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publications.html
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---
layout: page
title: Publications
---
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<span style="font-size:13px"><em>For more details, see our page on <a href="https://scholar.google.ca/citations?user=Svk1wjsAAAAJ&hl=en">Google Scholar</a></em></span>
<div id="2025" class="tabcontent">
{% include current-year-pubs.html %}
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<div id="2024" class="tabcontent">
<p class="2024">Gagalova KK, Yan Y, Wang S, Matzat T, Castellarin SD, Birol I, Edwards D, Schuetz M. 2024. Leaf pigmentation in Cannabis sativa: Characterization of anthocyanin biosynthesis in colorful Cannabis varieties. <a href=https://doi.org/10.1002/pld3.70016>Plant Direct. 8(11):e70016. https://doi.org/10.1002/pld3.70016</a></p>
<p class="2024">Porter VL, Ng M, O'Neill K, MacLennan S, Corbett RD, Culibrk L, Hamadeh Z, Iden M, Schmidt R, Tsaih SW, Nakisige C, Origa M, Orem J, Chang G, Fan J, Nip KM, Akbari V, Chan SK, Hopkins J, Moore RA, Chuah E, Mungall KL, Mungall AJ, Birol I, Jones SJM, Rader JS, Marra MA. 2024. Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation. <a href=https://doi.org/10.1101/gr.279041.124>Genome Res. https://doi.org/10.1101/gr.279041.124</a></p>
<p class="2024">Li C, Sutherland D, Richter A, Coombe L, Yanai A, Warren RL, Kotkoff M, Hof F, Hoang LMN, Helbing C, Birol I. 2024. De novo synthetic antimicrobial peptide design with a recurrent neural network. <a href=https://doi.org/10.1002/pro.5088> Protein Science. https://doi.org/10.1002/pro.5088</a></p>
<p class="2024">Ebrahimikondori H, Sutherland D, Yanai A, Richter A, Salehi A, Li C, Coombe L, Kotkoff M, Warren RL, Birol I. 2024. Structure-aware deep learning model for peptide toxicity prediction. <a href=https://doi.org/10.1002/pro.5076> Protein Science. https://doi.org/10.1002/pro.5076</a></p>
<p class="2024">Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. 2024. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. <a href=https://doi.org/10.1038/s41592-024-02298-3>Nat Methods. doi: 10.1038/s41592-024-02298-3. Epub ahead of print. PMID: 38849569.</a></p>
<p class="2024">Woudstra Y, Tumas H, van Ghelder C, Hung TH, Ilska JJ, Girardi S, A'Hara S, McLean P, Cottrell J, Bohlmann J, Bousquet J, Birol I, Woolliams JA, MacKay JJ. 2024. Conifers concentrate large numbers of NLR immune receptor genes on one chromosome. <a href=https://doi.org/10.1093/gbe/evae113>Genome Biol Evol. doi: 10.1093/gbe/evae113. PMID: 38787537.</a></p>
<p class="2024">Corrie LM, Kuecks-Winger H, Ebrahimikondori H, Birol I, Helbing CC. 2024. Transcriptomic profiling of Rana [Lithobates] catesbeiana back skin during natural and thyroid hormone-induced metamorphosis under different temperature regimes with particular emphasis on innate immune system components.<a href=https://doi.org/10.1016/j.cbd.2024.101238> Comp Biochem Physiol Part D Genomics Proteomics. 50:101238. doi: 10.1016/j.cbd.2024.101238. PMID: 38714098.</a></p>
<p class="2024">Acharya-Patel N, Groenwold E, Lemay MA, Clemente-Carvalho R, Morien E, Dudas S, Rubidge E, Yang CL, Coombe L, Warren RL, Frid A, Birol I, Helbing CC. 2024. Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada. <a href=https://doi.org/10.1016/j.ecolind.2024.111830>Ecol. Indic. 160, 111830. https://doi.org/10.1016/j.ecolind.2024.111830</a></p>
<p class="2024">Warren RL, Abraham R, Calingo M, Garant JM, Jones SJM, Birol I, CGEn HostSeq Initiative. 2024. Establishing association between HLA-C*04:01 and severe COVID-19. <a href=https://doi.org/10.1111/tan.15355>HLA, 103: e15355. DOI: 10.1111/tan.15355. PMID: 38273454</a></p>
<p class="2024">Hung TH, Wu ETY, Zeltiņš P, Jansons Ā, Ullah A, Erbilgin N, Bohlmann J, Bousquet J, Birol I, Clegg SM, MacKay JJ. 2024. Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce. <a href=https://doi.org/10.1186/s12864-024-09978-6>BMC genomics, 25(1), 118. https://doi.org/10.1186/s12864-024-09978-6</a></p>
</div>
<div id="2023" class="tabcontent">
<p class="2023">Wong J, Kazemi P, Coombe L, Warren RL, Birol I. 2023. aaHash: recursive amino acid sequence hashing.<a href=https://doi.org/10.1093/bioadv/vbad162> Bioinformatics Advances, vbad162, https://doi.org/10.1093/bioadv/vbad162</a></p>
<p class="2023">Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. 2023. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. <a href=https://doi.org/10.1093/g3journal/jkad247>G3 Genes|Genomes|Genetics, jkad247, https://doi.org/10.1093/g3journal/jkad247</a></p>
<p class="2023">Porter VL, O'Neill K, MacLennan S, Corbett RD, Ng M, Culibrk L, Hamadeh Z, Iden M, Schmidt R, Tsaih SW, Chang G, Fan J, Nip KM, Akbari V, Chan SK, Hopkins J, Moore RA, Chuah E, Mungall KL, Mungall AJ, Birol I, Jones SJM, Rader JS, Marra MA. 2023. Genomic structures and regulation patterns at HPV integration sites in cervical cancer.<a href=https://doi.org/10.1101/2023.11.04.564800>bioRxiv [Preprint]. 2023 Nov 5:2023.11.04.564800. doi: 10.1101/2023.11.04.564800. PMID: 37961641; PMCID: PMC10635144.</a></p>
<p class ="2023">Li JX, Fernandez KX, Ritland C, Jancsik S, Engelhardt DB, Coombe L, Warren RL, van Belkum MJ, Carroll AL, Vederas JC, Bohlmann J, Birol I. 2023. Genomic virulence features of Beauveria bassiana as a biocontrol agent for the mountain pine beetle population.<a href=https://doi.org/10.1186/s12864-023-09473-4> BMC Genomics 24, 390. https://doi.org/10.1186/s12864-023-09473-4</a></p>
<p class="2023">Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. 2023. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. <a href=https://doi.org/10.1101/2023.07.25.550582>bioRxiv [Preprint]. 2023 Jul 27:2023.07.25.550582. doi: 10.1101/2023.07.25.550582. PMID: 37546854; PMCID: PMC10402094.</a></p>
<p class="2023">Allison MJ, Warren RL, Lopez ML, Acharya-Patel N, Imbery JJ, Coombe L, Yang CL, Birol I, Helbing CC. 2023. Enabling robust environmental DNA assay design with “unikseq” for the identification of taxon-specific regions within whole mitochondrial genomes. <a href=https://doi.org/10.1002/edn3.438>Environmental DNA, 00, 1-16. https://doi.org/10.1002/edn3.438</a></p>
<p class="2023">Nip KM, Hafezqorani S, Gagalova KK, Chiu R, Yang C, Warren RL, Birol I. 2023. Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2. <a href=https://doi.org/10.1038/s41467-023-38553-y>Nat Commun 14, 2940. https://doi.org/10.1038/s41467-023-38553-y</a></p>
<p class="2023">Wong J, Coombe L, Nikolić V, Zhang E, Nip KM, Sidhu P, Warren RL, Birol I. 2023. Linear time complexity de novo long read genome assembly with GoldRush. <a href=https://doi.org/10.1038/s41467-023-38716-x>Nat Commun 14, 2906. https://doi.org/10.1038/s41467-023-38716-x</a></p>
<p class="2023">Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, Brooks JD, Bull SB, Gagnon F, Greenwood C, Lawless JF, Paterson AD, Sun L, Zawati MH, Lerner-Ellis J, Abraham R, Birol I, Bourque G, Garant JM, Gosselin C, Li J, Whitney J, Thiruvahindrapuram B, Herbrick JA, Lorenti M, Reuter MS, Adeoye OO, Liu S, Allen U, Bernier FP, Biggs CM, Cheung AM, Cowan J, Herridge M, Maslove DM, Modi BP, Mooser V, Morris SK, Ostrowski M, Parekh RS, Pfeffer G, Suchowersky O, Taher J, Upton J, Warren RL, Yeung R, Aziz N, Turvey SE, Knoppers BM, Lathrop M, Jones S, Scherer SW, Strug LJ. 2023. HostSeq: a Canadian whole genome sequencing and clinical data resource. <a href=https://doi.org/10.1186/s12863-023-01128-3>BMC Genom Data. 24(1):26. doi: 10.1186/s12863-023-01128-3. PMID: 37131148; PMCID: PMC10152008.</a></p>
<p class="2023">Coombe, L., Warren, R. L., Wong, J., Nikolic, V., Birol, I. 2023. ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads. <a href=https://doi.org/10.1002/cpz1.733> Current Protocols, 3(4), e733. https://doi.org/10.1002/cpz1.733</a></p>
