Hajirasouliha, Iman

Publications

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selected publications

AutoRadAI: a versatile artificial intelligence framework validated for detecting extracapsular extension in prostate cancer. Biology methods & protocols. 2025 Academic Article GET IT
A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer. NPJ precision oncology. 2025 Academic Article GET IT
Blackbird: structural variant detection using synthetic and low-coverage long-reads. 2024 GET IT
Automatic ploidy prediction and quality assessment of human blastocysts using time-lapse imaging. Nature communications. 2024 Academic Article GET IT
cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data. Bioinformatics (Oxford, England). 2024 Academic Article GET IT
Automatic Ploidy Prediction and Quality Assessment of Human Blastocyst Using Time-Lapse Imaging. 2023 GET IT
Ariadne: synthetic long read deconvolution using assembly graphs. Genome biology. 2023 Academic Article GET IT
Times cited: 3
Back in 3D-a report on Genome Informatics 2022. Genome biology. 2023 Academic Article GET IT
Cue: a deep-learning framework for structural variant discovery and genotyping. Nature methods. 2023 Academic Article GET IT
Times cited: 28
A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study. The Lancet. Digital health. 2023 Academic Article GET IT
Efficient detection and assembly of non-reference DNA sequences with synthetic long reads. Nucleic acids research. 2022 Academic Article GET IT
Times cited: 4
Weakly-supervised tumor purity prediction from frozen H&E stained slides. EBioMedicine. 2022 Academic Article GET IT
System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell reports. Medicine. 2022 Academic Article GET IT
Times cited: 31
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. Bioinformatics (Oxford, England). 2021 Academic Article GET IT
Times cited: 37
A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 2021 Academic Article GET IT
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. Bioinformatics (Oxford, England). 2021 Academic Article GET IT
Times cited: 25
A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion. Journal of magnetic resonance imaging : JMRI. 2021 Academic Article GET IT
Times cited: 77
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nature communications. 2021 Academic Article GET IT
Times cited: 100
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC bioinformatics. 2020 Academic Article GET IT
Times cited: 11
Precision medicine and artificial intelligence: overview and relevance to reproductive medicine. Fertility and sterility. 2020 Information Resource GET IT
Times cited: 4
Predictive modeling in reproductive medicine: Where will the future of artificial intelligence research take us?. Fertility and sterility. 2020 Information Resource GET IT
Times cited: 3
A robust benchmark for detection of germline large deletions and insertions. Nature biotechnology. 2020 Academic Article GET IT
Times cited: 34
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature medicine. 2020 Academic Article GET IT
Times cited: 172
VALOR2: characterization of large-scale structural variants using linked-reads. Genome biology. 2020 Academic Article GET IT
Times cited: 12
Meltos: multi-sample tumor phylogeny reconstruction for structural variants. Bioinformatics (Oxford, England). 2020 Academic Article GET IT
Times cited: 9
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. Genome research. 2019 Academic Article GET IT
Times cited: 55
BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples. BMC bioinformatics. 2019 Academic Article GET IT
Times cited: 11
BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs. Genome research. 2019 Academic Article GET IT
Times cited: 45
The tech for the next decade: promises and challenges in genome biology. Genome biology. 2019 Conference Paper GET IT
Times cited: 2
Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization. NPJ digital medicine. 2019 Academic Article GET IT
Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics. Genome research. 2018 Academic Article GET IT
Times cited: 14
Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees. Current protocols in bioinformatics. 2018 Academic Article GET IT
Times cited: 6
Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images. EBioMedicine. 2017 Academic Article GET IT
Times cited: 274
Fast and scalable inference of multi-sample cancer lineages. Genome biology. 2015 Academic Article GET IT
Times cited: 166
Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics (Oxford, England). 2014 Academic Article GET IT
Times cited: 46
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinformatics (Oxford, England). 2014 Academic Article GET IT
Times cited: 85
Detecting independent and recurrent copy number aberrations using interval graphs. Bioinformatics (Oxford, England). 2014 Academic Article GET IT
Times cited: 22
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature communications. 2014 Academic Article GET IT
Times cited: 308
MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics (Oxford, England). 2013 Academic Article GET IT
Times cited: 34
An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Academic Article GET IT
Times cited: 6169
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. The Journal of pathology. 2012 Academic Article GET IT
Times cited: 158
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. The Journal of pathology. 2012 Academic Article GET IT
Times cited: 63
Mirroring co-evolving trees in the light of their topologies. Bioinformatics (Oxford, England). 2012 Academic Article GET IT
Times cited: 4
Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome research. 2011 Academic Article GET IT
Times cited: 53
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics (Oxford, England). 2011 Academic Article GET IT
Times cited: 33
Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Academic Article GET IT
Times cited: 889
Alu repeat discovery and characterization within human genomes. Genome research. 2010 Academic Article GET IT
Times cited: 82
A map of human genome variation from population-scale sequencing. Nature. 2010 Academic Article GET IT
Times cited: 5281
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics (Oxford, England). 2010 Academic Article GET IT
Times cited: 165
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics (Oxford, England). 2010 Academic Article GET IT
Times cited: 83
smyRNA: a novel Ab initio ncRNA gene finder. PloS one. 2009 Academic Article GET IT
Times cited: 11
Biomolecular network motif counting and discovery by color coding. Bioinformatics (Oxford, England). 2008 Academic Article GET IT
Times cited: 184
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics (Oxford, England). 2008 Academic Article GET IT
Times cited: 16

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Research

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Co-investigator Network

Funding awarded

Improving metagenomic analysis with novel algorithms and technologies awarded by National Institute of General Medical Sciences Principal Investigator 2020 - 2026

The joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor Profiles awarded by National Cancer Institute Co-Principal Investigator 2021 - 2026

Cross-platform structural variant discovery with deep learning awarded by Bill & Melinda Gates Foundation Principal Investigator Subaward 2022 - 2027
Machine learning in the identification of ultrasonographic features of olycystic Ovarian Morphology awarded by National Institute of Mental Health Principal Investigator Subaward 2023 - 2025

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Background

education and training

Ph.D., Simon Fraser University (Canada) 2012
M.Sc., Simon Fraser University (Canada) 2007
B.Sc., Sharif University (Iran) 2005

Contact

full name

Iman Hajirasouliha

primary email

imh2003@med.cornell.edu

VIVO Weill Cornell Medical College

Iman Hajirasouliha Associate Professor of Physiology and Biophysics

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email

Phone

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email