Inanc Birol Publication List

  1. Campbell LJ, Hammond SA, Price SJ, Sharma MD, Garner TWJ, Birol I, Helbing CC, Wilfert L, Griffiths AGF. A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations. Mol Ecol. 2018 Feb 8. doi: 10.1111/mec.14528. [Epub ahead of print] PMID: 29420865.

  2. Khan H, Mohamadi H, Vandervalk BP, Warren RL, Chu J, Birol I. ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. Bioinformatics. 2017 Dec 29. doi: 10.1093/bioinformatics/btx839. [Epub ahead of print]. PMID: 29300846.

  3. Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Tse K, Li I, Cheung D, Mungall KL, Choo C, Ally A, Dhalla N, Tam AKY, Troussard A, Kirk H, Pandoh P, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Haulena M. The Genome of the Beluga Whale (Delphinapterus leucas). Genes (Basel). 2017 Dec 11;8(12). pii: E378. doi: 10.3390/genes8120378. PMID: 29232881.

  4. Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni). Genes (Basel).  2017 Dec 11;8(12). pii: E379. doi: 10.3390/genes8120379. PMID: 29232880.

  5. Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao Y, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I. The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7. PMID: 29127278.

  6. TCGA Research Network (including Inanc Birol & 170 collaborators). Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell. 2017 Oct 19;171(3):540-556.e25. doi: 10.1016/j.cell.2017.09.007. Epub 2017 Oct 5. PMID: 28988769.

  7. Hasan NA, Warren RL, Epperson LE, Malecha A, Alexander DC, Turenne CY, MacMillan D, Birol I, Pleasance S, Coope R, Jones SJM, Romney MG, Ng M, Chan T, Rodrigues M, Tang P, Gardy JL, Strong M. Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease. Genome Announc. 2017 Sep 14;5(37). pii: e00963-17. doi: 10.1128/genomeA.00963-17. PMID: 28912319.

  8. Kucuk E, Chu J, Vandervalk BP, Austin Hammond S, Warren RL, Birol I. Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics. 2017 Sep 1;33(17):2789. doi: 10.1093/bioinformatics/btx405. PMID: 28903539.

  9. Thibodeau ML, Steinraths M, Brown L, Zong Z, Shomer N, Taubert S, Mungall KL, Ma YP, Mueller R, Birol I, Lehman A. Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98. Cytogenet Genome Res. 2017 Aug 31. doi: 10.1159/000479463. PMID: 28854430.

  10. Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017 Aug 14;32(2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007. PMID: 28810144.

  11. Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell. 2017 Aug 14;32(2):204-220.e15. doi: 10.1016/j.ccell.2017.07.003. PMID: 28810145.

  12. Mohamadi H, Khan H, Birol, I. ntCard: A streaming algorithm for cardinality estimation in genomics data. Bioinformatics. 2017 May 1 ;33(9):1324-1330. doi: 10.1093/bioinformatics/btw832. PMID: 28453674.

  13. Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. Plant J.  2017 Apr;90(1):189-203. doi: 10.1111/tpj.13478. PMID: 28090692.

  14. Chu J, Mohamadi H, Warren RL, Yang C, Birol I. Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. Bioinformatics. 2017 Apr 15;33(8):1261-1270. doi: 10.1093/bioinformatics/btw811. PMID: 28003261.

  15. Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I. ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter. Genome Res. 2017 Feb 23. pii: gr.214346.116. doi: 10.1101/gr.214346.116. [Epub ahead of print]. PMID: 28232478.