<p class="2023">Yang C., Lo T., Nip K.M., Hafezqorani S., Warren R.L., Birol I. 2023. Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.<a href=https://doi.org/10.1093/gigascience/giad013> GigaScience, Volume 12, giad013, https://doi.org/10.1093/gigascience/giad013 PMID: 36939007; PMCID: PMC10025935</a></p>
<p class="2023">Li C., Warren R.L., Birol I. 2023. Models and data of AMPlify: a deep learning tool for antimicrobial peptide prediction. <a href=https://doi.org/10.1186/s13104-023-06279-1>BMC Res Notes 16, 11. https://doi.org/10.1186/s13104-023-06279-1</a></p>
</div>
<div id="2022" class="tabcontent">
<p class="2022">Richter A, Sutherland D, Ebrahimikondori H, Babcock A, Louie N, Li C, Coombe L, Lin D, Warren RL, Yanai A, Kotkoff M, Helbing CC, Hof F, Hoang LMN, Birol I. 2022. Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects. <a href=https://doi.org/10.3390/antibiotics11121710>Antibiotics. 11(12):1710. https://doi.org/10.3390/antibiotics11121710</a></p>
<p class="2022">Nikolic V, Kazemi P, Coombe L, Wong J, Afshinfard A, Chu J, Warren RL, Birol I. 2022. btllib: A C++ library with Python interface for efficient genomic sequence processing. <a href=https://doi.org/10.21105/joss.04720>Journal of Open Source Software. 7(79), 4720, https://doi.org/10.21105/joss.04720</a></p>
<p class="2022">Warren RL. 2022. HLA predictions from long sequence read alignments, streamed directly into HLAminer. <a href=https://doi.org/10.48550/arXiv.2209.09155>arXiv. https://doi.org/10.48550/arXiv.2209.09155</a></p>
<p class="2022">Shalev TJ, El-Dien OG, Yuen MMS, Shengqiang S, Jackman SD, Warren RL, Coombe L, van der Merwe L, Stewart A, Boston LB, Plott C, Jenkins J, He G, Yan J, Yan M, Guo J, Breinholt JW, Neves LG, Grimwood J, Rieseberg LH, Schmutz J, Birol I, Kirst M, Yanchuk AD, Ritland C, Russell JH, Bohlmann J. 2022. The western redcedar genome reveals low genetic diversity in a self-compatible conifer. <a href=https://doi.org/10.1101/gr.276358.121>Genome Res. gr.276358.121 Published in Advance September 15, 2022, doi:10.1101/gr.276358.121</a></p>
<p class="2022">Kazemi P, Wong J, Nikolic V, Mohamadi H, Warren RL, Birol I. 2022. ntHash2: recursive spaced seed hashing for nucleotide sequences.<a href=https://doi.org/10.1093/bioinformatics/btac564>Bioinformatics. https://doi.org/10.1093/bioinformatics/btac564</a></p>
<p class="2022">Warren RL. 2022. PASS: De novo assembler for short peptide sequences. <a href=https://arxiv.org/pdf/2208.05598.pdf>arXiv. https://doi.org/10.48550/arXiv.2208.05598</a></p>
<p class="2022">Lin D, Sutherland D, Aninta SI, Louie N, Nip KM, Li C, Yanai A, Coombe L, Warren RL, Helbing C, Hoang LMN, Birol I. 2022. Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage. <a href=https://doi.org/10.3390/antibiotics11070952>Antibiotics. 11:952. https://doi.org/10.3390/antibiotics11070952</a></p>
<p class="2022">Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill GA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. 2022. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. <a href=https://doi.org/10.1111/tpj.15889>The Plant Journal. https://doi.org/10.1111/tpj.15889</a></p>
<p class="2022">Nikolic V, Afshinfard A, Chu J, Wong J, Coombe L, Nip KM, Warren RL, Birol I. 2022. RResolver: efficient short-read repeat resolution within ABySS. <a href=https://doi.org/10.1186/s12859-022-04790-z>BMC bioinformatics. 23:246. https://doi.org/10.1186/s12859-022-04790-z</a></p>
<p class="2022">Wright K, Nip KM, Kim JE, Birol, I. 2022. Seasonal and sex-dependent gene expression in emu (Dromaius novaehollandiae) fat tissues. <a href=https://doi.org/10.1038/s41598-022-13681-5>Sci Rep 12:9419. https://doi.org/10.1038/s41598-022-13681-5</a></p>
<p class="2022">Afshinfard A, Jackman SD, Wong J, Coombe L, Chu J, Nikolic V, Dilek G, Malkoç Y, Warren RL, Birol I. 2022. Physlr: Next-Generation Physical Maps. <a href=https://doi.org/10.3390/dna2020009>DNA 2:116-130. https://doi.org/10.3390/dna2020009</a></p>
<p class="2022">Chiu R, Rajan-Babu IS, Birol I, Friedman JM. 2022. Linked-read sequencing for detecting short tandem repeat expansions. <a href=https://doi.org/10.1038/s41598-022-13024-4>Sci Rep 12:9352. https://doi.org/10.1038/s41598-022-13024-4</a></p>
<p class="2022">Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, Brooks JD, Bull SB, Gagnon F, Greenwood CMT, Lawless JF, Paterson AD, Sun L, Zawati MH, Lerner-Ellis J, Abraham RJS, Birol I, et al. 2022. HostSeq: A Canadian Whole Genome Sequencing and Clinical Data Resource. <a href=https://doi.org/10.1101/2022.05.06.22274627>medRxiv 2022.05.06.22274627; doi: https://doi.org/10.1101/2022.05.06.22274627</a></p>
<p class="2022">Li JX, Coombe L, Wong J, Birol I, Warren RL. 2022. ntEdit+Sealer: Efficient targeted error resolution and automated finishing of long-read genome assemblies. <a href=https://doi.org/10.1002/cpz1.442>Curr. Protocols. 2:e442 doi: 10.1002/cpz1.442</a></p>
<p class="2022">Gagalova KK, Whitehill JGA, Culibrk L, Lin D, Lévesque-Tremblay V, Keeling CI, Coombe L, Yuen MMS, Birol I, Bohlmann J, Jones SJM. 2022. The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont. <a href=https://doi.org/10.1093/g3journal/jkac038>G3 Genes|Genomes|Genetics. 12(4):jkac038 doi: 10.1093/g3journal/jkac038</a></p>
<p class="2022">Li C, Sutherland D, Hammond SA, Yang C, Taho F, Bergman L, Houston S, Warren RL, Wong T, Hoang LMN, Cameron CE, Helbing CC, Birol I. 2022. AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. <a href=https://doi.org/10.1186/s12864-022-08310-4>BMC genomics. 23:77. https://doi.org/10.1186/s12864-022-08310-4</a></p>
<p class="2022">Selinger AJ, Cavallin NA, Yanai A, Birol I, Hof F. 2022. Template-Directed Synthesis of Bivalent, Broad-Spectrum Hosts for Neuromuscular Blocking Agents. <a href=https://doi.org/10.1002/anie.202113235>Angew Chem Int Ed Engl. 61(4):e202113235. doi: 10.1002/anie.202113235</a></p>
</div>
<div id="2021" class="tabcontent">
<p class="2021">Stephenson M, Nip KM, HafezQorani S, Gagalova KK, Yang C, Warren RL, Birol I. 2021. RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. <a href=https://academic.oup.com/nargab/article-abstract/doi/10.1093/nargab/lqab105/6445923>NAR Genomics and Bioinformatics 3:4. lqab105 doi: https://doi.org/10.1093/nargab/lqab105</a></p>
<p class="2021">Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL, Birol I. 2021. LongStitch: high-quality genome assembly correction and scaffolding using long reads. <a href=https://doi.org/10.1186/s12859-021-04451-7>BMC Bioinformatics 22:534 https://doi.org/10.1186/s12859-021-04451-7</a></p>
<p class="2021">Warren RL and Birol I. 2021. HLA alleles measured from COVID-19 patient transcriptomes reveal associations with disease prognosis in a New York cohort. <a href=http://doi.org/10.7717/peerj.12368>PeerJ 9:e12368 http://doi.org/10.7717/peerj.12368</a></p>
<p class="2021">Chen E, Chu J, Zhang J, Warren RL, Birol I. 2021. GapPredict A Language Model for Resolving Gaps in Draft Genome Assemblies. <a href=https://ieeexplore.ieee.org/document/9528958>IEEE/ACM Trans Comput Biol Bioinform. doi: 10.1109/TCBB.2021.3109557</a></p>
<p class="2021">Haile S, Corbett RD, LeBlanc VG, Wei L, Pleasance S, Bilobram S, Nip KM, Brown K, Trinh E, Smith J, Trinh DL, Bala M, Chuah E, Coope RJN, Moore RA, Mungall AJ, Mungall KL, Zhao Y, Hirst M, Aparicio S, Birol I, Jones SJM, Marra MA. 2021. A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells. <a href=https://doi.org/10.3389/fgene.2021.665888>Front Genet. 12:665888. doi: 10.3389/fgene.2021.665888</a></p>
<p class="2021">Chiu R, Rajan-Babu IS, Friedman JM, Birol I. 2021. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. <a href=https://doi.org/10.1186/s13059-021-02447-3>Genome Biol. https://doi.org/10.1186/s13059-021-02447-3</a></p>
