Publications

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L Coombe, J Zhang, BP Vandervalk, J Chu, SD Jackman, I Birol, et. al. ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. 2018 Dec. BMC bioinformatics 19 (1), 234

LJ Campbell, SA Hammond, SJ Price, MD Sharma, TWJ Garner, I Birol, et. al. A novel approach to wildlife transcriptomics provides evidence of disease‐mediated differential expression and changes to the microbiome of amphibian populations. 2018 Mar. Molecular ecology 27 (6), 1413-1427

N Feau, S Beauseigle, MJ Bergeron, GJ Bilodeau, I Birol, et. al. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. 2018 Feb 22. PeerJ 6, e4392

H Khan, H Mohamadi, BP Vandervalk, RL Warren, J Chu, I Birol. ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. 2017 Dec 29. Bioinformatics, btx839

SJ Jones, M Haulena, GA Taylor, S Chan, S Bilobram, RL Warren, et. al. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni). 2017 Dec 11. Genes 8 (12), 379

SJM Jones, GA Taylor, S Chan, RL Warren, SA Hammond, S Bilobram, et. al. The Genome of the Beluga Whale (Delphinapterus leucas). 2017 Dec 11. Genes 8 (12), 378

SA Hammond, RL Warren, BP Vandervalk, E Kucuk, H Khan, EA Gibb, et. al. The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. 2017 Nov 10. Nature Communications 8 (1), 1433

S Yeo, L Coombe, RL Warren, J Chu, I Birol. Arcs: Scaffolding genome drafts with linked reads. 2017 Oct 23. Bioinformatics

AG Robertson, J Kim, H Al-Ahmadie, J Bellmunt, G Guo, AD Cherniack, et. al. Comprehensive molecular characterization of muscle-invasive bladder cancer. 2017 Oct 19. Cell 171 (3), 540-556. e25

NA Hasan, RL Warren, LE Epperson, A Malecha, DC Alexander, et. al. Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease. 2017 Sep 14. Genome announcements 5 (37), e00963-17

AG Robertson, J Shih, C Yau, EA Gibb, J Oba, KL Mungall, JM Hess, et. al. Integrative analysis identifies four molecular and clinical subsets in uveal melanoma. 2017 Aug 14. Cancer cell 32 (2), 204-220. e15

BJ Raphael, RH Hruban, AJ Aguirre, RA Moffitt, JJ Yeh, C Stewart, et. al. Integrated genomic characterization of pancreatic ductal adenocarcinoma. 2017 Aug 14. Cancer Cell 32 (2), 185-203. e13

SD Jackman, BP Vandervalk, H Mohamadi, J Chu, S Yeo, SA Hammond, et. al. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. 2017 May 01. Genome research 27 (5), 768-777

TM Brown, SA Hammond, B Behsaz, N Veldhoen, I Birol, CC Helbing. De novo assembly of the ringed seal (Pusa hispida) blubber transcriptome: A tool that enables identification of molecular health indicators associated with PCB expo.... 2017 Apr 01. Aquatic toxicology 185, 48-57

N Pavy, M Lamothe, B Pelgas, F Gagnon, I Birol, J Bohlmann, J Mackay, et. al. A high‐resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical dis.... 2017 Apr 01. The Plant Journal 90 (1), 189-203

C Yang, J Chu, RL Warren, I Birol. NanoSim: nanopore sequence read simulator based on statistical characterization. 2017 Feb 24. GigaScience 6 (4), 1-6

E Kucuk, J Chu, BP Vandervalk, SA Hammond, RL Warren, I Birol. Kollector: transcript-informed, targeted de novo assembly of gene loci. 2017 Feb 10. Bioinformatics 33 (12), 1782-1788

H Mohamadi, H Khan, I Birol. ntCard: a streaming algorithm for cardinality estimation in genomics data. 2017 Jan 05. Bioinformatics 33 (9), 1324-1330

ML Thibodeau, M Steinraths, L Brown, Z Zong, N Shomer, S Taubert, et. al. Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98. 2017. Cytogenetic and genome research 152 (3), 117-121

Z Xue, RL Warren, EA Gibb, D MacMillan, J Wong, R Chiu, SA Hammond, et. al. Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation. 2017 Jan 01. bioRxiv, 160960

