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Items: 27


VALOR2: characterization of large-scale structural variants using linked-reads.

Karaoğlanoğlu F, Ricketts C, Ebren E, Rasekh ME, Hajirasouliha I, Alkan C.

Genome Biol. 2020 Mar 19;21(1):72. doi: 10.1186/s13059-020-01975-8.


PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.

Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC.

Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18.


Meltos: multi-sample tumor phylogeny reconstruction for structural variants.

Ricketts C, Seidman D, Popic V, Hormozdiari F, Batzoglou S, Hajirasouliha I.

Bioinformatics. 2020 Feb 15;36(4):1082-1090. doi: 10.1093/bioinformatics/btz737.


Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization.

Khosravi P, Kazemi E, Zhan Q, Malmsten JE, Toschi M, Zisimopoulos P, Sigaras A, Lavery S, Cooper LAD, Hickman C, Meseguer M, Rosenwaks Z, Elemento O, Zaninovic N, Hajirasouliha I.

NPJ Digit Med. 2019 Apr 4;2:21. doi: 10.1038/s41746-019-0096-y. eCollection 2019.


BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples.

Toosi H, Moeini A, Hajirasouliha I.

BMC Bioinformatics. 2019 Jun 6;20(Suppl 11):282. doi: 10.1186/s12859-019-2824-3.


BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.

Meleshko D, Mohimani H, Tracanna V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA.

Genome Res. 2019 Aug;29(8):1352-1362. doi: 10.1101/gr.243477.118. Epub 2019 Jun 3.


The tech for the next decade: promises and challenges in genome biology.

Hajirasouliha I, Tilgner HU.

Genome Biol. 2019 Apr 30;20(1):86. doi: 10.1186/s13059-019-1695-2.


Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.

Danko DC, Meleshko D, Bezdan D, Mason C, Hajirasouliha I.

Genome Res. 2019 Jan;29(1):116-124. doi: 10.1101/gr.235499.118. Epub 2018 Dec 6.


Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees.

Ricketts C, Popic V, Toosi H, Hajirasouliha I.

Curr Protoc Bioinformatics. 2018 Jun;62(1):e49. doi: 10.1002/cpbi.49. Epub 2018 May 16.


Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images.

Khosravi P, Kazemi E, Imielinski M, Elemento O, Hajirasouliha I.

EBioMedicine. 2018 Jan;27:317-328. doi: 10.1016/j.ebiom.2017.12.026. Epub 2017 Dec 28.


Fast and scalable inference of multi-sample cancer lineages.

Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S.

Genome Biol. 2015 May 6;16:91. doi: 10.1186/s13059-015-0647-8.


Characterization of structural variants with single molecule and hybrid sequencing approaches.

Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.

Bioinformatics. 2014 Dec 15;30(24):3458-66. doi: 10.1093/bioinformatics/btu714. Epub 2014 Oct 28.


A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.

Hajirasouliha I, Mahmoody A, Raphael BJ.

Bioinformatics. 2014 Jun 15;30(12):i78-86. doi: 10.1093/bioinformatics/btu284.


Detecting independent and recurrent copy number aberrations using interval graphs.

Wu HT, Hajirasouliha I, Raphael BJ.

Bioinformatics. 2014 Jun 15;30(12):i195-203. doi: 10.1093/bioinformatics/btu276.


MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.

Marschall T, Hajirasouliha I, Schönhuth A.

Bioinformatics. 2013 Dec 15;29(24):3143-50. doi: 10.1093/bioinformatics/btt556. Epub 2013 Sep 25.


From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer.

Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC.

J Pathol. 2012 Jul;227(3):286-97. doi: 10.1002/path.4047.


Mirroring co-evolving trees in the light of their topologies.

Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC.

Bioinformatics. 2012 May 1;28(9):1202-8. doi: 10.1093/bioinformatics/bts109. Epub 2012 Mar 6.


Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.

Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC.

J Pathol. 2012 May;227(1):53-61. doi: 10.1002/path.3987. Epub 2012 Mar 21.


Simultaneous structural variation discovery among multiple paired-end sequenced genomes.

Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC.

Genome Res. 2011 Dec;21(12):2203-12. doi: 10.1101/gr.120501.111. Epub 2011 Nov 2.


Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC.

Bioinformatics. 2011 Jun 1;27(11):1481-8. doi: 10.1093/bioinformatics/btr184. Epub 2011 Apr 9.


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 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.


Alu repeat discovery and characterization within human genomes.

Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE.

Genome Res. 2011 Jun;21(6):840-9. doi: 10.1101/gr.115956.110. Epub 2010 Dec 3.


Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.

Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC.

Bioinformatics. 2010 Jun 15;26(12):i350-7. doi: 10.1093/bioinformatics/btq216.


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.


smyRNA: a novel Ab initio ncRNA gene finder.

Salari R, Aksay C, Karakoc E, Unrau PJ, Hajirasouliha I, Sahinalp SC.

PLoS One. 2009;4(5):e5433. doi: 10.1371/journal.pone.0005433. Epub 2009 May 5.


Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.

Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I.

Bioinformatics. 2008 Jul 1;24(13):i32-40. doi: 10.1093/bioinformatics/btn173.


Biomolecular network motif counting and discovery by color coding.

Alon N, Dao P, Hajirasouliha I, Hormozdiari F, Sahinalp SC.

Bioinformatics. 2008 Jul 1;24(13):i241-9. doi: 10.1093/bioinformatics/btn163.

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