<p class="2021">Rajan-Babu IS, Peng JJ, Chiu R; IMAGINE Study; CAUSES Study, Li C, Mohajeri A, Dolzhenko E, Eberle MA, Birol I, Friedman JM. 2021. Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions. <a href=https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00932-9>Genome Med. 13(1):126. doi: 10.1186/s13073-021-00932-9</a></p>
<p class="2021">Docking TR, Parker JDK, Jädersten M, Duns G, Chang L, Jiang J, Pilsworth JA, Swanson LA, Chan SK, Chiu R, Nip KM, Mar S, Mo A, Wang X, Martinez-Høyer S, Stubbins RJ, Mungall KL, Mungall AJ, Moore RA, Jones SJM, Birol İ, Marra MA, Hogge D, Karsan A. 2021. A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. <a href=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8087683/>Nat Commun. 12(1):2474. doi: 10.1038/s41467-021-22625-y</a></p>
<p class="2021">Warren RL and Birol I. 2021. Interactive SARS-CoV-2 mutation timemaps [version 1; peer review: awaiting peer review]. <a href=https://doi.org/10.12688/f1000research.50857.1>F1000Research. 10:68 (https://doi.org/10.12688/f1000research.50857.1)</a></p>
</div>
<div id="2020" class="tabcontent">
<p class="2020">Lo T, Coombe L, Lin D, Warren RL, et al. 2020. Complete chloroplast genome sequence of a black spruce (Picea mariana) from Eastern Canada. <a href=https://doi.org/10.1128/MRA.00877-20>Microbiol Resour Announc. https://doi.org/10.1128/MRA.00877-20</a></p>
<p class="2020">Warren RL and Birol I. 2020. HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset. <a href=https://doi.org/10.1093/bioinformatics/btaa756>Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa756</a></p>
<p class="2020">Nip KM, Chiu R, Yang C, Chu J, Mohamadi H, Warren RL, Birol I. 2019. RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes. <a href=http://www.genome.org/cgi/doi/10.1101/gr.260174.119>Genome Res. http://www.genome.org/cgi/doi/10.1101/gr.260174.119</a></p>
<p class="2020">Chu J, Mohamadi H, Erhan E, Tse J, Chiu R, Yeo S, Birol I. 2020. Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters. <a href=https://doi.org/10.1073/pnas.1903436117>Proc Natl Acad Sci USA. https://doi.org/10.1073/pnas.1903436117</a></p>
<p class="2020">Hafezqorani S, Yang C, Nip KM, Warren RL, <strong>Birol I</strong>. 2020. Trans-NanoSim characterizes and simulates nanopore RNA-seq data. <a href=https://doi.org/10.1093/gigascience/giaa061>GigaScience. 9:1-7 https://doi.org/10.1093/gigascience/giaa061</a></p>
<p class="2020">Jackman SD, Coombe L, Warren RL, Kirk H, Trinh E, McLeod T, Pleasance S, Pandoh P, Zhao Y, Coope RJ, Bousquet J, Bohlmann J, Jones SJM, Birol I. 2019. Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure. <a href="https://doi.org/10.1093/gbe/evaa108"> Genome Biol Evol. https://doi.org/10.1093/gbe/evaa108</a></p>
<p class="2020">Coombe L, Nikolic V, Chu J, Birol I, <strong>Warren RL</strong>. ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. 2020 Apr 20. <a href="https://doi.org/10.1093/bioinformatics/btaa253">Bioinformatics. doi: 10.1093/bioinformatics/btaa253.</a></p>
<p class="2020"><strong>Warren RL</strong>, Birol I. HLA predictions from the bronchoalveolar lavage fluid samples of five patients at the early stage of the Wuhan seafood market COVID-19 outbreak. 2020 Apr 15. <a href="https://arxiv.org/pdf/2004.07108">arXiv preprint arXiv:2004.07108</a></p>
<p class="2020">Law WD, Warren RL, McCallion AS. Establishment of an eHAP1 human haploid cell line hybrid reference genome assembled from short and long reads. Genomics. 2020;112(3):2379‐2384. <a href="https://doi.org/10.1016/j.ygeno.2020.01.009">doi:10.1016/j.ygeno.2020.01.009</a></p>
<p class="2020">Lin H, Rothe K, Chen M, Wu A, Babaian A, Yen R, Zeng J, Ruschmann J, et. al. The miR-185/PAK6 Axis Predicts Therapy Response and Regulates Survival of Drug-Resistant Leukemic Stem Cells in CML. 2020 Apr 08. <a href="https://ashpublications.org/blood/article-pdf/doi/10.1182/blood.2019003636/1723513/blood.2019003636.pdf">Blood Journal, blood-2019003636</a></p>
</div>
<div id="2019" class="tabcontent">
<p class="2019">Chiu R, Nip KM, Birol I. 2019. Fusion-Bloom: fusion detection in assembled transcriptomes <a href="https://doi.org/10.1093/bioinformatics/btz902">Bioinformatics. doi: 10.1093/bioinformatics/btz902.</a></p>
<p class="2019">Lin D, Coombe L, Jackman SD, Gagalova KK, Warren RL, Hammond SA, McDonald H, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Doerksen T, Jaquish B, Bousquet J, Jones SJM, Bohlmann J, Birol I. 2019. Complete Chloroplast Genome Sequence of an Engelmann Spruce (Picea engelmannii, Genotype Se404-851) from Western Canada. <a href="https://doi.org/10.1128/MRA.00382-19">Microbiol Resour Announc 8:e00382-19. doi: 10.1128/MRA.00382-19.</a></p>
<p class="2019">Lin D, Coombe L, Jackman SD, Gagalova KK, Warren RL, Hammond SA, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Jaquish B, Isabel N, Bousquet J, Jones SJM, Bohlmann J, Birol I. 2019. Complete chloroplast genome sequence of a white spruce (Picea glauca, genotype WS77111) from eastern Canada. <a href="https://doi.org/10.1128/MRA.00381-19">Microbiol Resour Announc 8:e00381-19. doi: 10.1128/MRA.00381-19.</a></p>
<p class="2019">Warren RL, Coombe L, Mohamadi H, Zhang J, Jaquish B, Isabel N, Jones SJM, Bousquet J, Bohlmann J, Birol I. 2019. ntEdit: scalable genome sequence polishing. <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz400/5490204">Bioinformatics. pii: btz400. doi: 10.1093/bioinformatics/btz400.</a></p>
<p class="2019">Jackman SD, Mozgacheva T, Chen S, O'Huiginn B, Bailey L, Birol I, Jones SJM. 2019. ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research. <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz278/5475597">Bioinformatics. pii: btz278. doi: 10.1093/bioinformatics/btz278.</a></p>
<p class="2019">Helbing CC, Hammond SA, Jackman SH, Houston S, Warren RL, Cameron CE, Birol I. 2019. Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles. <a href="https://rdcu.be/bqHPW">Sci. Reports. 9:1529</a></p>
</div>
<div id="2018" class="tabcontent">
<p class="2018">GA Taylor, H Kirk, L Coombe, SD Jackman, J Chu, K Tse, D Cheng, et. al. The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis. 2018 Dec. <a href="https://www.mdpi.com/2073-4425/9/12/598/pdf">Genes 9 (12), 598</a></p>
<p class="2018">Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM,<strong>Birol I</strong>.Tigmint: correcting assembly errors using linked reads from large molecules. 2018 <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2425-6">BMC Bioinformatics 19(1):393</a></p>
<p class="2018">R Chiu, KM Nip, J Chu, <strong>I Birol</strong>. TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data. 2018 Dec. <a href="https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-018-0402-6">BMC medical genomics 11 (1), 79</a></p>
<p class="2018">Z Xue, RL Warren, EA Gibb, D MacMillan, J Wong, R Chiu, SA Hammond, et. al. Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes. 2018 Dec. <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4903-7">BMC genomics 19 (1), 536</a></p>
<p class="2018">L Coombe, J Zhang, BP Vandervalk, J Chu, SD Jackman, <strong>I Birol</strong>, et. al. ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. 2018 Dec. <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2243-x">BMC bioinformatics 19 (1), 234</a></p>
<p class="2018">Warren RL. 2018. Visualizing genome synteny with xmatchview. <a href="https://joss.theoj.org/papers/10.21105/joss.00497">Journal of Open Source Software 3:497 doi:10.21105/joss.00497</a></p>
<p class="2018">G Sheikhshab, E Starks, A Karsan, R Chiu, A Sarkar, <strong>I Birol</strong>. Graphner: Using corpus level similarities and graph propagation for named entity recognition. 2018 May 21. <a href="http://www.hicomb.org/papers/HICOMB2018-03.pdf">2018 IEEE International Parallel and Distributed Processing Symposium …</a></p>
