Publications

A bit of history:
(the ACTION PLAN image) shows how Fereydoun and I were going to wrap up two projects simultaneously in only two months, under the fear of getting scooped.

2014-today

V Popic, R Salari, I Hajirasouliha, D Kashef-Haghighi, RB West, S Batzoglou
Fast and scalable inference of multi-sample cancer lineages
Genome biology (2015)16 (1), 91

Iman Hajirasouliha, Benjamin Raphael
Reconstructing mutational history in multiply sampled tumors using perfect phylogeny mixtures
WABI 2014 (14th Workshop on Algorithms in Bioinformatics), Wroclaw, Poland, September 8-10, 2014. Springer, pp. 354--367.
Errata slides from WABI 2014 presentaion.

Hsin-Ta Wu, Iman Hajirasouliha, Benjamin Raphael
Detecting independent and recurrent copy number aberrations using interval graphs
ISMB 2014 (The 22th Annual International Conference Intelligent Systems for Molecular Biology), Boston, USA, July 13-15, 2014.
(Also, Bioinformatics 30 (12), i195-i203)

Iman Hajirasouliha, Ahmad Mahmoody and Benjamin Raphael
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data
ISMB 2014 (The 22th Annual International Conference Intelligent Systems for Molecular Biology), Boston, USA, July 13-15, 2014.
(Also, Bioinformatics 30 (12), i78-i86)

Anna Ritz, Ali Bashir, Suzanne Sindi, David Hsu, Iman Hajirasouliha, Benjamin Raphael
Characterization of Complex Structural Variants with Single Molecule and Hybrid Sequencing Approaches
ISMB-HitSeq 2014(High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB'14), Boston, MA, USA, July 11-12 2014
(Also, Bioinformatics 30 (24), 3458-3466)

2010-2013

Tobias Marschall, Iman Hajirasouliha, Alexander Schönhuth
Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels
ISMB-HitSeq 2013(High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB'13), Berlin, Germany, July 19-20 2013.
(Also, Bioinformatics , 2013 Dec 15;29(24):3143-50.)
GoNL Supplement (Command Line Instructions, provided by Tobias and Alex)

The 1000 Genomes Project Consortium
An integrated map of genetic variation from 1,092 human genomes.
Nature (2012) 491: 56-65

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.
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer.
The Journal of Pathalogy, 2012 Jul;227(3):286-97. doi: 10.1002/path.4047

Iman Hajirasouliha, Alexander Schönhuth, David Juan, Alfonso Valencia and S. Cenk Sahinalp
Mirroring co-evolving trees in the light of their topologies
Bioinformatics (2012) 28 (9): 1202-1208. (First published online: March 6, 2012)

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.
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.
The Journal of Pathalogy, 2012 May;227(1):53-61. doi: 10.1002/path.3987. Epub 2012 Mar 21.

Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp
Simultaneous structural variation discovery in multiple paired-end sequenced genomes
RECOMB 2011 (15th Annual International Conference on Research in Computational Molecular Biology), Vancouver, Canada, March 28-31 2011
(Also full paper at Genome Research, 2011 Dec;21(12):2203-12. Epub 2011 Nov 2.)
Featured on the cover!
Highlighted in: Nature Biotechnology, 29, 1101 (2011)

Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, S. Cenk Sahinalp
Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data
ISMB-HitSeq 2011 (High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB'11), Vienna, Austria, July 15-16 2011.
Winner of the Best Paper Award
(Also, Bioinformatics 2011 Jun 1;27(11):1481-8. Epub 2011 Apr 9.)

Mills, R. E., K. Walter, D. A. Stewart, R. Handsaker, K. Chen, C. Alkan, A. Abyzov, S. C. Yoon, K. Ye, R. K. Cheetham, A. Chinwalla, D. F. Conrad, Y. Fu, F. Grubert., I. Hajirasouliha, F. Hormozdiari, L. M. Iakoucheva, Z. Iqbal, J. M. Kidd, M. K. Konkel, J. Korn, E. Khurana, D. Kura, H. J. K. Lam, J. Leng, R. Li, Y. Li, C.-Y. Lin, R. Luo, X. J. Mu, J. Nemesh, H. E. Peckham, T. Rausch, A. Scally, X. Shi, M. P. Stromberg, A. M. Stutz, A. E. Urban, J. A. Walker, J. Wu, Y. Zhang, Z. Zhang, M. A. Batzer, L. Ding, G. T. Marth, G. McVean, J. Sebat, M. Snyder, J. Wang, K. Ye, K. Ye, E. E. Eichler, M. B. Gerstein, M. E. Hurles, C. Lee, S. A. McCarroll and J. O. Korbel on behalf of the 1000 Genomes Project.
Mapping copy number variation at fine-scale by population-scale genome sequencing
Nature 470, 59-65 (03 February 2011)

