet Digit Health. 2023 Jan;5(1):e28-e40. doi: 10.1016/S2589-7500(22)00213-8. Lancet Digit Health. 2023. PMID: 36543475 Free PMC article.
Weakly-supervised tumor purity prediction from frozen H&E stained slides.
Brendel M, Getseva V, Assaad MA, Sigouros M, Sigaras A, Kane T, Khosravi P, Mosquera JM, Elemento O, Hajirasouliha I. Brendel M, et al. EBioMedicine. 2022 Jun;80:104067. doi: 10.1016/j.ebiom.2022.104067. Epub 2022 May 26. EBioMedicine. 2022. PMID: 35644123 Free PMC article.
FUNDING: Starr Cancer Consortium Grant (SCC I15-0027) to Iman Hajirasouliha....
FUNDING: Starr Cancer Consortium Grant (SCC I15-0027) to Iman Hajirasouliha....
Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples.
Hujdurovic A, Kacar U, Milanic M, Ries B, Tomescu AI. Hujdurovic A, et al. IEEE/ACM Trans Comput Biol Bioinform. 2018 Jan-Feb;15(1):96-108. doi: 10.1109/TCBB.2016.2606620. Epub 2016 Oct 13. IEEE/ACM Trans Comput Biol Bioinform. 2018. PMID: 28113405
Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. ...
Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throu …
Structural engineering from an inverse problems perspective.
Gallet A, Rigby S, Tallman TN, Kong X, Hajirasouliha I, Liew A, Liu D, Chen L, Hauptmann A, Smyl D. Gallet A, et al. Proc Math Phys Eng Sci. 2022 Jan;478(2257):20210526. doi: 10.1098/rspa.2021.0526. Epub 2022 Jan 26. Proc Math Phys Eng Sci. 2022. PMID: 35153609 Free PMC article. Review.
71 results