S Yeo, L Coombe, J Chu, RL Warren, I Birol. ARCS: assembly roundup by chromium scaffolding. 2017 Jan 01. bioRxiv, 100750

SA Hammond, RL Warren, BP Vandervalk, E Kucuk, H Khan, EA Gibb, et. al. It's okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana). 2017 Jan 01. bioRxiv, 100149

M Krzywinski, KM Nip, I Birol, M Marra. Differential Hive Plots: Seeing Networks Change. 2017. Leonardo 50 (5), 504-504

N Feau, G Taylor, AL Dale, B Dhillon, GJ Bilodeau, I Birol, SJM Jones, et. al. Genome sequences of six Phytophthora species threatening forest ecosystems. 2016 Dec 31. Genomics data 10, 85-88

J Chu, H Mohamadi, RL Warren, C Yang, I Birol. Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. 2016 Dec 21. Bioinformatics 33 (8), 1261-1270

L Coombe, RL Warren, SD Jackman, C Yang, BP Vandervalk, RA Moore, et. al. Assembly of the complete Sitka spruce chloroplast genome using 10X Genomics’ GemCode sequencing data. 2016 Sep 15. PloS one 11 (9), e0163059

D Bouneffouf, I Birol. Theoretical analysis of the Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. 2016 Jul 24. Neural Networks (IJCNN), 2016 International Joint Conference on, 3856-3862

D Bouneffouf, I Birol. Ensemble Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. 2016 Jul 24. Neural Networks (IJCNN), 2016 International Joint Conference on, 3851-3855

H Mohamadi, J Chu, BP Vandervalk, I Birol. ntHash: recursive nucleotide hashing. 2016 Jul 16. Bioinformatics 32 (22), 3492-3494

S Jackman, I Birol, S Jackman, I Birol. Linuxbrew and Homebrew for cross-platform package management. 2016. F1000Research 5, 1795

J Chu, H Mohamadi, R Warren, C Yang, I Birol. Overlapping long sequence reads: Current innovations and challenges in developing sensitive, specific and scalable algorithms. 2016 Jan 01. bioRxiv, 081596

G Sheikhshab, E Starks, A Karsan, A Sarkar, I Birol. Graph-based semi-supervised gene mention tagging. 2016. Proceedings of the 15th Workshop on Biomedical Natural Language Processing …

AS Morrissy, L Garzia, DJH Shih, S Zuyderduyn, X Huang, P Skowron, et. al. Divergent clonal selection dominates medulloblastoma at recurrence. 2016 Jan. Nature 529 (7586), 351

SD Jackman, RL Warren, EA Gibb, BP Vandervalk, H Mohamadi, J Chu, et. al. Organellar genomes of white spruce (Picea glauca): assembly and annotation. 2015 Dec 08. Genome biology and evolution 8 (1), 29-41

H Lin, J Zeng, K Rothe, J Ruschmann, O Petriv, K O'Neill, T Maetzig, et. al. Identification and Characterization of New Microrna Biomarkers and Target Genes in Drug-Insensitive CD34+ CML Stem/Progenitor Cells Using Global Comparative.... 2015 Dec 03. Blood 126 (23), 1567-1567

BP Vandervalk, C Yang, Z Xue, K Raghavan, J Chu, H Mohamadi, et. al. Konnector v2. 0: pseudo-long reads from paired-end sequencing data. 2015 Dec. BMC medical genomics 8 (3), S1

RL Warren, C Yang, BP Vandervalk, B Behsaz, A Lagman, SJM Jones, et. al. LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. 2015 Dec. GigaScience 4 (1), 35

D Paulino, RL Warren, BP Vandervalk, A Raymond, SD Jackman, I Birol. Sealer: a scalable gap-closing application for finishing draft genomes. 2015 Dec. BMC bioinformatics 16 (1), 230

I Birol, J Chu, H Mohamadi, SD Jackman, K Raghavan, BP Vandervalk, et. al. Spaced seed data structures for de novo assembly. 2015 Oct 11. International journal of genomics 2015

H Lin, K Rothe, J Ruschmann, O Petriv, K O'Neill, D Knapp, R Brinkman, et. al. Comparative RNA-seq analyses identify new microRNA biomarkers and candidate target genes in patients’ drug-resistant CD34+ CML stem/progenitor cells. 2015 Sep 01. Experimental Hematology 43 (9), S63

