Iman Hajirasouliha, Ph.D

Assistant Professor of Physiology and Biophysics

  • Assistant Professor of Computational Genomics in Computational Biomedicine in the Institute for Computational Biomedicine

646-962-7804

1305 York Avenue, Room Y-13.09
New York, NY 10021


Techniques

Research Areas


Research Summary:

Iman Hajirasouliha, Ph.D. is an Assistant Professor of Computational Genomics in Computational Biomedicine and an Assistant Professor of Physiology and Biophysics, Physiology and Biophysics. Dr. Hajirasouliha and his lab team are passionate about developing new algorithms, machine learning and deep learning methods, and their applications to genomics, metagenomics and cancer research. Some of the current projects in the lab include characterizing human genomes and metagenomes sequenced by exciting new technologies, quantifying cancer evolution, a study of tumor heterogeneity using genomics and digital pathology images.

Recent Publications:

  1. Segal, E, Zhang, F, Lin, X, King, G, Shalem, O, Shilo, S et al.. Publisher Correction: Building an international consortium for tracking coronavirus health status. Nat. Med. 2020; :. doi: 10.1038/s41591-020-0983-4. PubMed PMID:32591764 PubMed Central PMC7319223.
  2. Zook, JM, Hansen, NF, Olson, ND, Chapman, L, Mullikin, JC, Xiao, C et al.. A robust benchmark for detection of germline large deletions and insertions. Nat. Biotechnol. 2020; :. doi: 10.1038/s41587-020-0538-8. PubMed PMID:32541955 .
  3. Chng, KR, Li, C, Bertrand, D, Ng, AHQ, Kwah, JS, Low, HM et al.. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat. Med. 2020;26 (6):941-951. doi: 10.1038/s41591-020-0894-4. PubMed PMID:32514171 PubMed Central PMC7303012.
  4. Butler, DJ, Mozsary, C, Meydan, C, Danko, D, Foox, J, Rosiene, J et al.. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions. bioRxiv. 2020; :. doi: 10.1101/2020.04.20.048066. PubMed PMID:32511352 PubMed Central PMC7255793.
  5. Segal, E, Zhang, F, Lin, X, King, G, Shalem, O, Shilo, S et al.. Building an international consortium for tracking coronavirus health status. Nat. Med. 2020; :. doi: 10.1038/s41591-020-0929-x. PubMed PMID:32488218 .
  6. Karaoğlanoğlu, F, Ricketts, C, Ebren, E, Rasekh, ME, Hajirasouliha, I, Alkan, C et al.. VALOR2: characterization of large-scale structural variants using linked-reads. Genome Biol. 2020;21 (1):72. doi: 10.1186/s13059-020-01975-8. PubMed PMID:32192518 PubMed Central PMC7083023.
  7. Malikic, S, Mehrabadi, FR, Ciccolella, S, Rahman, MK, Ricketts, C, Haghshenas, E et al.. PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. Genome Res. 2019;29 (11):1860-1877. doi: 10.1101/gr.234435.118. PubMed PMID:31628256 PubMed Central PMC6836735.
  8. Ricketts, C, Seidman, D, Popic, V, Hormozdiari, F, Batzoglou, S, Hajirasouliha, I et al.. Meltos: multi-sample tumor phylogeny reconstruction for structural variants. Bioinformatics. 2020;36 (4):1082-1090. doi: 10.1093/bioinformatics/btz737. PubMed PMID:31584621 .
  9. Khosravi, P, Kazemi, E, Zhan, Q, Malmsten, JE, Toschi, M, Zisimopoulos, P et al.. Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization. NPJ Digit Med. 2019;2 :21. doi: 10.1038/s41746-019-0096-y. PubMed PMID:31304368 PubMed Central PMC6550169.
  10. Toosi, H, Moeini, A, Hajirasouliha, I. BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples. BMC Bioinformatics. 2019;20 (Suppl 11):282. doi: 10.1186/s12859-019-2824-3. PubMed PMID:31167637 PubMed Central PMC6551234.
  11. Meleshko, D, Mohimani, H, Tracanna, V, Hajirasouliha, I, Medema, MH, Korobeynikov, A et al.. BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs. Genome Res. 2019;29 (8):1352-1362. doi: 10.1101/gr.243477.118. PubMed PMID:31160374 PubMed Central PMC6673720.
  12. Hajirasouliha, I, Tilgner, HU. The tech for the next decade: promises and challenges in genome biology. Genome Biol. 2019;20 (1):86. doi: 10.1186/s13059-019-1695-2. PubMed PMID:31039798 PubMed Central PMC6492373.
  13. Danko, DC, Meleshko, D, Bezdan, D, Mason, C, Hajirasouliha, I. Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics. Genome Res. 2019;29 (1):116-124. doi: 10.1101/gr.235499.118. PubMed PMID:30523036 PubMed Central PMC6314158.
  14. Ricketts, C, Popic, V, Toosi, H, Hajirasouliha, I. Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees. Curr Protoc Bioinformatics. 2018;62 (1):e49. doi: 10.1002/cpbi.49. PubMed PMID:29927069 PubMed Central PMC6020047.
  15. Khosravi, P, Kazemi, E, Imielinski, M, Elemento, O, Hajirasouliha, I. Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images. EBioMedicine. 2018;27 :317-328. doi: 10.1016/j.ebiom.2017.12.026. PubMed PMID:29292031 PubMed Central PMC5828543.
  16. Popic, V, Salari, R, Hajirasouliha, I, Kashef-Haghighi, D, West, RB, Batzoglou, S et al.. Fast and scalable inference of multi-sample cancer lineages. Genome Biol. 2015;16 :91. doi: 10.1186/s13059-015-0647-8. PubMed PMID:25944252 PubMed Central PMC4501097.
  17. Delaneau, O, Marchini, J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun. 2014;5 :3934. doi: 10.1038/ncomms4934. PubMed PMID:25653097 PubMed Central PMC4338501.
  18. Ritz, A, Bashir, A, Sindi, S, Hsu, D, Hajirasouliha, I, Raphael, BJ et al.. Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics. 2014;30 (24):3458-66. doi: 10.1093/bioinformatics/btu714. PubMed PMID:25355789 PubMed Central PMC4253835.
  19. Colonna, V, Ayub, Q, Chen, Y, Pagani, L, Luisi, P, Pybus, M et al.. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol. 2014;15 (6):R88. doi: 10.1186/gb-2014-15-6-r88. PubMed PMID:24980144 PubMed Central PMC4197830.
  20. Hajirasouliha, I, Mahmoody, A, Raphael, BJ. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinformatics. 2014;30 (12):i78-86. doi: 10.1093/bioinformatics/btu284. PubMed PMID:24932008 PubMed Central PMC4058927.
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Selected Publications:

  1. Mapping copy number variation by population-scale genome sequencing. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.Nature. 2011. PMID:21293372
  2. 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.Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Erratum in: Nature. 2011 May 26;473(7348):544. Xue, Yali [added]; Cartwright, Reed A [added]; Altshuler, David L [corrected to Altshuler, David]; Kebbel, Andrew [corrected to Keebler, Jonathan]; Koko-Gonzales, Paula [corrected to Kokko-Gonzales, Paula]; Nickerson, Debbie A [corrected to Nickerson, Debo. PMID: 20981092 

  3. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC.Bioinformatics. 2010 May 15;26(10):1277-83. doi: 10.1093/bioinformatics/btq152. Epub 2010 Apr 12.PMID: 20385726