Iman Hajirasouliha, Ph.D

Associate Professor of Physiology and Biophysics

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


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


Research Areas

Research Summary:

Iman Hajirasouliha, Ph.D. is an Associate Professor of Computational Genomics in Computational Biomedicine and an Associate 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 using multiple sequencing platforms, quantifying cancer evolution, the study of tumor heterogeneity using genomics and imaging, and AI in In Vitro Fertilization (IVF).

Recent Publications:

  1. Meleshko, D, Prjbelski, AD, Raiko, M, Tomescu, AI, Tilgner, H, Hajirasouliha, I et al.. cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data. Bioinformatics. 2024;40 (2):. doi: 10.1093/bioinformatics/btad781. PubMed PMID:38262343 PubMed Central PMC10868327.
  2. Rajendran, S, Brendel, M, Barnes, J, Zhan, Q, Malmsten, JE, Zisimopoulos, P et al.. Automatic Ploidy Prediction and Quality Assessment of Human Blastocyst Using Time-Lapse Imaging. bioRxiv. 2023; :. doi: 10.1101/2023.08.31.555741. PubMed PMID:37693566 PubMed Central PMC10491146.
  3. Mak, L, Meleshko, D, Danko, DC, Barakzai, WN, Maharjan, S, Belchikov, N et al.. Ariadne: synthetic long read deconvolution using assembly graphs. Genome Biol. 2023;24 (1):197. doi: 10.1186/s13059-023-03033-5. PubMed PMID:37641111 PubMed Central PMC10463629.
  4. Meleshko, D, Prjbelski, AD, Raiko, M, Tomescu, AI, Tilgner, H, Hajirasouliha, I et al.. cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data. bioRxiv. 2023; :. doi: 10.1101/2023.07.25.550587. PubMed PMID:37546844 PubMed Central PMC10402000.
  5. Mak, L, Tierney, B, Ronkowski, C, Toomey, M, Martinez, JSA, Zimmerman, S et al.. A modular metagenomics analysis system for integrated multi-step data exploration. bioRxiv. 2023; :. doi: 10.1101/2023.04.09.536171. PubMed PMID:37066359 PubMed Central PMC10104186.
  6. Hajirasouliha, I, Semrau, S. Back in 3D-a report on Genome Informatics 2022. Genome Biol. 2023;24 (1):57. doi: 10.1186/s13059-023-02870-8. PubMed PMID:36978161 PubMed Central PMC10053082.
  7. Popic, V, Rohlicek, C, Cunial, F, Hajirasouliha, I, Meleshko, D, Garimella, K et al.. Cue: a deep-learning framework for structural variant discovery and genotyping. Nat Methods. 2023;20 (4):559-568. doi: 10.1038/s41592-023-01799-x. PubMed PMID:36959322 PubMed Central PMC10152467.
  8. Barnes, J, Brendel, M, Gao, VR, Rajendran, S, Kim, J, Li, Q et al.. A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study. Lancet Digit Health. 2023;5 (1):e28-e40. doi: 10.1016/S2589-7500(22)00213-8. PubMed PMID:36543475 PubMed Central PMC10193126.
  9. Meleshko, D, Yang, R, Marks, P, Williams, S, Hajirasouliha, I. Efficient detection and assembly of non-reference DNA sequences with synthetic long reads. Nucleic Acids Res. 2022;50 (18):e108. doi: 10.1093/nar/gkac653. PubMed PMID:35924489 PubMed Central PMC9561269.
  10. Brendel, M, Getseva, V, Assaad, MA, Sigouros, M, Sigaras, A, Kane, T et al.. Weakly-supervised tumor purity prediction from frozen H&E stained slides. EBioMedicine. 2022;80 :104067. doi: 10.1016/j.ebiom.2022.104067. PubMed PMID:35644123 PubMed Central PMC9157012.
  11. Park, J, Foox, J, Hether, T, Danko, DC, Warren, S, Kim, Y et al.. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Rep Med. 2022;3 (2):100522. doi: 10.1016/j.xcrm.2022.100522. PubMed PMID:35233546 PubMed Central PMC8784611.
  12. Meleshko, D, Hajirasouliha, I, Korobeynikov, A. coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. Bioinformatics. 2021;38 (1):1-8. doi: 10.1093/bioinformatics/btab597. PubMed PMID:34406356 PubMed Central PMC10060723.
  13. 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.
  14. 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.
  15. 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 PubMed Central PMC8360022.
  16. 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.
  17. 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.
  18. 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.
  19. 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 .
  20. 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 .
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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