<p class="2018">LJ Campbell, SA Hammond, SJ Price, MD Sharma, TWJ Garner, <strong>I Birol</strong>, 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. <a href="https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14528">Molecular ecology 27 (6), 1413-1427</a></p>
<p class="2018">N Feau, S Beauseigle, MJ Bergeron, GJ Bilodeau, <strong>I Birol</strong>, et. al. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. 2018 Feb 22. <a href="https://peerj.com/articles/4392">PeerJ 6, e4392</a></p>
<p class="2018">G Sheikhshabbafghi, <strong>I Birol</strong>, A Sarkar. In-domain Context-aware Token Embeddings Improve Biomedical Named Entity Recognition. 2018. <a href="http://www.aclweb.org/anthology/W18-5618">Proceedings of the Ninth International Workshop on Health Text Mining and …</a></p>
<p class="2018">KJ Lesack, <strong>I Birol</strong>. Nomenclature Errors in Public 16S rRNA Gene Reference Databases. 2018 Jan 01. <a href="https://www.biorxiv.org/content/biorxiv/early/2018/10/13/441576.full.pdf">bioRxiv, 441576</a></p>
<p class="2018">J Chu, H Mohamadi, E Erhan, J Tse, R Chiu, S Yeo, <strong>I Birol</strong>. Improving on hash-based probabilistic sequence classification using multiple spaced seeds and multi-index Bloom filters. 2018 Jan 01. <a href="https://www.biorxiv.org/content/biorxiv/early/2018/10/05/434795.full.pdf">bioRxiv, 434795</a></p>
<p class="2018">SD Jackman, L Coombe, J Chu, RL Warren, BP Vandervalk, S Yeo, Z Xue, et. al. Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules. 2018 Jan 01. <a href="https://www.biorxiv.org/content/biorxiv/early/2018/04/20/304253.full.pdf">bioRxiv, 304253</a></p>
</div>
<div id="2017" class="tabcontent">
<p class="2017">H Khan, H Mohamadi, BP Vandervalk, RL Warren, J Chu, <strong>I Birol</strong>. ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. 2017 Dec 29. <a href="https://www.researchgate.net/profile/Hamid_Mohamadi2/publication/322210982_ChopStitch_exon_annotation_and_splice_graph_construction_using_transcriptome_assembly_and_whole_genome_sequencing_data/links/5a4e4db40f7e9b234d9d06fe/ChopStitch-exon-annotation-and-splice-graph-construction-using-transcriptome-assembly-and-whole-genome-sequencing-data.pdf">Bioinformatics, btx839</a></p>
<p class="2017">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. <a href="http://www.mdpi.com/2073-4425/8/12/379/html">Genes 8 (12), 379</a></p>
<p class="2017">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. <a href="http://www.mdpi.com/2073-4425/8/12/378/htm">Genes 8 (12), 378</a></p>
<p class="2017">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. <a href="https://www.nature.com/articles/s41467-017-01316-7">Nature Communications 8 (1), 1433</a></p>
<p class="2017">S Yeo, L Coombe, RL Warren, J Chu, <strong>I Birol</strong>. Arcs: Scaffolding genome drafts with linked reads. 2017 Oct 23. <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btx675/4562503">Bioinformatics</a></p>
<p class="2017">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. <a href="https://www.sciencedirect.com/science/article/pii/S0092867417310565">Cell 171 (3), 540-556. e25</a></p>
<p class="2017">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. <a href="http://genomea.asm.org/content/5/37/e00963-17.full">Genome announcements 5 (37), e00963-17</a></p>
<p class="2017">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. <a href="https://www.sciencedirect.com/science/article/pii/S1535610817302957">Cancer cell 32 (2), 204-220. e15</a></p>
<p class="2017">BJ Raphael, RH Hruban, AJ Aguirre, RA Moffitt, JJ Yeh, C Stewart, et. al. Integrated genomic characterization of pancreatic ductal adenocarcinoma. 2017 Aug 14. <a href="https://www.sciencedirect.com/science/article/pii/S1535610817302994">Cancer Cell 32 (2), 185-203. e13</a></p>
<p class="2017">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. <a href="http://genome.cshlp.org/content/27/5/768.full">Genome research 27 (5), 768-777</a></p>
<p class="2017">TM Brown, SA Hammond, B Behsaz, N Veldhoen, <strong>I Birol</strong>, 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. <a href="https://www.sciencedirect.com/science/article/pii/S0166445X17300358">Aquatic toxicology 185, 48-57</a></p>
<p class="2017">N Pavy, M Lamothe, B Pelgas, F Gagnon, <strong>I Birol</strong>, 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. <a href="http://onlinelibrary.wiley.com/doi/10.1111/tpj.13478/full">The Plant Journal 90 (1), 189-203</a></p>
<p class="2017">C Yang, J Chu, RL Warren, <strong>I Birol</strong>. NanoSim: nanopore sequence read simulator based on statistical characterization. 2017 Feb 24. <a href="https://academic.oup.com/gigascience/article/3051934">GigaScience 6 (4), 1-6</a></p>
<p class="2017">E Kucuk, J Chu, BP Vandervalk, SA Hammond, RL Warren, <strong>I Birol</strong>. Kollector: transcript-informed, targeted de novo assembly of gene loci. 2017 Feb 10. <a href="https://academic.oup.com/bioinformatics/article/2982053">Bioinformatics 33 (12), 1782-1788</a></p>
<p class="2017">H Mohamadi, H Khan, <strong>I Birol</strong>. ntCard: a streaming algorithm for cardinality estimation in genomics data. 2017 Jan 05. <a href="https://academic.oup.com/bioinformatics/article/2832780">Bioinformatics 33 (9), 1324-1330</a></p>
<p class="2017">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. <a href="https://academic.oup.com/bioinformatics/article/2832780">Cytogenetic and genome research 152 (3), 117-121</a></p>
<p class="2017">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. <a href="https://www.biorxiv.org/content/biorxiv/early/2017/07/08/160960.full.pdf">bioRxiv, 160960</a></p>
<p class="2017">S Yeo, L Coombe, J Chu, RL Warren, <strong>I Birol</strong>. ARCS: assembly roundup by chromium scaffolding. 2017 Jan 01. <a href="https://www.biorxiv.org/content/biorxiv/early/2017/01/17/100750.full.pdf">bioRxiv, 100750</a></p>
<p class="2017">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. <a href="https://www.biorxiv.org/content/biorxiv/early/2017/01/13/100149.full.pdf">bioRxiv, 100149</a></p>
<p class="2017">M Krzywinski, KM Nip, <strong>I Birol</strong>, M Marra. Differential Hive Plots: Seeing Networks Change. 2017. <a href="https://muse.jhu.edu/article/670962">Leonardo 50 (5), 504-504</a></p>
</div>
<div id="2016" class="tabcontent">
<p class="2016">N Feau, G Taylor, AL Dale, B Dhillon, GJ Bilodeau, <strong>I Birol</strong>, SJM Jones, et. al. Genome sequences of six Phytophthora species threatening forest ecosystems. 2016 Dec 31. <a href="https://www.sciencedirect.com/science/article/pii/S2213596016301283">Genomics data 10, 85-88</a></p>
<p class="2016">J Chu, H Mohamadi, RL Warren, C Yang, <strong>I Birol</strong>. Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. 2016 Dec 21. <a href="https://academic.oup.com/bioinformatics/article/33/8/1261/2730233">Bioinformatics 33 (8), 1261-1270</a></p>
<p class="2016">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. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163059">PloS one 11 (9), e0163059</a></p>
<p class="2016">D Bouneffouf, <strong>I Birol</strong>. Theoretical analysis of the Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. 2016 Jul 24. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163059">Neural Networks (IJCNN), 2016 International Joint Conference on, 3856-3862</a></p>
<p class="2016">D Bouneffouf, <strong>I Birol</strong>. Ensemble Minimum Sum of Squared Similarities sampling for Nyström-based spectral clustering. 2016 Jul 24. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163059">Neural Networks (IJCNN), 2016 International Joint Conference on, 3851-3855</a></p>
<p class="2016">H Mohamadi, J Chu, BP Vandervalk, <strong>I Birol</strong>. ntHash: recursive nucleotide hashing. 2016 Jul 16. <a href="https://academic.oup.com/bioinformatics/article/32/22/3492/2525588">Bioinformatics 32 (22), 3492-3494</a></p>