A Chu, G Robertson, D Brooks, AJ Mungall, I Birol, R Coope, Y Ma, et. al. Large-scale profiling of microRNAs for the cancer genome atlas. 2015 Aug 13. Nucleic acids research 44 (1), e3-e3

D Bouneffouf, I Birol. Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering.. 2015 Jul 25. IJCAI, 2313-2319

RL Warren, CI Keeling, MMS Yuen, A Raymond, GA Taylor, et. al. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. 2015 Jul 01. The Plant Journal 83 (2), 189-212

I Birol, B Behsaz, SA Hammond, E Kucuk, N Veldhoen, CC Helbing. De novo transcriptome assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis tadpole livers for comparative genomics without reference genomes. 2015 Jun 29. PloS one 10 (6), e0130720

SD Jackman, J Bohlmann, I Birol. UniqTag: Content-derived unique and stable identifiers for gene annotation. 2015 May 28. PloS one 10 (5), e0128026

H Mohamadi, BP Vandervalk, A Raymond, SD Jackman, J Chu, et. al. DIDA: Distributed Indexing Dispatched Alignment. 2015 Apr 29. PloS one 10 (4), e0126409

E Shoshan, AK Mobley, RR Braeuer, T Kamiya, L Huang, ME Vasquez, et. al. Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis. 2015 Mar. Nature cell biology 17 (3), 311

ARMA Basher, AS Purdy, I Birol. Event Extraction from Biomedical Literature. 2015 Jan 01. bioRxiv, 034397

RL Warren, BP Vandervalk, SJM Jones, I Birol. LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads. 2015 Jan 01. bioRxiv, 016519

H Lin, K Rothe, J Ruschmann, O Petriv, K O'Neill, DJHF Knapp, et. al. Identification of new microRNA biomarkers and candidate target genes in primitive CML cells using global comparative RNA analyses. 2014 Dec 06. Blood 124 (21), 3133-3133

R Amanda, I Birol, J Bousquet, PK Ingvarsson, S Jansson, SJM Jones, et. al. Insights into conifer giga-genomes. 2014 Dec 01. Plant physiology 166 (4), 1724-1732

JS Sena, I Giguère, B Boyle, P Rigault, I Birol, A Zuccolo, K Ritland, et. al. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. 2014 Dec. BMC plant biology 14 (1), 95

I Birol, H Mohamadi, A Raymond, K Raghavan, J Chu, BP Vandervalk, et. al. Spaced seed data structures. 2014 Nov 02. Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on …

BP Vandervalk, SD Jackman, A Raymond, H Mohamadi, C Yang, et. al. Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph. 2014 Nov 02. Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on …

M Parfenov, CS Pedamallu, N Gehlenborg, SS Freeman, L Danilova, et. al. Characterization of HPV and host genome interactions in primary head and neck cancers. 2014 Oct 28. Proceedings of the National Academy of Sciences 111 (43), 15544-15549

CF Davis, CJ Ricketts, M Wang, L Yang, AD Cherniack, H Shen, C Buhay, et. al. The somatic genomic landscape of chromophobe renal cell carcinoma. 2014 Sep 08. Cancer cell 26 (3), 319-330

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. 2014 Sep. Nature 513 (7517), 202

J Chu, S Sadeghi, A Raymond, SD Jackman, KM Nip, R Mar, et. al. BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. 2014 Aug 20. Bioinformatics 30 (23), 3402-3404

YS Butterfield, M Kreitzman, N Thiessen, RD Corbett, Y Li, J Pang, YP Ma, et. al. JAGuaR: junction alignments to genome for RNA-seq reads. 2014 Jul 25. PloS one 9 (7), e102398

I Birol, A Raymond, R Chiu, KM Nip, SD Jackman, M Kreitzman, et. al. Kleat: cleavage site analysis of transcriptomes. 2014. Pacific Symposium on Biocomputing Co-Chairs, 347-358

L Swanson, G Robertson, KL Mungall, YS Butterfield, R Chiu, RD Corbett, et. al. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. 2013 Dec. BMC genomics 14 (1), 550

S Haridas, Y Wang, L Lim, SM Alamouti, S Jackman, R Docking, et. al. The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera. 2013 Dec. BMC genomics 14 (1), 373