Petra Berenbrink, Tom Friedetzky, Iman Hajirasouliha and Zengjian Hu
Convergence to Equilibria in Distributed,Selfish Reallocation Processes with Weighted Tasks
Algorithmica, DOI: 10.1007/s00453-010-9482-1, Online First, 24 December 2010
A preliminary version of this work was appeared in the ESA'07 (15th Annual European Symposium on Algorithms), October 8-10, 2007

Fereydoun Hormozdiari, Can Alkan, Mario Ventura, Iman Hajirasouliha, Maika Malig, Faraz Hach, Deniz Yorukoglu, Phuong Dao, Marzieh Bakhshi, S. Cenk Sahinalp, Evan E. Eichler
Alu repeat discovery and characterization within human genomes
Genome Research, June 2011 21: 840-849; Published in Advance December 3, 2010, doi:10.1101/gr.115956.110

The 1000 Genomes Project Consortium
A map of human genome variation from population-scale sequencing
Nature 467, 1061-1073 (28 October 2010)
Featured on the cover!
Comment in: Nature 2010 Oct 28;467(7319):1050-1.
(For a list of related publications, please see the 1000 Genomes Project special page in Nature.)

Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yorukoglu, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp
Next Generation VariationHunter: Combinatorial Algorithms for Transposon Insertion Discovery
ISMB 2010 (18th Annual International Conference Intelligent Systems for Molecular Biology), Boston, USA, July 11-13 2010
(Also, Bioinformatics 2010 Jun 15;26(12):i350-i357)

Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanc Birol, Evan E. Eichler, S. Cenk Sahinalp
Detection and characterization of sequence insertions using paired-end next-generation sequencing
ISMB-HiTSeq 2010 (High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB'10), Boston, USA, July 9-10 2010
(Also, Bioinformatics 2010 May 15;26(10):1277-83. Epub 2010 Apr 12.)

2007-2009

Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, S. Cenk Sahinalp, Martin Ester
Quantifying systemic evolutionary changes by color coding confidence-sored PPI networks
WABI 2009 (9th Workshop on Algorithms in Bioinformatics), Philadelphia, USA, September 12-13 2009
Lecture Notes in Computer Science, volume 5724, pages 37-48

Rahele Salari, Cagri Aksay, Emre Karakoc, Peter Unrau, Iman Hajirasouliha, and S. Cenk Sahinalp
smyRNA: A novel ab initio ncRNA gene finder
PLoS ONE, (5): e5433, doi:10.1371/journal.pone.0005433, May 2009

Iman Hajirasouliha, Fereydoun Hormozdiari, S. Cenk Sahinalp, and Inanc Birol
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies
ISMB 2008 (16th Annual International Conference Intelligent Systems for Molecular Biology), Toronto, Canada, July 19-23 2008
(Also, Bioinformatics 2008 Jul 1;24 (13):i32-40)

Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari and S. Cenk Sahinalp
Biomolecular Network Motif Counting and Discovery by Color Coding
ISMB 2008 (16th Annual International Conference Intelligent Systems for Molecular Biology), Toronto, Canada, July 19-23 2008
(Also, Bioinformatics 2008 Jul 1;24 (13):i241-9)

Petra Berenbrink, Tom Friedetzky, Iman Hajirasouliha and Zengjian Hu
Convergence to Equilibria in Distributed, Selfish Reallocation Processes with Weighted Tasks
ESA 2007 (15th Annual European Symposium on Algorithms), October 8-10, 2007
Lecture Notes in Computer Science Volume 4698, 2007, pages 41-52

Iman Hajirasouliha, Hossein Jowhari, Ravi Kumar, and Ravi Sundaram
On Completing Latin Squares
STACS 2007 (24th Annual Symposium on Theoretical Aspects of Computer Science), Aachen, Germany, February 22-24 2007
Lecture Notes in Computer Science, volume 4393, pages 524-535