<p class="2016">Warren RL. 2016. RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences. <a href=https://joss.theoj.org/papers/10.21105/joss.00116>The Journal of Open Source Software. doi: 10.21105/joss.00116</a></p>
<p class="2016">S Jackman, <strong>I Birol</strong>, S Jackman, <strong>I Birol</strong>. Linuxbrew and Homebrew for cross-platform package management. 2016. <a href="https://academic.oup.com/bioinformatics/article/32/22/3492/2525588">F1000Research 5, 1795</a></p>
<p class="2016">J Chu, H Mohamadi, R Warren, C Yang, <strong>I Birol</strong>. Overlapping long sequence reads: Current innovations and challenges in developing sensitive, specific and scalable algorithms. 2016 Jan 01. <a href="https://www.biorxiv.org/content/biorxiv/early/2016/10/17/081596.full.pdf">bioRxiv, 081596</a></p>
<p class="2016">G Sheikhshab, E Starks, A Karsan, A Sarkar, <strong>I Birol</strong>. Graph-based semi-supervised gene mention tagging. 2016. <a href="http://www.aclweb.org/anthology/W16-2904">Proceedings of the 15th Workshop on Biomedical Natural Language Processing …</a></p>
<p class="2016">AS Morrissy, L Garzia, DJH Shih, S Zuyderduyn, X Huang, P Skowron, et. al. Divergent clonal selection dominates medulloblastoma at recurrence. 2016 Jan. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936195/">Nature 529 (7586), 351</a></p>
</div>
<div id="old" class="tabcontent">
<p class="old">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. <a href="https://academic.oup.com/gbe/article/8/1/29/2574158">Genome biology and evolution 8 (1), 29-41</a></p>
<p class="old">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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=H&aulast=Lin&atitle=Identification+and+Characterization+of+New+Microrna+Biomarkers+and+Target+Genes+in+Drug-Insensitive+CD34%2B+CML+Stem/Progenitor+Cells+Using+Global+Comparative+RNA-Seq+Analyses&title=Blood&volume=126&issue=23&date=2015&spage=1567&issn=0006-4971">Blood 126 (23), 1567-1567</a></p>
<p class="old">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. <a href="https://bmcmedgenomics.biomedcentral.com/articles/10.1186/1755-8794-8-S3-S1">BMC medical genomics 8 (3), S1</a></p>
<p class="old">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. <a href="https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0076-3">GigaScience 4 (1), 35</a></p>
<p class="old">D Paulino, RL Warren, BP Vandervalk, A Raymond, SD Jackman, <strong>I Birol</strong>. Sealer: a scalable gap-closing application for finishing draft genomes. 2015 Dec. <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0663-4">BMC bioinformatics 16 (1), 230</a></p>
<p class="old"><strong>I Birol</strong>, J Chu, H Mohamadi, SD Jackman, K Raghavan, BP Vandervalk, et. al. Spaced seed data structures for de novo assembly. 2015 Oct 11. <a href="https://www.hindawi.com/journals/ijg/aa/196591/">International journal of genomics 2015</a></p>
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<p class="old">A Chu, G Robertson, D Brooks, AJ Mungall, <strong>I Birol</strong>, R Coope, Y Ma, et. al. Large-scale profiling of microRNAs for the cancer genome atlas. 2015 Aug 13. <a href="https://academic.oup.com/nar/article/44/1/e3/2499678">Nucleic acids research 44 (1), e3-e3</a></p>
<p class="old">D Bouneffouf, <strong>I Birol</strong>. Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering.. 2015 Jul 25. <a href="http://www.aaai.org/ocs/index.php/IJCAI/IJCAI15/paper/download/10716/10984">IJCAI, 2313-2319</a></p>
<p class="old">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. <a href="http://www.academia.edu/download/39573202/Improved_white_spruce__Picea_glauca__g20151031-20140-1bc35ge.pdf">The Plant Journal 83 (2), 189-212</a></p>
<p class="old"><strong>I Birol</strong>, 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. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130720">PloS one 10 (6), e0130720</a></p>
<p class="old">SD Jackman, J Bohlmann, <strong>I Birol</strong>. UniqTag: Content-derived unique and stable identifiers for gene annotation. 2015 May 28. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128026">PloS one 10 (5), e0128026</a></p>
<p class="old">H Mohamadi, BP Vandervalk, A Raymond, SD Jackman, J Chu, et. al. DIDA: Distributed Indexing Dispatched Alignment. 2015 Apr 29. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126409">PloS one 10 (4), e0126409</a></p>
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<p class="old">ARMA Basher, AS Purdy, <strong>I Birol</strong>. Event Extraction from Biomedical Literature. 2015 Jan 01. <a href="https://www.biorxiv.org/content/biorxiv/early/2015/12/15/034397.full.pdf">bioRxiv, 034397</a></p>
<p class="old">RL Warren, BP Vandervalk, SJM Jones, <strong>I Birol</strong>. LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads. 2015 Jan 01. <a href="https://www.biorxiv.org/content/biorxiv/early/2015/03/20/016519.full.pdf">bioRxiv, 016519</a></p>
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<p class="old">R Amanda, <strong>I Birol</strong>, J Bousquet, PK Ingvarsson, S Jansson, SJM Jones, et. al. Insights into conifer giga-genomes. 2014 Dec 01. <a href="http://www.plantphysiol.org/content/166/4/1724">Plant physiology 166 (4), 1724-1732</a></p>
<p class="old">JS Sena, I Giguère, B Boyle, P Rigault, <strong>I Birol</strong>, 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. <a href="https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-14-95">BMC plant biology 14 (1), 95</a></p>
<p class="old"><strong>I Birol</strong>, H Mohamadi, A Raymond, K Raghavan, J Chu, BP Vandervalk, et. al. Spaced seed data structures. 2014 Nov 02. <a href="https://www.researchgate.net/profile/Hamid_Mohamadi2/publication/288724735_Spaced_seed_data_structures/links/58bef7ccaca272bd2a3ace11/Spaced-seed-data-structures.pdf">Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on …</a></p>
<p class="old">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. <a href="https://www.researchgate.net/profile/Hamid_Mohamadi2/publication/286723441_Konnector_Connecting_paired-end_reads_using_a_bloom_filter_de_Bruijn_graph/links/58bef7744585151c70304962/Konnector-Connecting-paired-end-reads-using-a-bloom-filter-de-Bruijn-graph.pdf">Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on …</a></p>
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<p class="old">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. <a href="https://academic.oup.com/bioinformatics/article/30/23/3402/207237">Bioinformatics 30 (23), 3402-3404</a></p>
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<p class="old"><strong>I Birol</strong>, A Raymond, R Chiu, KM Nip, SD Jackman, M Kreitzman, et. al. Kleat: cleavage site analysis of transcriptomes. 2014. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350765/">Pacific Symposium on Biocomputing Co-Chairs, 347-358</a></p>
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<p class="old">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. <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-373">BMC genomics 14 (1), 373</a></p>
<p class="old">AH Khodabakhshi, AP Fejes, <strong>I Birol</strong>, SJM Jones. Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. 2013 Dec. <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-167">BMC bioinformatics 14 (1), 167</a></p>
<p class="old">KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, <strong>I Birol</strong>, et. al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. 2013 Dec. <a href="https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-2-10">GigaScience 2 (1), 10</a></p>
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<p class="old">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. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071328">PLoS One 8 (8), e71328</a></p>