AH Khodabakhshi, AP Fejes, I Birol, SJM Jones. Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. 2013 Dec. BMC bioinformatics 14 (1), 167

KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, et. al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. 2013 Dec. GigaScience 2 (1), 10

IE Bosdet, TR Docking, YS Butterfield, AJ Mungall, T Zeng, RJ Coope, et. al. A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations. 2013 Nov 01. The Journal of Molecular Diagnostics 15 (6), 796-809

JN Weinstein, EA Collisson, GB Mills, KRM Shaw, BA Ozenberger, et. al. The cancer genome atlas pan-cancer analysis project. 2013 Sep 26. Nature genetics 45 (10), 1113

M Lenassi, C Gostincar, S Jackman, M Turk, I Sadowski, C Nislow, et. al. Whole genome duplication and enrichment of cation transporters are associated with the halotolerant lifestyle of the black yeast Hortaea werneckii. 2013 Sep 01. YEAST 30, 190-190

M Lenassi, C Gostinčar, S Jackman, M Turk, I Sadowski, C Nislow, et. al. Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea wer.... 2013 Aug 15. PLoS One 8 (8), e71328

RD Morin, K Mungall, E Pleasance, AJ Mungall, R Goya, RD Huff, et. al. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. 2013 Aug 15. Blood 122 (7), 1256-1265

A Fentiman, J Parker, L Swanson, K Mungall, I Birol, A Karsan. Endothelial-hematopoietic transition: from the dorsal aorta to the dish. 2013 Aug 01. Experimental Hematology 41 (8), S26

K Kasaian, SM Wiseman, N Thiessen, KL Mungall, RD Corbett, JQ Qian, et. al. Complete genomic landscape of a recurring sporadic parathyroid carcinoma. 2013 Jul 01. The Journal of pathology 230 (3), 249-260

Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. 2013 May 30. New England Journal of Medicine 368 (22), 2059-2074

I Birol, A Raymond, SD Jackman, S Pleasance, R Coope, GA Taylor, et. al. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. 2013 May 22. Bioinformatics 29 (12), 1492-1497

DA Levine, Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. 2013 May. Nature 497 (7447), 67

CI Keeling, MMS Yuen, NY Liao, TR Docking, SK Chan, GA Taylor, et. al. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. 2013 Mar. Genome biology 14 (3), R27

TJ Pugh, O Morozova, EF Attiyeh, S Asgharzadeh, JS Wei, D Auclair, et. al. The genetic landscape of high-risk neuroblastoma. 2013 Mar. Nature genetics 45 (3), 279

AH Khodabakhshi, RD Morin, AP Fejes, AJ Mungall, KL Mungall, et. al. Recurrent targets of aberrant somatic hypermutation in lymphoma. 2012 Nov. Oncotarget 3 (11), 1308

Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. 2012 Oct. Nature 490 (7418), 61

Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. 2012 Sep. Nature 489 (7417), 519

KG Roberts, RD Morin, J Zhang, M Hirst, Y Zhao, X Su, SC Chen, et. al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. 2012 Aug 14. Cancer cell 22 (2), 153-166

PA Northcott, DJH Shih, J Peacock, L Garzia, AS Morrissy, T Zichner, et. al. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. 2012 Aug. Nature 488 (7409), 49

CI Keeling, H Henderson, M Li, M Yuen, EL Clark, JD Fraser, DPW Huber, et. al. Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests. 2012 Aug 01. Insect biochemistry and molecular biology 42 (8), 525-536

Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. 2012 Jul. Nature 487 (7407), 330

D Yorukoglu, F Hach, L Swanson, CC Collins, I Birol, SC Sahinalp. Dissect: detection and characterization of novel structural alterations in transcribed sequences. 2012 Jun 09. Bioinformatics 28 (12), i179-i187

SP Shah, A Roth, R Goya, A Oloumi, G Ha, Y Zhao, G Turashvili, J Ding, et. al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. 2012 Jun. Nature 486 (7403), 395

SD Jackman, AG Raymond, İ Birol. Scaffolding a genome sequence assembly using ABySS. 2012. No Journal Information

PA Dimitriu, JV Gosselink, WM Elliott, MM Moore, S Adams, J Friedman, et. al. A Preliminary Assessment Of Fungi In The Lung Microbiome. 2012. Am J Respir Crit Care Med 185, A4537