  16. Kucuk E, Chu J, Vandervalk BP, Austin Hammond S, Warren RL, Birol I. Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics. 2017 Feb 10. doi: 10.1093/bioinformatics/btx078. [Epub ahead of print]. PMID: 28186221.
  17. Mohamadi H, Khan H, Birol I. ntCard: A streaming algorithm for cardinality estimation in genomics data. Bioinformatics. 2017 Jan 5. pii: btw832. doi: 10.1093/bioinformatics/btw832. [Epub ahead of print].
  18. Chu J, Mohamadi H, Warren RL, Yang C, Birol I. Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. Bioinformatics. 2016 Dec 21. pii: btw811. doi: 10.1093/bioinformatics/btw811. [Epub ahead of print]. PMID: 28003261
  19. Feau N, Taylor G, Dale AL, Dhillon B, Bilodeau GJ, Birol I, Jones SJ, Hamelin RC. Genome sequences of six Phytophthora species threatening forest ecosystems. Genomics Data. 2016 Oct 3;10:85-88. eCollection 2016. PMID: 27752469
  20. Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJ, Birol I. Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data. PLoS One. 2016 Sep 15;11(9):e0163059. doi: 10.1371/journal.pone.0163059. eCollection 2016. PMID: 27632164
  21. Mohamadi H, Chu J, Vandervalk BP, Birol I. ntHash: recursive nucleotide hashing. Bioinformatics. 2016 Jul 16. pii: btw397. [Epub ahead of print] PMID: 27423894
  22. Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD. Divergent clonal selection dominates medulloblastoma at recurrence.  Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13. PMID: 26760213
  23. Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJ, Bohlmann J, Birol I. Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244. PMID: 26645680
  24. Birol I, Chu J, Mohamadi H, Jackman SD, Raghavan K, Vandervalk BP, Raymond A, Warren RL. Spaced Seed Data Structures for De Novo Assembly. Int J Genomics. 2015;2015:196591. doi: 10.1155/2015/196591. Epub 2015 Oct 11. PMID: 26539459
  25. Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I. Konnector v2.0: pseudo-long reads from paired-end sequencing data. BMC Med Genomics. 2015;8 Suppl 3:S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23. PMID: 26399504
  26. Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA. Nucleic Acids Res. Large-scale profiling of microRNAs for The Cancer Genome Atlas. 2015 Aug 13. pii: gkv808. [Epub ahead of print] PMID: 26271990.
  27. Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ,Birol I. LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience. 2015 Aug 4;4:35. doi: 10.1186/s13742-015-0076-3. eCollection 2015. PMID: 26244089
  28. Birol I, Behsaz B, Hammond SA, Kucuk E, Veldhoen N, Helbing CC. De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes. PLoS One. 2015 Jun 29;10(6):e0130720. doi: 10.1371/journal.pone.0130720. eCollection 2015. PMID:26121473
  29. Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I. Sealer: a scalable gap-closing application for finishing draft genomes. BMC Bioinformatics. 2015 Jul 25;16:230. doi: 10.1186/s12859-015-0663-4.PMID: 26209068
  30. Jackman SD, Bohlmann J, Birol İ. UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.  PLoS One. 2015 May 28;10(5):e0128026. doi: 10.1371/journal.pone.0128026. eCollection 2015. PMID: 26020645
  31. Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJ, MacKay J, Birol I, Bohlmann J. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. Plant J.  2015 Jul;83(2):189-212. doi: 10.1111/tpj.12886. Epub 2015 Jun 19. PMID: 26017574
  32. Mohamadi H, Vandervalk BP, Raymond A, Jackman SD, Chu J, Breshears CP, Birol I. DIDA: Distributed Indexing Dispatched Alignment PLoS One. 2015 Apr 29;10(4):e0126409. doi: 10.1371/journal.pone.0126409. eCollection 2015. PMID:25923767