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<p class="old">A Fentiman, J Parker, L Swanson, K Mungall, <strong>I Birol</strong>, A Karsan. Endothelial-hematopoietic transition: from the dorsal aorta to the dish. 2013 Aug 01. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=A&aulast=Fentiman&atitle=Endothelial-hematopoietic+transition:+from+the+dorsal+aorta+to+the+dish&id=doi:10.1016/j.exphem.2013.05.104&title=Experimental+hematology&volume=41&issue=8&date=2013&spage=S26">Experimental Hematology 41 (8), S26</a></p>
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<p class="old"><strong>I Birol</strong>, 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. <a href="https://academic.oup.com/bioinformatics/article-abstract/29/12/1492/291965">Bioinformatics 29 (12), 1492-1497</a></p>
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<p class="old">D Yorukoglu, F Hach, L Swanson, CC Collins, <strong>I Birol</strong>, SC Sahinalp. Dissect: detection and characterization of novel structural alterations in transcribed sequences. 2012 Jun 09. <a href="https://academic.oup.com/bioinformatics/article/28/12/i179/268298">Bioinformatics 28 (12), i179-i187</a></p>
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<p class="old">SD Jackman, AG Raymond, İ Birol. Scaffolding a genome sequence assembly using ABySS. 2012. <a href="http://sjackman.ca/abyss-scaffold-paper/">No Journal Information</a></p>
<p class="old">PA Dimitriu, JV Gosselink, WM Elliott, MM Moore, S Adams, J Friedman, et. al. A Preliminary Assessment Of Fungi In The Lung Microbiome. 2012. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=PA&aulast=Dimitriu&atitle=A+Preliminary+Assessment+Of+Fungi+In+The+Lung+Microbiome&id=doi:10.1164/ajrccm-conference.2012.185.1_MeetingAbstracts.A4537&title=American+journal+of+respiratory+and+critical+care+medicine&volume=185&date=2012&spage=A4537&issn=1073-449X">Am J Respir Crit Care Med 185, A4537</a></p>
<p class="old">M Krzywinski, <strong>I Birol</strong>, S Jones, M Marra. Getting into visualization of large biological data sets. 2012. <a href="http://web.cse.ohio-state.edu/~machiraju.1/teaching/CSE5544/Visweek2012/biovis/posters/krzywinski.pdf">2nd IEEE Symposium on Biological Data Visualization (BioVis2012), Seattle, WA</a></p>
<p class="old">K Kasaian, A He, N Thiessen, K Mungall, J Qian, R Varhol, Y Zhao, <strong>I Birol</strong>, et. al. Profiling thyroid cancers on the molecular level. 2012. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=K&aulast=Kasaian&atitle=Profiling+thyroid+cancers+on+the+molecular+level&title=Genome&volume=55&date=2012&spage=705&issn=0831-2796">GENOME 55, 705-705</a></p>
<p class="old">S Yip, YS Butterfield, O Morozova, S Chittaranjan, MD Blough, J An, <strong>I Birol</strong>, et. al. Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. 2012 Jan 01. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246739/">The Journal of pathology 226 (1), 7-16</a></p>
<p class="old">M Krzywinski, <strong>I Birol</strong>, SJM Jones, MA Marra. Hive plots—rational approach to visualizing networks. 2011 Dec 09. <a href="https://academic.oup.com/bib/article/13/5/627/412507">Briefings in bioinformatics 13 (5), 627-644</a></p>
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<p class="old">QWT Chan, RS Cornman, <strong>I Birol</strong>, 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. <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-450">Bmc Genomics 12 (1), 450</a></p>
<p class="old">Y Chu, P Gao, P Zhao, Y He, N Liao, S Jackman, Y Zhao, <strong>I Birol</strong>, X Duan, et. al. Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601. 2011 Nov 01. <a href="http://jb.asm.org/content/193/21/6098.long">Journal of bacteriology 193 (21), 6098-6099</a></p>
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<p class="old">O Morozova, <strong>I Birol</strong>, 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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=O&aulast=Morozova&atitle=Whole+genome+and+transcriptome+sequencing+defines+the+spectrum+of+somatic+changes+in+high-risk+neuroblastoma&id=doi:10.1158/1538-7445.AM2011-926&title=Cancer+research+(Chicago,+Ill.)&volume=71&issue=8+Supplement&date=2011&spage=926&issn=0008-5472">Cancer Research 71 (8 Supplement), 926-926</a></p>
<p class="old">AP Fejes, AH Khodabakhshi, <strong>I Birol</strong>, SJM Jones. Human variation database: an open-source database template for genomic discovery. 2011 Mar 02. <a href="https://academic.oup.com/bioinformatics/article/27/8/1155/228730">Bioinformatics 27 (8), 1155-1156</a></p>
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<p class="old">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. <a href="http://search.ebscohost.com/login.aspx?direct=true&profile=ehost&scope=site&authtype=crawler&jrnl=15487091&AN=54725616&h=Gfdd7tEe1NU4YoIYwDkx%2FbCIDkU05NgaX8Z2rykh9XICn9LqhtDWi2921O%2Bhsjugj2uLbUe%2FtQPObHE4%2Bk9hyA%3D%3D&crl=f">Nature methods 7 (11), 909</a></p>
<p class="old">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. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-8-r82">Genome biology 11 (8), R82</a></p>
<p class="old">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. <a href="http://genome.cshlp.org/content/20/8/1037.full">Genome research 20 (8), 1037-1051</a></p>
<p class="old">F Hach, F Hormozdiari, C Alkan, F Hormozdiari, <strong>I Birol</strong>, EE Eichler, et. al. mrsFAST: a cache-oblivious algorithm for short-read mapping. 2010 Aug. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115707/">Nature methods 7 (8), 576</a></p>
<p class="old">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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=SJM&aulast=Jones&atitle=Genomic+analysis+of+a+rare+human+tumor&id=doi:10.1186/1471-2105-11-S4-O3&title=BMC+bioinformatics&volume=11&issue=S4&date=2010&spage=O3&issn=1471-2105">BMC bioinformatics 11 (S4), O3</a></p>
<p class="old">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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=RTF&aulast=Wong&atitle=LaneRuler:+automated+lane+tracking+for+dna+electrophoresis+gel+images&id=doi:10.1109/TASE.2009.2035437&title=IEEE+transactions+on+automation+science+and+engineering&volume=7&issue=3&date=2010&spage=706&issn=1545-5955">IEEE transactions on automation science and engineering 7 (3), 706-708</a></p>
<p class="old">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. <a href="http://genome.cshlp.org/content/20/6/791.full">Genome research 20 (6), 791-803</a></p>
<p class="old">I Hajirasouliha, F Hormozdiari, C Alkan, JM Kidd, <strong>I Birol</strong>, EE Eichler, et. al. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. 2010 Apr 12. <a href="https://academic.oup.com/bioinformatics/article/26/10/1277/194099">Bioinformatics 26 (10), 1277-1283</a></p>
<p class="old">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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/pmc2850970/">Nature genetics 42 (2), 181</a></p>
<p class="old"><strong>I Birol</strong>, M Champ, J Cant. GENOME INFORMATICS. 2010. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/pmc2850970/">No Journal Information</a></p>
<p class="old">RF Murphy, A Bateman, UK Hinxton, T Lengauer, Y Moreau, D Durand, et. al. ISMB 2010 ORGANIZATION. 2010. <a href="https://pdfs.semanticscholar.org/18db/be41ce4b67b5c562f195e6567a3d298eacb5.pdf">No Journal Information</a></p>
<p class="old">SD Jackman, İ Birol. Assembling genomes using short-read sequencing technology. 2010 Jan. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-1-202">Genome biology 11 (1), 202</a></p>
<p class="old">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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=R&aulast=Morin&atitle=Tyrosine+641+of+the+EZH2+Oncogene+Is+Frequently+Mutated+in+Follicular+and+Diffuse+Large+B-Cell+Lymphomas+of+Germinal+Center+Origin.&title=Blood&volume=114&issue=22&date=2009&spage=139&issn=0006-4971">Blood 114 (22), 139-139</a></p>