M Krzywinski, I Birol, S Jones, M Marra. Getting into visualization of large biological data sets. 2012. 2nd IEEE Symposium on Biological Data Visualization (BioVis2012), Seattle, WA

K Kasaian, A He, N Thiessen, K Mungall, J Qian, R Varhol, Y Zhao, I Birol, et. al. Profiling thyroid cancers on the molecular level. 2012. GENOME 55, 705-705

S Yip, YS Butterfield, O Morozova, S Chittaranjan, MD Blough, J An, I Birol, et. al. Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. 2012 Jan 01. The Journal of pathology 226 (1), 7-16

M Krzywinski, I Birol, SJM Jones, MA Marra. Hive plots—rational approach to visualizing networks. 2011 Dec 09. Briefings in bioinformatics 13 (5), 627-644

D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, et. al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. 2011 Dec 01. Genome research 21 (12), 2224-2241

QWT Chan, RS Cornman, I Birol, NY Liao, SK Chan, TR Docking, et. al. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. 2011 Dec. Bmc Genomics 12 (1), 450

Y Chu, P Gao, P Zhao, Y He, N Liao, S Jackman, Y Zhao, I Birol, X Duan, et. al. Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601. 2011 Nov 01. Journal of bacteriology 193 (21), 6098-6099

RD Morin, M Mendez-Lago, AJ Mungall, R Goya, KL Mungall, RD Corbett, et. al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. 2011 Aug. Nature 476 (7360), 298

M Sze, JV Gosselink, JE McDonough, M Elliott, S Adam, J Friedman, et. al. The lung microbiome in COPD. 2011 May. A14. DEFINING CLINICAL PHENOTYPES OF COPD, A1017-A1017

O Morozova, I Birol, R Corbett, K Mungall, EF Attiyeh, S Asgharzadeh, et. al. Whole genome and transcriptome sequencing defines the spectrum of somatic changes in high-risk neuroblastoma. 2011 Apr 15. Cancer Research 71 (8 Supplement), 926-926

AP Fejes, AH Khodabakhshi, I Birol, SJM Jones. Human variation database: an open-source database template for genomic discovery. 2011 Mar 02. Bioinformatics 27 (8), 1155-1156

A Geraldes, J Pang, N Thiessen, T Cezard, R Moore, YJ Zhao, A Tam, et. al. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. 2011 Mar 01. Molecular Ecology Resources 11 (s1), 81-92

JL Gardy, JC Johnston, SJH Sui, VJ Cook, L Shah, E Brodkin, S Rempel, et. al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. 2011 Feb 24. New England Journal of Medicine 364 (8), 730-739

S DiGuistini, Y Wang, NY Liao, G Taylor, P Tanguay, N Feau, B Henrissat, et. al. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. 2011 Feb 08. Proceedings of the National Academy of Sciences 108 (6), 2504-2509

RD Morin, M Mendez-Lago, AJ Mungall, NA Johnson, R Goya, et. al. Identification of genes frequently mutated in FL and DLBCL with transcriptome, genome and exome sequencing. 2010 Nov 19. Blood 116 (21), 804-804

SJM Jones, J Laskin, YY Li, OL Griffith, J An, M Bilenky, YS Butterfield, et. al. Personalized oncogenomics. 2010 Nov. Genome biology 11 (1), I5

G Robertson, J Schein, R Chiu, R Corbett, M Field, SD Jackman, et. al. De novo assembly and analysis of RNA-seq data. 2010 Nov. Nature methods 7 (11), 909

SJM Jones, J Laskin, YY Li, OL Griffith, J An, M Bilenky, YS Butterfield, et. al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. 2010 Aug. Genome biology 11 (8), R82

BG Hoffman, G Robertson, B Zavaglia, M Beach, R Cullum, S Lee, et. al. Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. 2010 Aug 01. Genome research 20 (8), 1037-1051

F Hach, F Hormozdiari, C Alkan, F Hormozdiari, I Birol, EE Eichler, et. al. mrsFAST: a cache-oblivious algorithm for short-read mapping. 2010 Aug. Nature methods 7 (8), 576

SJM Jones, J Laskin, YY Li, OL Griffith, J An, M Bilenky, YS Butterfield, et. al. Genomic analysis of a rare human tumor. 2010 Jul 01. BMC bioinformatics 11 (S4), O3