  33. Shoshan E, Mobley AK, Braeuer RR, Kamiya T, Huang L, Vasquez ME, Salameh A, Lee HJ, Kim SJ, Ivan C, Velazquez-Torres G, Nip KM, Zhu K, Brooks D, Jones SJ, Birol I, Mosqueda M, Wen YY, Eterovic AK, Sood AK, Hwu P, Gershenwald JE, Gordon Robertson A, Calin GA, Markel G, Fidler IJ, Bar-Eli M. Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis. Nat Cell Biol. 2015 Mar;17(3):311-21.2015 Feb 16. doi: 10.1038/ncb3110. PMID: 25686251
  34. Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A. Kleat: cleavage site analysis of transcriptomes Pac Symp Biocomput. 2015;20:347-58. PMID: 25592595
  35. Cancer Genome Atlas Network. (348 Collaborators including) , Ally A, Balasundaram M, Birol I,  Bowlby R, Brooks D, Butterfield YS, Carlsen R, Cheng D, Chu A, Dhalla N, Guin R, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Robertson AG, Schein JE,  Sipahimalani P, Tam A, Thiessen N, Wong T. Comprehensive genomic characterization of the head and neck squamous cell carcinoma Nature. 2015 Jan 29;517(7536):576-82. doi: 10.1038/nature14129. PMID: 25631445
  36. De La Torre AR, Birol I, Bousquet J, Ingvarsson PK, Jansson S, Jones SJ, Keeling CI, MacKay J, Nilsson O, Ritland K, Street N, Yanchuk A, Zerbe P, Bohlmann J. Insights into conifer giga-genomes. Plant Physiol. 2014 Dec;166(4):1724-32. doi: 10.1104/pp.114.248708. Epub 2014 Oct 27. PMID: 25349325
  37. Cancer Genome Atlas Network. (340 Collaborators including) Ally A, Balasundaram M, Birol I, Bowlby R, Butterfield YS, Carlsen R, Cheng D, Chu A, Dhalla N, Guin R, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Robertson AG, Schein JE, Sipahimalani P, Tam A, Thiessen N, Wong T, Characterization of HPV and host genome interactions in primary head and neck cancers.  Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13. PMID: 25313082
  38. The Cancer Genome Atlas Research Network  (223 Collaborators including)  Davis CF, Ricketts CJ, Wang M, Yang L,  Ally A, Balasundaram M, Birol I, Brooks D, Butterfield YS, Chuah E, Clarke A, Dhalla N, Guin R, Holt RA, Kasaian K, Lee D, Li HI, Lim E, Ma Y, Mayo M, Moore RA, Mungall AJ, Schein JE, Sipahimalani P, Tam A, Thiessen N, Wong T, Jones SJ, Marra MA. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. 2014 Sep 8;26(3):319-30. PMID: 25155756 
  39. The Cancer Genome Atlas Research Network; Analysis Working Group (318 Collaborators including) Birol I, BC Cancer Agency. Comprehensive  molecular  characterization of  gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. PMID: 25079317
  40. Cancer Genome Atlas Research Network, (307 Collaborators including) Birol I. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14;158(4):929-44. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7. PMID: 25109877
  41. Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, Mar R, Mohamadi H, Butterfield YS, Robertson AG, Birol I. BioBloom Tools: Fast, accurate and memory-efficient host species sequence screening using Bloom filters. Bioinformatics. 2014 Aug 20. pii: btu558. [Epub ahead of print]. PMID: 25143290
  42. Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, Ma YP, Jones SJ, Birol I. JAGuaR: Junction Alignments to Genome for RNA-Seq Reads. PLoS One. 2014 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. eCollection 2014. PMID: 25062255
  43. 318 collaborators including: Ally A, Balasundaram M, Birol I, Bowlby R, Brooks D, Butterfield YS, Carlsen R, Chu A, Chu J, Chuah E, Chun HJ, Clarke A, Dhalla N, Guin R, Holt RA, Jones SJ, Kasaian K, Lee D, Li HA, Lim E, Ma Y, Marra MA, Mayo M, Moore RA, Mungall AJ, Mungall KL, Ming Nip K, Gordon Robertson A, Schein JE, Sipahimalani P, Tam A, Thiessen N. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Jul 23. doi: 10.1038/nature13480. [Epub ahead of print]. PMID: 25079317