<p class="old">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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=AJ&aulast=Mungall&atitle=Base-Pair+Resolution+of+Somatic+and+Germline-Derived+Genome+Rearrangement+Breakpoints+in+Follicular+Lymphoma.&title=Blood&volume=114&issue=22&date=2009&spage=439&issn=0006-4971">Blood 114 (22), 439-439</a></p>
<p class="old">CB Nielsen, SD Jackman, <strong>I Birol</strong>, SJM Jones. ABySS-Explorer: visualizing genome sequence assemblies. 2009 Nov. <a href="https://www.researchgate.net/profile/Shaun_Jackman/publication/38015408_ABySS-Explorer_Visualizing_Genome_Sequence_Assemblies/links/0046351be924889453000000.pdf">IEEE transactions on visualization and computer graphics 15 (6), 881-888</a></p>
<p class="old">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. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-9-r94">Genome biology 10 (9), R94</a></p>
<p class="old">M Krzywinski, J Schein, <strong>I Birol</strong>, J Connors, R Gascoyne, D Horsman, et. al. Circos: an information aesthetic for comparative genomics. 2009 Sep 01. <a href="http://genome.cshlp.org/content/19/9/1639.long">Genome research 19 (9), 1639-1645</a></p>
<p class="old"><strong>I Birol</strong>, SD Jackman, CB Nielsen, JQ Qian, R Varhol, G Stazyk, RD Morin, et. al. De novo transcriptome assembly with ABySS. 2009 Jun 15. <a href="https://academic.oup.com/bioinformatics/article/25/21/2872/2111463">Bioinformatics 25 (21), 2872-2877</a></p>
<p class="old">JT Simpson, K Wong, SD Jackman, JE Schein, SJM Jones, <strong>I Birol</strong>. ABySS: a parallel assembler for short read sequence data. 2009 Jun 01. <a href="http://genome.cshlp.org/content/19/6/1117.full.htmlref-list-1This">Genome research 19 (6), 1117-1123</a></p>
<p class="old">CB Nielsen, SD Jackman, <strong>I Birol</strong>, SJM Jones. Papers of the IEEE Information Visualization Conference 2009-Session 1: Bioinformatics Visualization-Best Paper Award: ABySS-Explorer: Visualizing Genome Seq.... 2009. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=CB&aulast=Nielsen&atitle=Papers+of+the+IEEE+Information+Visualization+Conference+2009-Session+1:+Bioinformatics+Visualization-Best+Paper+Award:+ABySS-Explorer:+Visualizing+Genome+Sequence+Assemblies&title=IEEE+transactions+on+visualization+and+computer+graphics&volume=15&issue=6&date=2009&spage=881&issn=1077-2626">IEEE Transactions on Visualization and Computer Graphics 15 (6), 881</a></p>
<p class="old">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. <a href="http://genome.cshlp.org/content/18/12/1906.full">Genome research 18 (12), 1906-1917</a></p>
<p class="old">I Hajirasouliha, F Hormozdiari, SC Sahinalp, <strong>I Birol</strong>. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. 2008 Jul 01. <a href="https://academic.oup.com/bioinformatics/article/24/13/i32/234056">Bioinformatics 24 (13), i32-i40</a></p>
<p class="old">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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=J&aulast=Schein&atitle=Structural+rearrangement+discovery+in+follicular+lymphoma+genomes&title=Annals+of+oncology&volume=19&date=2008&spage=178&issn=0923-7534">ANNALS OF ONCOLOGY 19, 178-179</a></p>
<p class="old">A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, <strong>I Birol</strong>, 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. <a href="http://link.aps.org/pdf/10.1103/PhysRevSTAB.11.041001">Physical Review Special Topics-Accelerators and Beams 11 (4), 041001</a></p>
<p class="old">M Marra, J Schein, M Krzywinski, <strong>I Birol</strong>, R Chiu, M Field, K Wong, et. al. High-resolution genome rearrangement discovery in follicular lymphoma. 2007 Mar 01. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=M&aulast=Marra&atitle=High-resolution+genome+rearrangement+discovery+in+follicular+lymphoma&title=Acta+cytologica&volume=51&issue=2&date=2007&spage=266&issn=0001-5547">ACTA CYTOLOGICA 51 (2), 266-267</a></p>
<p class="old">MA Marra, M Krzywinski, R Chiu, M Field, <strong>I Birol</strong>, 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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=MA&aulast=Marra&atitle=Towards+the+Human+Cancer+Genome+Project:+A+Sequence-Ready+Physical+Map+of+a+Follicular+Lymphoma+Genome.&title=Blood&volume=106&issue=11&date=2005&spage=605&issn=0006-4971">Blood 106 (11), 605-605</a></p>
<p class="old">A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, <strong>I Birol</strong>, P Cenci, et. al. Results on the coherent interaction of high energy electrons and photons in oriented single crystals. 2005 May 01. <a href="https://www.sciencedirect.com/science/article/pii/S0168583X05001692">Nuclear Instruments and Methods in Physics Research Section B: Beam …</a></p>
<p class="old">E Tatara, İ Birol, F Teymour, A Çınar. Agent-based control of autocatalytic replicators in networks of reactors. 2005 Mar 15. <a href="https://www.sciencedirect.com/science/article/pii/S0098135404002844">Computers & Chemical Engineering 29 (4), 807-815</a></p>
<p class="old">L Wang, <strong>I Birol</strong>, V Hatzimanikatis. Metabolic control analysis under uncertainty: framework development and case studies. 2004 Dec 01. <a href="https://www.sciencedirect.com/science/article/pii/S0006349504738436">Biophysical journal 87 (6), 3750-3763</a></p>
<p class="old">G Unel, <strong>I Birol</strong>, S Ballestrero. The trigger and DAQ systems of the Na59 experiment. 2004 Aug. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=G&aulast=Unel&atitle=The+trigger+and+DAQ+systems+of+the+Na59+experiment&id=doi:10.1109/TNS.2004.832303&title=IEEE+transactions+on+nuclear+science&volume=51&issue=4&date=2004&spage=1482&issn=0018-9499">IEEE Transactions on Nuclear Science 51 (4), 1482-1487</a></p>
<p class="old">G Unel, <strong>I Birol</strong>, S Eichblatt. Software aspects of the Na59 experiment. 2004 Aug. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=G&aulast=Unel&atitle=Software+aspects+of+the+Na59+experiment&id=doi:10.1109/TNS.2004.832297&title=IEEE+transactions+on+nuclear+science&volume=51&issue=4&date=2004&spage=1449&issn=0018-9499">IEEE Transactions on Nuclear Science 51 (4), 1449-1455</a></p>
<p class="old">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. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=G&aulast=Unel&atitle=Software+aspects+of+the+Na59+experiment&id=doi:10.1109/TNS.2004.832297&title=IEEE+transactions+on+nuclear+science&volume=51&issue=4&date=2004&spage=1449&issn=0018-9499">rXiv preprint hep-ex/0406026</a></p>
<p class="old">G Ünel, Na59 Collaboration. Measuring the linear polarization of γs in 20–170 GeV range. 2003 Jun 30. <a href="https://arxiv.org/pdf/hep-ex/0212001$$yFulltext">Nuclear Physics A 721, C1071-C1074</a></p>
<p class="old">A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, <strong>I Birol</strong>, P Cenci, et. al. Linear to Circular Polarisation Conversion using Birefringent Properties of Aligned Crystals for Multi-GeV Photons. 2003 Jun 18. <a href="https://arxiv.org/pdf/hep-ex/0306041">rXiv preprint hep-ex/0306041</a></p>
<p class="old">A Apyan, RO Avakian, B Badelek, S Ballestrero, C Biino, <strong>I Birol</strong>, P Cenci, et. al. Coherent pair production by photons in the 20-170 GeV energy range incident on crystals and birefringence. 2003 Jun 11. <a href="https://arxiv.org/pdf/hep-ex/0306028">rXiv preprint hep-ex/0306028</a></p>
<p class="old">NZ Perdahçı, A Hacınlıyan. Normal forms and nonlocal chaotic behavior in Sprott systems. 2003 Jun 01. <a href="https://www.sciencedirect.com/science/article/pii/S0020722502003257">International journal of engineering science 41 (10), 1085-1108</a></p>