RTF Wong, S Flibotte, R Corbett, P Saeedi, SJM Jones, MA Marra, et. al. LaneRuler: automated lane tracking for dna electrophoresis gel images. 2010 Jul. IEEE transactions on automation science and engineering 7 (3), 706-708

SS Atanur, İ Birol, V Guryev, M Hirst, O Hummel, C Morrissey, et. al. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. 2010 Jun 01. Genome research 20 (6), 791-803

I Hajirasouliha, F Hormozdiari, C Alkan, JM Kidd, I Birol, EE Eichler, et. al. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. 2010 Apr 12. Bioinformatics 26 (10), 1277-1283

RD Morin, NA Johnson, TM Severson, AJ Mungall, J An, R Goya, JE Paul, et. al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. 2010 Feb. Nature genetics 42 (2), 181

I Birol, M Champ, J Cant. GENOME INFORMATICS. 2010. No Journal Information

RF Murphy, A Bateman, UK Hinxton, T Lengauer, Y Moreau, D Durand, et. al. ISMB 2010 ORGANIZATION. 2010. No Journal Information

SD Jackman, İ Birol. Assembling genomes using short-read sequencing technology. 2010 Jan. Genome biology 11 (1), 202

R Morin, N Johnson, T Severson, AJ Mungall, J An, J Paul, M Boyle, et. al. Tyrosine 641 of the EZH2 Oncogene Is Frequently Mutated in Follicular and Diffuse Large B-Cell Lymphomas of Germinal Center Origin.. 2009 Nov 20. Blood 114 (22), 139-139

AJ Mungall, A Chu, R Chiu, R Corbett, MA Field, SD Jackman, KL Mungall, et. al. Base-Pair Resolution of Somatic and Germline-Derived Genome Rearrangement Breakpoints in Follicular Lymphoma.. 2009 Nov 20. Blood 114 (22), 439-439

CB Nielsen, SD Jackman, I Birol, SJM Jones. ABySS-Explorer: visualizing genome sequence assemblies. 2009 Nov. IEEE transactions on visualization and computer graphics 15 (6), 881-888

S DiGuistini, NY Liao, D Platt, G Robertson, M Seidel, SK Chan, et. al. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. 2009 Sep. Genome biology 10 (9), R94

M Krzywinski, J Schein, I Birol, J Connors, R Gascoyne, D Horsman, et. al. Circos: an information aesthetic for comparative genomics. 2009 Sep 01. Genome research 19 (9), 1639-1645

I Birol, SD Jackman, CB Nielsen, JQ Qian, R Varhol, G Stazyk, RD Morin, et. al. De novo transcriptome assembly with ABySS. 2009 Jun 15. Bioinformatics 25 (21), 2872-2877

JT Simpson, K Wong, SD Jackman, JE Schein, SJM Jones, I Birol. ABySS: a parallel assembler for short read sequence data. 2009 Jun 01. Genome research 19 (6), 1117-1123

CB Nielsen, SD Jackman, I Birol, SJM Jones. Papers of the IEEE Information Visualization Conference 2009-Session 1: Bioinformatics Visualization-Best Paper Award: ABySS-Explorer: Visualizing Genome Seq.... 2009. IEEE Transactions on Visualization and Computer Graphics 15 (6), 881

AG Robertson, M Bilenky, A Tam, Y Zhao, T Zeng, N Thiessen, T Cezard, et. al. Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. 2008 Dec 01. Genome research 18 (12), 1906-1917

I Hajirasouliha, F Hormozdiari, SC Sahinalp, I Birol. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. 2008 Jul 01. Bioinformatics 24 (13), i32-i40

J Schein, M Krzywinski, C Hirst, R Chiu, A Chu, R Corbett, M Field, et. al. Structural rearrangement discovery in follicular lymphoma genomes. 2008 Jun 01. ANNALS OF ONCOLOGY 19, 178-179

A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, I Birol, P Cenci, et. al. Coherent bremsstrahlung, coherent pair production, birefringence, and polarimetry in the 20–170 GeV energy range using aligned crystals. 2008 Apr 16. Physical Review Special Topics-Accelerators and Beams 11 (4), 041001