  44. Stival Sena J, Giguère I, Boyle B, Rigault P, Birol I, Zuccolo A, Ritland K, Ritland C, Bohlmann J, Jones S, Bousquet J, Mackay J. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC Plant Biol. 2014 Apr 16;14(1):95. [Epub ahead of print]. PMID: 24734980.
  45. Bosdet IE, Docking TR, Butterfield YS, Mungall AJ, Zeng T, Coope RJ, Yorida E, Chow K, Bala M, Young SS, Hirst M, Birol I, Moore RA, Jones SJ, Marra MA, Holt R, Karsan A. A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations. J Mol Diagn. 2013 Nov;15(6):796-809. doi: 10.1016/j.jmoldx.2013.07.004. Epub 2013 Oct 4. PMID: 24094589
  46. Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM, Birol I. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764. PMID:24071849
  47. Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JD, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, Hoodless PA, Sahinalp SC, Karsan A, Birol I. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. BMC Genomics. 2013 Aug 14;14(1):550 [Epub ahead of print]. PMID: 23941359.
  48. Lenassi M, Gostin C, Jackman S, Turk M, Sadowski I, Nislow C, Jones S, Birol I, Cimerman NG, Plemenita A. Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by de novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii. PLOS ONE. 2013 Aug 15; 8(8): e71328.  doi:10.1371/journal.pone.0071328.  PMID: 23977017.
  49. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.  Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10. PMID: 23870653
  50. Kasaian K, Wiseman SM, Thiessen N, Mungall KL, Corbett RD, Qian JQ, Nip KM, He A, Tse K, Chuah E, Varhol RJ, Pandoh P, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao Y, Hirst M, Marra MA, Walker BA, Jones SJ. Complete Genomic Landscape of a Recurring Sporadic Parathyroid Carcinoma. J Pathol. 2013 Jul;230(3):249-60.  PMID: 23616356.
  51. The Cancer Genome Atlas Research Network (139 Collaborators including) Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013 May 30;368(22):2059-74. doi: 10.1056/NEJMoa1301689. Epub 2013 May 1. Erratum in: N Engl J Med. 2013 Jul 4;369(1):98. PMID: 23634996
  52. The Cancer Genome Atlas Research Network (200+ authors) Gordon Robertson A, Chu A, Chun HJ, Mungall AJ, Sipahimalani P, Stoll D, Ally A, Balasundaram M, Butterfield YS, Carlsen R, Carter C, Chuah E, Coope RJ, Dhalla N, Gorski S, Guin R, Hirst C, Hirst M, Holt RA, Lebovitz C, Lee D, Li HI, Mayo M, Moore RA, Pleasance E, Plettner P, Schein JE, Shafiei A, Slobodan JR, Tam A, Thiessen N, Varhol RJ, Wye N, Zhao Y, Birol I, Jones SJ, Marra MA. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 4;499(7456):43-9. PMID:23792563
  53. Haridas S, Wang Y, Lim L, Massoumi Alamouti S, Jackman S, Docking R, Robertson G, Birol I, Bohlmann J, Breuil C. The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera. BMC Genomics. 2013 Jun 2;14:373. PMID: 23725015
  54. Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B, Yanchuk A, Ritland C, Boyle B, Bousquet J,Ritland K, Mackay J, Bohlmann J, Jones SJ. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genomeshotgun sequencing data. Bioinformatics. 2013 Jun 15;29(12):1492-1497. Epub 2013 May 22. PMID: 23698863.
  55. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff R, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim E, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole genome sequencing.  Blood. 2013 May 22. [Epub ahead of print] PMID: 23699601. 
  56. Hadj Khodabakhshi A, Fejes AP, Birol I, Jones SJ. Identifying cancer mutation targets across thousands of samples MuteProc, a high throughput mutation analysis pipeline. BMC Bioinformatics. 2013 May 28;14:167. PMID: 23714400 [PubMed - in process].
  57. Cancer Genome Atlas Research Network, (313 collaborators).  Ally A, Balasundaram M, Birol I, Butterfield YS, Carlsen R, Carter C, Chu A, Chuah E, Chuah HJ, Dhalla N, Guin R, Hirst C, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Plettner P, Schein JE, Sipahimalani P, Tam A, Varhol RJ, Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/Nature12113. PMID: 23636398.
