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Complete Chloroplast Genome Sequence of an Engelmann Spruce (Picea engelmannii, Genotype Se404-851) from Western Canada.

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.

Microbiol Resour Announc. 2019 Jun 13;8(24). pii: e00382-19. doi: 10.1128/MRA.00382-19.


Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada.

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.

Microbiol Resour Announc. 2019 Jun 6;8(23). pii: e00381-19. doi: 10.1128/MRA.00381-19.


ntEdit: scalable genome sequence polishing.

Warren RL, Coombe L, Mohamadi H, Zhang J, Jaquish B, Isabel N, Jones SJM, Bousquet J, Bohlmann J, Birol I.

Bioinformatics. 2019 May 16. pii: btz400. doi: 10.1093/bioinformatics/btz400. [Epub ahead of print]


Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles.

Helbing CC, Hammond SA, Jackman SH, Houston S, Warren RL, Cameron CE, Birol I.

Sci Rep. 2019 Feb 6;9(1):1529. doi: 10.1038/s41598-018-38442-1.


Tigmint: correcting assembly errors using linked reads from large molecules.

Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol I.

BMC Bioinformatics. 2018 Oct 26;19(1):393. doi: 10.1186/s12859-018-2425-6.


Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

Xue Z, Warren RL, Gibb EA, MacMillan D, Wong J, Chiu R, Hammond SA, Yang C, Nip KM, Ennis CA, Hahn A, Reynolds S, Birol I.

BMC Genomics. 2018 Jul 13;19(1):536. doi: 10.1186/s12864-018-4903-7.


ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.

BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x.


Static length changes of cochlear outer hair cells can tune low-frequency hearing.

Ciganović N, Warren RL, Keçeli B, Jacob S, Fridberger A, Reichenbach T.

PLoS Comput Biol. 2018 Jan 19;14(1):e1005936. doi: 10.1371/journal.pcbi.1005936. eCollection 2018 Jan.


ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Khan H, Mohamadi H, Vandervalk BP, Warren RL, Chu J, Birol I.

Bioinformatics. 2018 May 15;34(10):1697-1704. doi: 10.1093/bioinformatics/btx839.


The Genome of the Beluga Whale (Delphinapterus leucas).

Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Jones SJ, 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.

Genes (Basel). 2017 Dec 11;8(12). pii: E378. doi: 10.3390/genes8120378.


The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).

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, Jones SJM.

Genes (Basel). 2017 Dec 11;8(12). pii: E379. doi: 10.3390/genes8120379.


The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.

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.

Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7.


ARCS: scaffolding genome drafts with linked reads.

Yeo S, Coombe L, Warren RL, Chu J, Birol I.

Bioinformatics. 2018 Mar 1;34(5):725-731. doi: 10.1093/bioinformatics/btx675.


Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease.

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.

Genome Announc. 2017 Sep 14;5(37). pii: e00963-17. doi: 10.1128/genomeA.00963-17.


Kollector: transcript-informed, targeted de novo assembly of gene loci.

Kucuk E, Chu J, Vandervalk BP, Austin Hammond S, Warren RL.

Bioinformatics. 2017 Sep 1;33(17):2789. doi: 10.1093/bioinformatics/btx405. No abstract available.


NanoSim: nanopore sequence read simulator based on statistical characterization.

Yang C, Chu J, Warren RL, Birol I.

Gigascience. 2017 Apr 1;6(4):1-6. doi: 10.1093/gigascience/gix010.


ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.

Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I.

Genome Res. 2017 May;27(5):768-777. doi: 10.1101/gr.214346.116. Epub 2017 Feb 23.


Kollector: transcript-informed, targeted de novo assembly of gene loci.

Kucuk E, Chu J, Vandervalk BP, Hammond SA, Warren RL, Birol I.

Bioinformatics. 2017 Jun 15;33(12):1782-1788. doi: 10.1093/bioinformatics/btx078. Erratum in: Bioinformatics. 2017 Sep 1;33(17 ):2789.


Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art.

Chu J, Mohamadi H, Warren RL, Yang C, Birol I.

Bioinformatics. 2017 Apr 15;33(8):1261-1270. doi: 10.1093/bioinformatics/btw811. Review.


Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJ, Birol I.

PLoS One. 2016 Sep 15;11(9):e0163059. doi: 10.1371/journal.pone.0163059. eCollection 2016.