M Marra, J Schein, M Krzywinski, I Birol, R Chiu, M Field, K Wong, et. al. High-resolution genome rearrangement discovery in follicular lymphoma. 2007 Mar 01. ACTA CYTOLOGICA 51 (2), 266-267

MA Marra, M Krzywinski, R Chiu, M Field, I Birol, B D’Souza, I Bosdet, et. al. Towards the Human Cancer Genome Project: A Sequence-Ready Physical Map of a Follicular Lymphoma Genome.. 2005 Nov 16. Blood 106 (11), 605-605

A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, I Birol, P Cenci, et. al. Results on the coherent interaction of high energy electrons and photons in oriented single crystals. 2005 May 01. Nuclear Instruments and Methods in Physics Research Section B: Beam …

E Tatara, İ Birol, F Teymour, A Çınar. Agent-based control of autocatalytic replicators in networks of reactors. 2005 Mar 15. Computers & Chemical Engineering 29 (4), 807-815

L Wang, I Birol, V Hatzimanikatis. Metabolic control analysis under uncertainty: framework development and case studies. 2004 Dec 01. Biophysical journal 87 (6), 3750-3763

G Unel, I Birol, S Ballestrero. The trigger and DAQ systems of the Na59 experiment. 2004 Aug. IEEE Transactions on Nuclear Science 51 (4), 1482-1487

G Unel, I Birol, S Eichblatt. Software aspects of the Na59 experiment. 2004 Aug. IEEE Transactions on Nuclear Science 51 (4), 1449-1455

NA Collaboration, A Apyan, RO Avakian, B Badelek, S Ballestrero, et. al. Measurement of Coherent Emission and Linear Polarization of Photons by Electrons in the Strong Fields of Aligned Crystals. 2004 Jun. rXiv preprint hep-ex/0406026

G Ünel, Na59 Collaboration. Measuring the linear polarization of γs in 20–170 GeV range. 2003 Jun 30. Nuclear Physics A 721, C1071-C1074

A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, I Birol, P Cenci, et. al. Linear to Circular Polarisation Conversion using Birefringent Properties of Aligned Crystals for Multi-GeV Photons. 2003 Jun 18. rXiv preprint hep-ex/0306041

A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, I Birol, P Cenci, et. al. Coherent pair production by photons in the 20-170 GeV energy range incident on crystals and birefringence. 2003 Jun 11. rXiv preprint hep-ex/0306028

NZ Perdahçı, A Hacınlıyan. Normal forms and nonlocal chaotic behavior in Sprott systems. 2003 Jun 01. International journal of engineering science 41 (10), 1085-1108

V Hatzimanikatis, I Birol, J Shi, L Wang. Quantification and characterization of uncertainty in metabolic engineering. 2003. Abstracts of Papers, 225th ACS National Meeting, New Orleans, LA, United …

E Eskut, A Kayis, G Onengüt, R van Dantzig, M de Jong, J Konijn, et. al. A search for ν μ→ ν τ oscillation. 1998 Apr 02. Physics Letters B 424 (1), 202-212

I Birol, A Hacinliyan, NZ Perdahçi. Simulating a dynamical system in the presence of a 1/f noise. 1998 Feb 01. International journal of engineering science 36 (3), 265-271

E Eskut, A Kayis, G Onengüt, R Van Dantzig, J Konijn, RGC Oldeman, et. al. The CHORUS experiment to search for νμ→ ντ oscillation. 1997 Dec 11. Nuclear Instruments and Methods in Physics Research Section A: Accelerators …

E Eskut, A Kayis, G Onengüt, R Van Dantzig, J Konijn, RGC Oldeman, et. al. The CHORUS experiment to search for νμ→ ντ oscillation. 1997 Dec 11. Nuclear Instruments and Methods in Physics Research Section A: Accelerators …

E Eskut, A Kayis, G Onengüt, R van Dantzig, M de Jong, J Konijn, et. al. A Search for. 1997 Nov 28. No Journal Information

İ Birol, A Hacinliyan. Signs and approximate magnitudes of Lyapunov exponents in continuous time dynamical systems. 1997 Sep. Journal of Mathematical Physics 38 (9), 4594-4605

İ Birol, A Hacinliyan. Determining Zero Lyapunov Exponents in Continuous Time Dynamical Systems. 1997 Jan 10. International Journal of Modern Physics A 12 (01), 131-135