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  59. Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefle E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao Y, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Auvil JM, Gerhard DS, Hogarty MD, Jones SJ, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM. “The genetic landscape of high-risk neuroblastoma.” Nat Genet. 2013 Mar;45(3):279-84. doi: 10.1038/ng.2529.
  60. Khodabakhshi AH, Morin RD, Fejes AP, Mungall AJ, Mungall KL, Bolger-Munro M, Johnson NA, Connors JM, Gascoyne RD, Marra MA, Birol I, Jones SJ. “Recurrent targets of aberrant somatic hypermutation in lymphoma.” Oncotarget. 2012 Nov;3(11):1308-19.
  61. Cancer Genome Atlas Network. “Comprehensive molecular portraits of human breast tumours.” Nature. 2012 Oct 4;490(7418):61-70. doi: 10.1038/nature11412.
  62. Cancer Genome Atlas Research Network. “Comprehensive genomic characterization of squamous cell lung cancers.” Nature. 2012 Sep 27;489(7417):519-25. doi: 10.1038/nature11404.
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  65. Cancer Genome Atlas Network. “Comprehensive molecular characterization of human colon and rectal cancer.” Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252.
  66. Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC. “Dissect: detection and characterization of novel structural alterations in transcribed sequences.” Bioinformatics. 2012 Jun 15;28(12):i179-87. doi: 10.1093/bioinformatics/bts214.
  67. Keeling CI, Henderson H, Li M, Yuen M, Clark EL, Fraser JD, Huber DP, Liao NY, Docking TR, Birol I, Chan SK, Taylor GA, Palmquist D, Jones SJ, Bohlmann J. “Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests.” Insect Biochem Mol Biol. 2012 Aug;42(8):525-36. doi: 10.1016/j.ibmb.2012.03.010.
  68. Roberts KG, Morin RD, Zhang J, Hirst M, Zhao Y, Su X, Chen SC, Payne-Turner D, Churchman ML, Harvey RC, Chen X, Kasap C, Yan C, Becksfort J, Finney RP, Teachey DT, Maude SL, Tse K, Moore R, Jones S, Mungall K, Birol I, Edmonson MN, Hu Y, Buetow KE, Chen IM, Carroll WL, Wei L, Ma J, Kleppe M, Levine RL, Garcia-Manero G, Larsen E, Shah NP, Devidas M, Reaman G, Smith M, Paugh SW, Evans WE, Grupp SA, Jeha S, Pui CH, Gerhard DS, Downing JR, Willman CL, Loh M, Hunger SP, Marra MA, Mullghan CG. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell. 2012 Aug 14;22(2):153-66. [PubMed - in process]
  69. Northcott PA, Shih DJ, Peacock J, Garzia L, Sorana Morrissy A, Zichner T, Stutz AM, Korshunov A, Reimand J, Schumaucher SE, Beroukhim R, Ellisson DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall Kl, Ming Nip K, Qian JQ, Raymond AG, Thiessen N, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fevre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Yancey Gillespie G, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognar L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa Sk, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, JOnes SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012 Jul 25.doi:10.1038/nature11327.
  70. Chu A, Chun HJ, Mungall AJ, Pleasance E, Robertson A, Stoll D, Balasundaram M, Birol I, Butterfield YS, Chuah E, Coope RJ, Dhalla N, Guin R, Hirst C, Hirst M, Holt RA, Lee D, Li HI, Mayo M, Moore RA, Schein JE, Slobodan JR, Tam A, Thiessen N, Varhol R, Zeng T, Zhao Y, Jones SJ, Marra MA and the Cancer Genome Atlast Network. (297 collaborators). Comprehensive molecular characterization of human colon and rectal cancer. Nature.2012 Jul 18;487(7407):330-7.doi:10.1038/nature/11327. [Epub ahead of print]