Minimal basilar membrane motion in low-frequency hearing.

Warren RL, Ramamoorthy S, Ciganović N, Zhang Y, Wilson TM, Petrie T, Wang RK, Jacques SL, Reichenbach T, Nuttall AL, Fridberger A.

Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):E4304-10. doi: 10.1073/pnas.1606317113. Epub 2016 Jul 12.


XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination.

IJspeert H, Rozmus J, Schwarz K, Warren RL, van Zessen D, Holt RA, Pico-Knijnenburg I, Simons E, Jerchel I, Wawer A, Lorenz M, Patıroğlu T, Akar HH, Leite R, Verkaik NS, Stubbs AP, van Gent DC, van Dongen JJ, van der Burg M.

Blood. 2016 Aug 4;128(5):650-9. doi: 10.1182/blood-2016-02-701029. Epub 2016 Jun 8.


Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

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.

Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244.


Spaced Seed Data Structures for De Novo Assembly.

Birol I, Chu J, Mohamadi H, Jackman SD, Raghavan K, Vandervalk BP, Raymond A, Warren RL.

Int J Genomics. 2015;2015:196591. doi: 10.1155/2015/196591. Epub 2015 Oct 11.


Konnector v2.0: pseudo-long reads from paired-end sequencing data.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.

BMC Med Genomics. 2015;8 Suppl 3:S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23.


Complicated and Advanced Atherosclerosis in a Young Woman With Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia: Success and Challenges of BCR/ABL1-Targeted Cancer Therapy.

Herrmann J, Bell MR, Warren RL, Lerman A, Fleming MD, Patnaik M.

Mayo Clin Proc. 2015 Aug;90(8):1167-8. doi: 10.1016/j.mayocp.2015.05.013. No abstract available.


LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.

Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ, Birol I.

Gigascience. 2015 Aug 4;4:35. doi: 10.1186/s13742-015-0076-3. eCollection 2015.


Sealer: a scalable gap-closing application for finishing draft genomes.

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.

BMC Bioinformatics. 2015 Jul 25;16:230. doi: 10.1186/s12859-015-0663-4.


Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJ, MacKay J, Birol I, Bohlmann J.

Plant J. 2015 Jul;83(2):189-212. doi: 10.1111/tpj.12886. Epub 2015 Jun 19.


Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.

Gibb EA, Warren RL, Wilson GW, Brown SD, Robertson GA, Morin GB, Holt RA.

Genome Med. 2015 Mar 5;7(1):22. doi: 10.1186/s13073-015-0142-6. eCollection 2015.


Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity.

Watson CT, Steinberg KM, Graves TA, Warren RL, Malig M, Schein J, Wilson RK, Holt RA, Eichler EE, Breden F.

Genes Immun. 2015 Jan-Feb;16(1):24-34. doi: 10.1038/gene.2014.56. Epub 2014 Oct 23.


Enhancing nutritional environments through access to fruit and vegetables in schools and homes among children and youth: a systematic review.

Ganann R, Fitzpatrick-Lewis D, Ciliska D, Peirson LJ, Warren RL, Fieldhouse P, Delgado-Noguera MF, Tort S, Hams SP, Martinez-Zapata MJ, Wolfenden L.

BMC Res Notes. 2014 Jul 4;7:422. doi: 10.1186/1756-0500-7-422. Review.


Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.

Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, Nelson BH, Holt RA.

Genome Res. 2014 May;24(5):743-50. doi: 10.1101/gr.165985.113. Epub 2014 Apr 29.


Co-occurrence of anaerobic bacteria in colorectal carcinomas.

Warren RL, Freeman DJ, Pleasance S, Watson P, Moore RA, Cochrane K, Allen-Vercoe E, Holt RA.

Microbiome. 2013 May 15;1(1):16. doi: 10.1186/2049-2618-1-16.


Y-balance test: a reliability study involving multiple raters.

Shaffer SW, Teyhen DS, Lorenson CL, Warren RL, Koreerat CM, Straseske CA, Childs JD.

Mil Med. 2013 Nov;178(11):1264-70. doi: 10.7205/MILMED-D-13-00222.


Genome Sequence of Burkholderia pseudomallei NCTC 13392.

Sahl JW, Stone JK, Gelhaus HC, Warren RL, Cruttwell CJ, Funnell SG, Keim P, Tuanyok A.

