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Inanc Birol Publication List

by Kirsten San Juan — last modified Nov 03, 2011 09:48 AM
  1. 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.
  2. 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.
  3. 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.
  4. Fejes AP, Hadj Khodabakhshi A, Birol I, Jones SJM, "Human Variation Database: An open source database template for genomic discovery", Bioinformatics. 2011 Mar 2.
  5. 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].
  6. 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-
  7. 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.
  8. 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..
  9. 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.]
  10. 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.]
  11. 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.
  12. 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.]
  13. 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.
  14. 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.
  15. 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.
  16. Jackman SD, Birol I, “Assembling genomes using short-read sequencing technology.” Genome Biol. 2010 Jan 28; 11(1):202.
  17. 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.
  18. 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.
  19. 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.
  20. 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.]
  21. 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.
  22. 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.
  23. 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.]
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.]
  29. Birol I, Unel G, for NA59 Collaboration, “Software Aspects of the NA59 Experiment”, Trans. Nuclear Science, (51), 1449 – 1455, August 2004.
  30. Unel G, Birol I, for NA59 Collaboration, “Data Acquisition System of NA59 Experiment”, Trans. Nuclear Science, (51), 1482 – 1487, August 2004.
  31. 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.
  32. 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.
  33. Birol I, “Evolutionary Pressures in Multi-Species Competition”, Environmental Informatics Archives, (1) 228 – 235, 2003.
  34. 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.
  35. Chaivorapoj W, Birol I, Cinar A, Teymour F, “Controlling the Competition Between Multiple Autocatalytic Replicators”, Industrial and Eng. Chem. Research, (42), 3765 – 3785, 2003.
  36. Birol I, Parulekar SJ, Teymour F, “Effect of Environment Partitioning on the Survival and Coexistence of Autocatalytic Replicators”, Physical Review E, (66), 051916, 2002.
  37. Chaivorapoj W, Birol I, Teymour F, “Competition Between Robust and Nonrobust Cubic Autocatalytic Replicators”, Industrial and Eng. Chem. Research, (41), 3630 – 3641, 2002.
  38. 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.
  39. Birol I, Birol G, Undey C, Cinar A, “A Web-Based Simulator for Penicillin Fermentation”, Int. J. of Engineering Simulation, (1), 24 – 30, 2001.
  40. Birol G, Birol I, Cinar A, “Student Performance Enhancement by Cross-Course Project Assignments”, Chemical Engineering Education, 35 (2), 2001.
  41. Birol I, Teymour F, “Statics and Dynamics of Autocatalytic Reactions”, Physica D, (144), 279 – 297, 2000.
  42. 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.
  43. CHORUS Collaboration, “A New Search for nm®nt Oscillation”, Phys. Lett., B, (424) 202 – 212, 1998.
  44. Birol G, Birol I, Kirdar B, Onsan ZI. "Modeling of recombinant yeast cells: reduction of phase space." Biomed Sci Instrum. 1997;34:163-8.
  45. Birol I, Hacinliyan A, “Signs and Approximate Magnitudes of Lyapunov Exponents in Continuous Time Dynamical Systems”, J. of Math. Phys., (38) 4594 – 4605, 1997.
  46. Birol I, Edgu E, “Parameter Dependent Study of Liapunov Exponents in Lorenz and Rossler Systems”, Tr. J. of Physics, (21) 1233 – 1245, 1997.
  47. Birol I, Hacinliyan A, “Some Algebraic Properties of Continuous Time Dynamical Systems”, Int. J. of Modern Physics A, (1), 137 – 142, 1997.
  48. Birol I, Hacinliyan A, “Determining Zero Lyapunov Exponent of Continuous Time Dynamical Systems”, Int. J. of Modern Physics A, (1), 131 – 135, 1997.
  49. Umur A, Birol I, Hacinliyan A, “Chaos Mechanisms of Third Order Continuous Time Dynamical Systems”, Balkan Phys. Let., (5), 188 – 197, 1997.
  50. CHORUS Collaboration, “The CHORUS Experiment to Search for nm®nt Oscillation”, Nucl. Instrum. Methods Phys. Res. A, (401) 7 – 44, 1997.
  51. Birol I, Hacinliyan A, “Approximately Conserved Quantity in the Henon-Heiles Problem”, Phys. Rev. E, (52), 4750 – 4753, 1995.
  52. 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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