  71. Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC. Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinformatics. 2012 jun 15;28(12):i179-il87.
  72. Keeling CI, Henderson H, Li M, Yuen M, Clark EL, Fraser JD, Huber DP, Liao NY, Docking RT, Birol I, Chan SK, Taylor GA, Palmquist D, Jones SJ, Bohlmann J. Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests. Insect Biochem Mol Biol. 2012 Apr 7.[Epub ahead of print]
  73. Shah SP, Roth A, Goya R, Oloumi A, Ha g, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashshati A, Prentice L, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan S, Chin SF, Curtis C, Rueda O, Pharoah P, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Caldas C, Marra MA, Aparicio S. The clonal mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012 Apr 4. doi: 10.1038/nature10933.Epub 2011 Nov 10.
  74. Yip S, Butterfield YS, Morozova O, Chittaranjan S, Blough MD, An J, Birol I, Chesnelong C, Chiu R, Chuah E, Corbett R, Docking R, Firme M, Hirst M, Jackman S, Karsan A, Li H, Louis DN, Maslova A, Moore R, Moradian A, Mungall KL, Perizzolo M, Qian J, Roldan G, Smith EE, Tamura-Wells J, Thiessen N, Varhol R, Weiss S, Wu W, Young S, Zhao YJ, Mungall AJ, Jones SJM, Morin GB, Chan JA, Cairncross JG, Marra MA. Concurrent CIC muttions, IDH mutations and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol. 2012 Jan;226(1):7-16.Epub 2011 Sep 16.
  75. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonesca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledstov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MaLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec;21(12):2224-41. Epub 2011 Sep 16.
  76. Krzywinski M, Birol I, Jones S, Marra M. Hive Plots - Rational Approach to Visualizing Networks. Brief Bioinform. 2011 Dec 9. [Epub ahead of print]
  77. Chu Y, Gao P, Zhao P, He Y, Liao N, Jackman S, Zhao Y, Birol I, Duan X, Lu Z. Genome sequence of Mycoplasma capricolum subsp. capripneumonaie strain M1601. J Bacteriol. 2011 Nov; 193(21):6098-9.
  78. Chan QW, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, jackman SD, Taylor GA, Jones SJ, de Graaf DC, Evans JD, Foster LJ. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. BMC Genomics. 2011 Sep 16;12;450.
  79. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, HIrst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Aug 18; 476(7360):298-303.
  80. Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour. 2011 Mar 1;11 Suppl 1:81-92.
  81. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJM, Brinkman FSL, Brunham RC, Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011 Feb 24; 364(8):730-9.
  82. Fejes AP, Hadj Khodabakhshi A, Birol I, Jones SJM. Human Variation Database: An open source database template for genomic discovery. Bioinformatics. 2011 Mar 2.
  83. Earl DA, Bradnam K, St John J, Darling A, Lin D, Faas J, Yu HOK, Vince B, Zerbino DR, Diekhans M, Nguyen N, Nuwantha P, Sung AW-K, Ning Z, Haimel M, Simpson JT, Fronseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelly DR, Phillippy AM, Koren S, Yang S-P, Wu W, Chou W-C, Srivastava A, SHaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, Maclean D, Xia F, Luo R, L Z, Xie Y, Liu B, Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, Derisi JL, Caccamo M, Li Y, Jaffe DB, Green R, Haussler D, Korf I, Paten B. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Res. 2011 Sep 16. [Epub ahead of print].
  84. DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CKM, Docking RT, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, Hirst M, Jones SJM, Bohlmann J, Breuil C. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci USA. 2011 Feb 8;108(6):2504-
  85. Chan QW, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, Jackman SD, Taylor GA, Jones SJM, de Graaf DC, Evans JD, Foster LJ. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. BMC Genomics. 2011 Sep 16;12:450.