İ Birol, A Hacinliyan. Some Algebraic Properties of Continuous Time Dynamical Systems. 1997 Jan 10. International Journal of Modern Physics A 12 (01), 137-142

İ BİROL, A Hacinliyan. Choice of Time Step in the Simulation of Continuous Time Dynamical Systems. 1997 Jan 01. Turkish Journal of Physics 21 (1), 147-147

İ BİROL, A Hacinliyan. Algebraic Approach to the Calculation of Lyapunov Exponents. 1997 Jan 01. Turkish Journal of Physics 21 (1), 31-42

S Alam, B Athar, AH Mahmood, S Ovunc, H Severini, S Timm, F Wappler, et. al. ATLAS. 1997. Experiments at CERN in 1997, 338-351

E Eskut, M Litmaath, J Hérin, T Kawamura, O Sato, T Hara, MT Muciaccia, et. al. The CHORUS neutrino oscillation search experiment. 1996 Dec 13. No Journal Information

R van Dantzig, J Konijn, RGC Oldeman, C van der Poel, JWE Uiterwijk, et. al. THE CHORUS NEUTRINO OSCILLATION SEARCH EXPERIMENT. 1996 Dec 13. No Journal Information

A Airapetian, FI Olness, V Dodonov, L Micu, D Axen, V Vinogradov, F Bosi, et. al. ATLAS calorimeter performance Technical Design Report. 1996. No Journal Information

J Konijn, RGC Oldeman, C Van der Poel, JWE Uiterwijk, E Eskut, et. al. The CHORUS experiment. 1996. Nuclear Physics B-Proceedings Supplements 48 (1-3), 183-187

A Airapetian, FI Olness, V Dodonov, L Micu, D Axen, V Vinogradov, F Bosi, et. al. ATLAS computing technical proposal. 1996. No Journal Information

A Airapetian, V Grabsky, H Hakopian, A Vartapetian, F Fares, et. al. ATLAS calorimeter performance. 1996. No Journal Information

İ Birol, A Hacinliyan. Approximately conserved quantity in the Henon-Heiles problem. 1995 Nov 01. Physical Review E 52 (5), 4750

D Macina, D Rondeshagen, C Weinheimer, JL Visschers, R Ferreira, et. al. The CHORUS experiment. 1995. Nucl. Phys. Proc. Suppl. 48, 183-187

WW Armstrong, FI Olness, V Dodonov, L Micu, G Chiefari, F Bosi, O Dahl, et. al. ATLAS: technical proposal for a general-purpose pp experiment at the Large Hadron Collider at CERN. 1994. No Journal Information

M Krzywinski, K Kasaian, O Morozova, I Birol, S Jones, M Marra. mkweb. bcgsc. ca/linnet. . No Journal Information

E Eskut, M Litmaath, J Hérin, A Di Bartolomeo, O Melzer, O Sato, T Hara, et. al. A New Search for $\nu_ {\mu}-\nu_ {\tau} $ Oscillations. . Experim. CERN, 34-37

N Feau, G Taylor, AL Dale, B Dhillon, GJ Bilodeau, I Birol, SJM Jones, et. al. Genomics Data. . No Journal Information

A Chu, G Robertson, D Brooks, AJ Mungall, I Birol, R Coope, Y Ma, et. al. Supplementary material for Large-‐scale profiling of microRNAs for The Cancer Genome Atlas. . No Journal Information

RD Morin, M Mendez-Lago, AJ Mungall, R Goya, KL Mungall, R Corbett, et. al. Supplementary Figures Figure S1: Overview of strategy. Figure S2: N-terminal truncation of FOXO1 protein with mutation affecting initial codon. Figure S3: Recurrent.... . No Journal Information

B Addad, S Akella, K Akesson, H Alla, A Allahham, S Amari, et. al. 2010 Index IEEE Transactions on Automation Science and Engineering Vol. 7. . No Journal Information

JT Simpson, K Wong, SD Jackman, JE Schein, SJM Jones, İ Birol. ABySS: A parallel assembler for short read sequence data–Supplemental Material. . No Journal Information

S Diguistini, NY Liao, D Platt, G Robertson, M Seidel, SK Chan, et. al. Genome biology Volume: 10 ISSN: 1465-6914 ISO Abbreviation: Genome Biol. Publication Date: 2009. .