<p class="old">V Hatzimanikatis, <strong>I Birol</strong>, J Shi, L Wang. Quantification and characterization of uncertainty in metabolic engineering. 2003. <a href="https://www.sciencedirect.com/science/article/pii/S0020722502003257">Abstracts of Papers, 225th ACS National Meeting, New Orleans, LA, United …</a></p>
<p class="old">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. <a href="https://www.sciencedirect.com/science/article/pii/S0370269398000811">Physics Letters B 424 (1), 202-212</a></p>
<p class="old"><strong>I Birol</strong>, A Hacinliyan, NZ Perdahçi. Simulating a dynamical system in the presence of a 1/f noise. 1998 Feb 01. <a href="https://www.sciencedirect.com/science/article/pii/S0020722597000670">International journal of engineering science 36 (3), 265-271</a></p>
<p class="old">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. <a href="http://cds.cern.ch/record/324550/files/ppe-97-033.pdf">Nuclear Instruments and Methods in Physics Research Section A: Accelerators …</a></p>
<p class="old">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. <a href="http://cds.cern.ch/record/324550/files/ppe-97-033.pdf">Nuclear Instruments and Methods in Physics Research Section A: Accelerators …</a></p>
<p class="old">E Eskut, A Kayis, G Onengüt, R van Dantzig, M de Jong, J Konijn, et. al. A Search for. 1997 Nov 28. <a href="http://cds.cern.ch/record/324550/files/ppe-97-033.pdf">No Journal Information</a></p>
<p class="old">İ Birol, A Hacinliyan. Signs and approximate magnitudes of Lyapunov exponents in continuous time dynamical systems. 1997 Sep. <a href="http://aip.scitation.org/doi/pdf/10.1063/1.532109">Journal of Mathematical Physics 38 (9), 4594-4605</a></p>
<p class="old">İ Birol, A Hacinliyan. Determining Zero Lyapunov Exponents in Continuous Time Dynamical Systems. 1997 Jan 10. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=%C4%B0&aulast=Birol&atitle=Determining+Zero+Lyapunov+Exponents+in+Continuous+Time+Dynamical+Systems&id=doi:10.1142/S0217751X97000165&title=International+journal+of+modern+physics.+B,+Condensed+matter+physics,+statistical+physics,+applied+physics&volume=12&issue=01&date=1997&spage=131">International Journal of Modern Physics A 12 (01), 131-135</a></p>
<p class="old">İ Birol, A Hacinliyan. Some Algebraic Properties of Continuous Time Dynamical Systems. 1997 Jan 10. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=%C4%B0&aulast=Birol&atitle=Some+Algebraic+Properties+of+Continuous+Time+Dynamical+Systems&id=doi:10.1142/S0217751X97000177&title=International+journal+of+modern+physics.+B,+Condensed+matter+physics,+statistical+physics,+applied+physics&volume=12&issue=01&date=1997&spage=137">International Journal of Modern Physics A 12 (01), 137-142</a></p>
<p class="old">İ BİROL, A Hacinliyan. Choice of Time Step in the Simulation of Continuous Time Dynamical Systems. 1997 Jan 01. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=%C4%B0&aulast=Birol&atitle=Some+Algebraic+Properties+of+Continuous+Time+Dynamical+Systems&id=doi:10.1142/S0217751X97000177&title=International+journal+of+modern+physics.+B,+Condensed+matter+physics,+statistical+physics,+applied+physics&volume=12&issue=01&date=1997&spage=137">Turkish Journal of Physics 21 (1), 147-147</a></p>
<p class="old">İ BİROL, A Hacinliyan. Algebraic Approach to the Calculation of Lyapunov Exponents. 1997 Jan 01. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=%C4%B0&aulast=Birol&atitle=Some+Algebraic+Properties+of+Continuous+Time+Dynamical+Systems&id=doi:10.1142/S0217751X97000177&title=International+journal+of+modern+physics.+B,+Condensed+matter+physics,+statistical+physics,+applied+physics&volume=12&issue=01&date=1997&spage=137">Turkish Journal of Physics 21 (1), 31-42</a></p>
<p class="old">S Alam, B Athar, AH Mahmood, S Ovunc, H Severini, S Timm, F Wappler, et. al. ATLAS. 1997. <a href="https://hal.archives-ouvertes.fr/tel-00011376/file/soutenance4.pdf">Experiments at CERN in 1997, 338-351</a></p>
<p class="old">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. <a href="http://cds.cern.ch/record/319824/files/ppe-96-196.pdf">No Journal Information</a></p>
<p class="old">R van Dantzig, J Konijn, RGC Oldeman, C van der Poel, JWE Uiterwijk, et. al. THE CHORUS NEUTRINO OSCILLATION SEARCH EXPERIMENT. 1996 Dec 13. <a href="http://cds.cern.ch/record/319824/files/ppe-96-196.pdf">No Journal Information</a></p>
<p class="old">A Airapetian, FI Olness, V Dodonov, L Micu, D Axen, V Vinogradov, F Bosi, et. al. ATLAS calorimeter performance Technical Design Report. 1996. <a href="http://inspirehep.net/record/432293/">No Journal Information</a></p>
<p class="old">J Konijn, RGC Oldeman, C Van der Poel, JWE Uiterwijk, E Eskut, et. al. The CHORUS experiment. 1996. <a href="http://gw2jh3xr2c.scholar.serialssolutions.com/?sid=google&auinit=J&aulast=Konijn&atitle=The+CHORUS+experiment&title=Nuclear+Physics+B&volume=48&issue=1-3&date=1996&spage=183">Nuclear Physics B-Proceedings Supplements 48 (1-3), 183-187</a></p>
<p class="old">A Airapetian, FI Olness, V Dodonov, L Micu, D Axen, V Vinogradov, F Bosi, et. al. ATLAS computing technical proposal. 1996. <a href="http://inspirehep.net/record/432292/">No Journal Information</a></p>
<p class="old">A Airapetian, V Grabsky, H Hakopian, A Vartapetian, F Fares, et. al. ATLAS calorimeter performance. 1996. <a href="http://hal.univ-grenoble-alpes.fr/in2p3-00011367/">No Journal Information</a></p>
<p class="old">İ Birol, A Hacinliyan. Approximately conserved quantity in the Henon-Heiles problem. 1995 Nov 01. <a href="http://link.aps.org/pdf/10.1103/PhysRevE.52.4750">Physical Review E 52 (5), 4750</a></p>
<p class="old">D Macina, D Rondeshagen, C Weinheimer, JL Visschers, R Ferreira, et. al. The CHORUS experiment. 1995. <a href="http://link.aps.org/pdf/10.1103/PhysRevE.52.4750">Nucl. Phys. Proc. Suppl. 48, 183-187</a></p>
<p class="old">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. <a href="http://inspirehep.net/record/386786/">No Journal Information</a></p>
<p class="old">M Krzywinski, K Kasaian, O Morozova, <strong>I Birol</strong>, S Jones, M Marra. mkweb. bcgsc. ca/linnet. . <a href="https://pdfs.semanticscholar.org/1bde/df92665e69edca289c382895418d491f5c67.pdf">No Journal Information</a></p>
<p class="old">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. . <a href="https://pdfs.semanticscholar.org/1bde/df92665e69edca289c382895418d491f5c67.pdf">Experim. CERN, 34-37</a></p>
<p class="old">N Feau, G Taylor, AL Dale, B Dhillon, GJ Bilodeau, <strong>I Birol</strong>, SJM Jones, et. al. Genomics Data. . <a href="https://pdfs.semanticscholar.org/219d/7399353cbcfbbb673a9c69e3a84d7962402a.pdf">No Journal Information</a></p>
<p class="old">A Chu, G Robertson, D Brooks, AJ Mungall, <strong>I Birol</strong>, R Coope, Y Ma, et. al. Supplementary material for Large-‐scale profiling of microRNAs for The Cancer Genome Atlas. . <a href="https://pdfs.semanticscholar.org/219d/7399353cbcfbbb673a9c69e3a84d7962402a.pdf">No Journal Information</a></p>
<p class="old">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.... . <a href="https://pdfs.semanticscholar.org/219d/7399353cbcfbbb673a9c69e3a84d7962402a.pdf">No Journal Information</a></p>
<p class="old">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. . <a href="http://ieeexplore.ieee.org/iel5/8856/5581178/05594799.pdf">No Journal Information</a></p>
<p class="old">JT Simpson, K Wong, SD Jackman, JE Schein, SJM Jones, İ Birol. ABySS: A parallel assembler for short read sequence data–Supplemental Material. . <a href="http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/abyss/GenomeRes_19-1117!2009_ABySS%20A%20parallel%20assembler%20for%20short%20read%20sequence%20data_Supp%20Material.doc">No Journal Information</a></p>
<p class="old">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. . <a href="http://www.biomedsearch.com/nih/De-novo-genome-sequence-assembly/19747388.html"></a></p>
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