  86. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJM, Brinkman FSL, Brunham RC, Tang P. Whole Genome Sequencing and Social Network Analysis of a Tuberculosis Outbreak. NEJM. 2011 Feb 24;364(8):730-9..
  87. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield Y, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao YJ, Moore R, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I. De novo Assembly and Analysis of RNA-seq Data. Nat Methods. 2010 Nov;7(11):909-12. [Epub 2010 Oct 10.]
  88. Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes A, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010;11(8):R82. [Epub 2010 Aug 9.]
  89. Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods. 2010 Aug;7(8):576-7.
  90. Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD, Marra MA, Jones SJ, Hoodless PA. Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res. 2010 Aug;20(8):1037-51. [Epub 2010 Jun 15.]
  91. Wong RTF, Flibotte S, Corbett R, Saeedi P, Jones SJM, Marra MA, Schein JE, Birol I. LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. IEEE Tr Automation Sci and Eng. July 2010, 7(3):706-708.
  92. Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res. 2010 Jun; 20(6):791-803.
  93. Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics. 2010 May 15; 26(10):1277-83.
  94. Jackman SD, Birol I. Assembling genomes using short-read sequencing technology. Genome Biol. 2010 Jan 28; 11(1):202.
  95. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet. 2010 Feb; 42(2):181-5.
  96. Nielsen CB, Jackman SD, Birol I, Jones SJ. ABySS-Explorer: visualizing genome sequence assemblies. IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):881-8.
  97. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJM. De novo assembly of a genome sequence for the filamentous fungus, Grosmannia clavigera, assembled using Sanger, 454 and Illumina sequence data. Genome Biology. 2009; 10(9):R94.
  98. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra M. Circos: an Information Aesthetic for Comparative Genomics. Genome Res. 2009 Sep;19(9):1639-45. [Epub 2009 Jun 18.]
  99. Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ. De novo Transcriptome Assembly with ABySS. Bioinformatics 2009 Nov 1; 25(21):2872-7.
  100. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: A parallel assembler for short read sequence data. Genome Research. 2009 Jun; 19(6):1117-23.
  101. Robertson GA, Bilenky M, Tam A, Zhao YJ, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM. Genome wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. Genome Research. 2008 Dec;18(12):1906-17. [Epub 2008 Sep 11.]
  102. Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics. 2008 Jul 1; 24(13):i32-40.
  103. Tatara E, Birol I, Teymour F, Cinar A. Agent-Based Control of Autocatalytic Replicators in Networks of Reactors. Computers and Chemical Engineering. (29), 807 – 815, March 2005.
  104. Tatara E, Birol I, Cinar A, Teymour F. Measuring Complexity in Reactor Networks with Cubic Autocatalytic Reactions. Industrial and Eng. Chem. Research. (44), 2781 – 2791 February 2005.
  105. Apyan A, Avakian R.O, Badelek B, Ballestrero S, Biino C, Birol I, Cenci P, Connell S.H, Eichblatt S, Fonseca T, Freund A, Gorini B, Groess R, Ispirian K, Ketel T. J, Kononets Yu. V, Lopez A, Mangiarotti A, van Rens B, Sellschop J.P.F, Shieh M, Sona P, Strakhovenko V, Uggerhoj E, Uggerhoj U.I, Unel G, Velasco M, Vilakazi Z.Z, Wessely O. Results on the Coherent Interaction of High Energy Electrons and Photons in Oriented Single Crystals. Nucl. Instrum. Meth. B234 128-137, 2005.
  106. Wang L, Birol I, Hatzimanikatis V. Metabolic Control Analysis Under Uncertainty: Framework Development and Case Studies. Biophysics J. 2004 Dec; 87(6):3750-63. [Epub 2004 Oct 1.]
