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. Danko, D, Bezdan, D, Afshin, EE, Ahsanuddin, S, Bhattacharya, C, Butler, DJ et al.. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 2021;184 (13):3376-3393.e17. doi: 10.1016/j.cell.2021.05.002. PubMed PMID:34043940 PubMed Central PMC8238498.
  2. Park, J, Foox, J, Hether, T, Danko, D, Warren, S, Kim, Y et al.. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps. bioRxiv. 2021; :. doi: 10.1101/2021.03.08.434433. PubMed PMID:33758858 PubMed Central PMC7987017.
  3. Khosravi, P, Lysandrou, M, Eljalby, M, Li, Q, Kazemi, E, Zisimopoulos, P et al.. A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion. J Magn Reson Imaging. 2021;54 (2):462-471. doi: 10.1002/jmri.27599. PubMed PMID:33719168 .
  4. Butler, D, Mozsary, C, Meydan, C, Foox, J, Rosiene, J, Shaiber, A et al.. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun. 2021;12 (1):1660. doi: 10.1038/s41467-021-21361-7. PubMed PMID:33712587 PubMed Central PMC7954844.
  5. Carrot-Zhang, J, Yao, X, Devarakonda, S, Deshpande, A, Damrauer, JS, Silva, TC et al.. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep. 2021;34 (5):108707. doi: 10.1016/j.celrep.2021.108707. PubMed PMID:33535033 PubMed Central PMC8009291.
  6. Ciccolella, S, Soto Gomez, M, Patterson, MD, Della Vedova, G, Hajirasouliha, I, Bonizzoni, P et al.. gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC Bioinformatics. 2020;21 (Suppl 1):413. doi: 10.1186/s12859-020-03736-7. PubMed PMID:33297943 PubMed Central PMC7725124.
  7. Curchoe, CL, Malmsten, J, Bormann, C, Shafiee, H, Flores-Saiffe Farias, A, Mendizabal, G et al.. Predictive modeling in reproductive medicine: Where will the future of artificial intelligence research take us?. Fertil Steril. 2020;114 (5):934-940. doi: 10.1016/j.fertnstert.2020.10.040. PubMed PMID:33160516 .
  8. Hajirasouliha, I, Elemento, O. Precision medicine and artificial intelligence: overview and relevance to reproductive medicine. Fertil Steril. 2020;114 (5):908-913. doi: 10.1016/j.fertnstert.2020.09.156. PubMed PMID:33160512 .
  9. Ciccolella, S, Ricketts, C, Soto Gomez, M, Patterson, M, Silverbush, D, Bonizzoni, P et al.. Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. Bioinformatics. 2021;37 (3):326-333. doi: 10.1093/bioinformatics/btaa722. PubMed PMID:32805010 PubMed Central PMC8058767.
  10. Zook, JM, Hansen, NF, Olson, ND, Chapman, L, Mullikin, JC, Xiao, C et al.. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020;38 (11):1357. doi: 10.1038/s41587-020-0640-y. PubMed PMID:32699374 .
  11. 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;26 (8):1309. doi: 10.1038/s41591-020-0983-4. PubMed PMID:32591764 PubMed Central PMC7319223.
  12. 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;38 (11):1347-1355. doi: 10.1038/s41587-020-0538-8. PubMed PMID:32541955 .
  13. 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.
  14. 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.
  15. 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;26 (8):1161-1165. doi: 10.1038/s41591-020-0929-x. PubMed PMID:32488218 .
  16. 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.
  17. 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.
  18. 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 PubMed Central PMC8215921.
  19. 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.
  20. 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.
Search PubMed

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