Genome Announc. 2013 May 23;1(3). pii: e00183-13. doi: 10.1128/genomeA.00183-13.


Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation.

Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, Schein J, Willsey AJ, Joy JB, Scott JK, Graves TA, Wilson RK, Holt RA, Eichler EE, Breden F.

Am J Hum Genet. 2013 Apr 4;92(4):530-46. doi: 10.1016/j.ajhg.2013.03.004. Epub 2013 Mar 28.


Accumulation of CD11b⁺Gr-1⁺ cells in the lung, blood and bone marrow of mice infected with highly pathogenic H5N1 and H1N1 influenza viruses.

Long JP, Kotur MS, Stark GV, Warren RL, Kasoji M, Craft JL, Albrecht RA, García-Sastre A, Katze MG, Waters KM, Vasconcelos D, Sabourin PJ, Bresler HS, Sabourin CL.

Arch Virol. 2013 Jun;158(6):1305-22. doi: 10.1007/s00705-012-1593-3. Epub 2013 Feb 9.


Brain microbial populations in HIV/AIDS: α-proteobacteria predominate independent of host immune status.

Branton WG, Ellestad KK, Maingat F, Wheatley BM, Rud E, Warren RL, Holt RA, Surette MG, Power C.

PLoS One. 2013;8(1):e54673. doi: 10.1371/journal.pone.0054673. Epub 2013 Jan 23.


Derivation of HLA types from shotgun sequence datasets.

Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA.

Genome Med. 2012 Dec 10;4(12):95. doi: 10.1186/gm396. eCollection 2012.


An objective approach for Burkholderia pseudomallei strain selection as challenge material for medical countermeasures efficacy testing.

Van Zandt KE, Tuanyok A, Keim PS, Warren RL, Gelhaus HC.

Front Cell Infect Microbiol. 2012 Sep 26;2:120. doi: 10.3389/fcimb.2012.00120. eCollection 2012. Review.


The pathophysiology of inhalational brucellosis in BALB/c mice.

Henning LN, Gillum KT, Fisher DA, Barnewall RE, Krile RT, Anderson MS, Ryan MJ, Warren RL.

Sci Rep. 2012;2:495. doi: 10.1038/srep00495. Epub 2012 Jul 6.


Pathophysiology of the rhesus macaque model for inhalational brucellosis.

Henning LN, Miller SM, Pak DH, Lindsay A, Fisher DA, Barnewall RE, Briscoe CM, Anderson MS, Warren RL.

Infect Immun. 2012 Jan;80(1):298-310. doi: 10.1128/IAI.05878-11. Epub 2011 Nov 7.


Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma.

Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA.

Genome Res. 2012 Feb;22(2):299-306. doi: 10.1101/gr.126516.111. Epub 2011 Oct 18.


The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue.

Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chénard C, Friedman JM, Suttle CA, Zhao Y, Holt RA.

PLoS One. 2011;6(5):e19838. doi: 10.1371/journal.pone.0019838. Epub 2011 May 13.


Targeted assembly of short sequence reads.

Warren RL, Holt RA.

PLoS One. 2011 May 11;6(5):e19816. doi: 10.1371/journal.pone.0019816.


Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes.

Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA.

Genome Res. 2011 May;21(5):790-7. doi: 10.1101/gr.115428.110. Epub 2011 Feb 24.


Genistein, a general kinase inhibitor, as a potential antiviral for arenaviral hemorrhagic fever as described in the Pirital virus-Syrian golden hamster model.

Vela EM, Knostman KA, Mott JM, Warren RL, Garver JN, Vela LJ, Stammen RL.

Antiviral Res. 2010 Sep;87(3):318-28. doi: 10.1016/j.antiviral.2010.06.007. Epub 2010 Jun 25.


Attenuation of defined Brucella melitensis wboA mutants.

Nikolich MP, Warren RL, Lindler LE, Izadjoo MJ, Hoover DL.

Vaccine. 2010 Oct 1;28 Suppl 5:F12-6. doi: 10.1016/j.vaccine.2010.03.058. Epub 2010 Apr 1.


A census of predicted mutational epitopes suitable for immunologic cancer control.

Warren RL, Holt RA.

Hum Immunol. 2010 Mar;71(3):245-54. doi: 10.1016/j.humimm.2009.12.007. Epub 2010 Jan 9.


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