  107. Unel G, Birol I, for NA59 Collaboration. Data Acquisition System of NA59 Experiment. Trans. Nuclear Science. (51), 1482 – 1487, August 2004.
  108. Unel G, Birol I, Ballestrero S. The trigger and DAQ systems of the Na59 experiment Nuclear Science. IEEE Transactions on 51, 4, 1 DOI: 10.1109/TNS.2004.832303, 1482 – 1487 2004.
  109. Tatara E, Birol I, Teymour F, Cinar A. Static and Dynamic Behavior of Autocatalytic Replicators in Reactor Networks. Industrial and Eng. Chem. Research. (43), 3972 – 3993, February 2004.
  110. Birol I. Evolutionary Pressures in Multi-Species Competition. Environmental Informatics Archives. (1) 228 – 235, 2003.
  111. Birol G, Birol I, Kirdar B, Onsan ZI. Investigating the Fermentation Dynamics Structure of Recombinant Saccharomyces cerevisiae, YPB-G. Computers and Chemical Engineering. (27), 45 – 54, 2003.
  112. Chaivorapoj W, Birol I, Cinar A, Teymour F. Controlling the Competition Between Multiple Autocatalytic Replicators. Industrial and Eng. Chem. Research. (42), 3765 – 3785, 2003.
  113. Birol I, Parulekar SJ, Teymour F. Effect of Environment Partitioning on the Survival and Coexistence of Autocatalytic Replicators. Physical Review E. (66), 051916, 2002.
  114. Chaivorapoj W, Birol I, Teymour F. Competition Between Robust and Nonrobust Cubic Autocatalytic Replicators. Industrial and Eng. Chem. Research, (41), 3630 – 3641, 2002.
  115. Papavasiliou G, Birol I, Teymour F. Calculation of Molecular Weight Distributions in Non-Linear Free-Radical Polymerization Using the Numerical Fractionation Technique. Macromolecular Theory and Simulations. (11) 533 – 548, 2002.
  116. Birol I, Birol G, Undey C, Cinar A. A Web-Based Simulator for Penicillin Fermentation.  Int. J. of Engineering Simulation. (1), 24 – 30, 2001.
  117. Birol G, Birol I, Cinar A. Student Performance Enhancement by Cross-Course Project Assignments. Chemical Engineering Education. 35 (2), 2001.
  118. Birol I, Teymour F. Statics and Dynamics of Autocatalytic Reactions. Physica D. (144), 279 – 297, 2000.
  119. Birol I, Hacinliyan A, Perdahci NZ. Simulating a Dynamical System in the Presence of a 1/f Noise. Int. J. of Eng. Science. (36) 265 – 271, 1998.
  120. CHORUS Collaboration. A New Search for nm®nt Oscillation. Phys. Lett. B.(424) 202 – 212, 1998.
  121. Birol G, Birol I, Kirdar B, Onsan ZI. Modeling of recombinant yeast cells: reduction of phase space. Biomed Sci Instrum. 1997;34:163-8.
  122. Birol I, Hacinliyan A. Signs and Approximate Magnitudes of Lyapunov Exponents in Continuous Time Dynamical Systems. J. of Math. Phys. (38) 4594 – 4605, 1997.
  123. Birol I, Edgu E. Parameter Dependent Study of Liapunov Exponents in Lorenz and Rossler Systems. Tr. J. of Physics. (21) 1233 – 1245, 1997.
  124. Birol I, Hacinliyan A. Some Algebraic Properties of Continuous Time Dynamical Systems. Int. J. of Modern Physics A. (1), 137 – 142, 1997.
  125. Birol I, Hacinliyan A. Determining Zero Lyapunov Exponent of Continuous Time Dynamical Systems. Int. J. of Modern Physics A.(1), 131 – 135, 1997.
  126. Umur A, Birol I, Hacinliyan A. Chaos Mechanisms of Third Order Continuous Time Dynamical Systems. Balkan Phys. Let.(5), 188 – 197, 1997.
  127. CHORUS Collaboration. The CHORUS Experiment to Search for nm®nt Oscillation. Nucl. Instrum. Methods Phys. Res. A. (401) 7 – 44, 1997.
  128. Birol I, Hacinliyan A. Approximately Conserved Quantity in the Henon-Heiles Problem. Phys. Rev. E.(52), 4750 – 4753, 1995.
  129. Birol I, Hacinliyan A. An Approach to System Modeling: Least Squares with Exponential Forgetting. Bull. Ist. Tech. Univ. (Invited Paper in the Special Issue: Suhubi and Continuum Mechanics), (47) 313 – 320, 1994.
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