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Items: 40

1.

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations.

Salazar AN, Abeel T.

Bioinformatics. 2018 Sep 1;34(17):i732-i742. doi: 10.1093/bioinformatics/bty614.

2.

SynerClust: a highly scalable, synteny-aware orthologue clustering tool.

Georgescu CH, Manson AL, Griggs AD, Desjardins CA, Pironti A, Wapinski I, Abeel T, Haas BJ, Earl AM.

Microb Genom. 2018 Nov 12. doi: 10.1099/mgen.0.000231. [Epub ahead of print]

3.

Patterns of Conservation and Diversification in the Fungal Polarization Network.

Diepeveen ET, Gehrmann T, Pourquié V, Abeel T, Laan L.

Genome Biol Evol. 2018 Jul 1;10(7):1765-1782. doi: 10.1093/gbe/evy121.

4.

Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs.

Gehrmann T, Pelkmans JF, Ohm RA, Vos AM, Sonnenberg ASM, Baars JJP, Wösten HAB, Reinders MJT, Abeel T.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4429-4434. doi: 10.1073/pnas.1721381115. Epub 2018 Apr 11.

5.

Reply to Lee and Howden.

Manson AL, Abeel T, Galagan J, Sundaramurthi JC, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM.

Clin Infect Dis. 2018 Jan 6;66(1):160-161. doi: 10.1093/cid/cix751. No abstract available.

PMID:
29040415
6.

Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D.

Salazar AN, Gorter de Vries AR, van den Broek M, Wijsman M, de la Torre Cortés P, Brickwedde A, Brouwers N, Daran JG, Abeel T.

FEMS Yeast Res. 2017 Nov 1;17(7). doi: 10.1093/femsyr/fox074.

7.

Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics.

Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM.

Clin Infect Dis. 2017 Jun 1;64(11):1494-1501. doi: 10.1093/cid/cix169.

8.

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.

Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE 3rd, Brand J; TBResist Global Genome Consortium, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM.

Nat Genet. 2017 Mar;49(3):395-402. doi: 10.1038/ng.3767. Epub 2017 Jan 16.

9.

Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus.

Wollenberg KR, Desjardins CA, Zalutskaya A, Slodovnikova V, Oler AJ, Quiñones M, Abeel T, Chapman SB, Tartakovsky M, Gabrielian A, Hoffner S, Skrahin A, Birren BW, Rosenthal A, Skrahina A, Earl AM.

J Clin Microbiol. 2017 Feb;55(2):457-469. doi: 10.1128/JCM.02116-16. Epub 2016 Nov 30.

10.

Schizophyllum commune has an extensive and functional alternative splicing repertoire.

Gehrmann T, Pelkmans JF, Lugones LG, Wösten HA, Abeel T, Reinders MJ.

Sci Rep. 2016 Sep 23;6:33640. doi: 10.1038/srep33640.

11.

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.

Desjardins CA, Cohen KA, Munsamy V, Abeel T, Maharaj K, Walker BJ, Shea TP, Almeida DV, Manson AL, Salazar A, Padayatchi N, O'Donnell MR, Mlisana KP, Wortman J, Birren BW, Grosset J, Earl AM, Pym AS.

Nat Genet. 2016 May;48(5):544-51. doi: 10.1038/ng.3548. Epub 2016 Apr 11.

12.

Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage.

Malinga LA, Abeel T, Desjardins CA, Dlamini TC, Cassell G, Chapman SB, Birren BW, Earl AM, van der Walt M.

Genome Announc. 2016 Mar 3;4(2). pii: e01771-15. doi: 10.1128/genomeA.01771-15.

13.

Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization.

Velayati AA, Abeel T, Shea T, Konstantinovich Zhavnerko G, Birren B, Cassell GH, Earl AM, Hoffner S, Farnia P.

Int J Mycobacteriol. 2016 Mar;5(1):66-73. doi: 10.1016/j.ijmyco.2015.12.001. Epub 2015 Dec 28.

14.

Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction.

Winglee K, Manson McGuire A, Maiga M, Abeel T, Shea T, Desjardins CA, Diarra B, Baya B, Sanogo M, Diallo S, Earl AM, Bishai WR.

PLoS Negl Trop Dis. 2016 Jan 11;10(1):e0004332. doi: 10.1371/journal.pntd.0004332. eCollection 2016 Jan.

15.

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.

Cohen KA, Abeel T, Manson McGuire A, Desjardins CA, Munsamy V, Shea TP, Walker BJ, Bantubani N, Almeida DV, Alvarado L, Chapman SB, Mvelase NR, Duffy EY, Fitzgerald MG, Govender P, Gujja S, Hamilton S, Howarth C, Larimer JD, Maharaj K, Pearson MD, Priest ME, Zeng Q, Padayatchi N, Grosset J, Young SK, Wortman J, Mlisana KP, O'Donnell MR, Birren BW, Bishai WR, Pym AS, Earl AM.

PLoS Med. 2015 Sep 29;12(9):e1001880. doi: 10.1371/journal.pmed.1001880. eCollection 2015 Sep.

16.

Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing.

Williams OM, Abeel T, Casali N, Cohen K, Pym AS, Mungall SB, Desjardins CA, Banerjee A, Drobniewski F, Earl AM, Cooke GS.

Emerg Infect Dis. 2015 Jun;21(6):1082-4. doi: 10.3201/eid2106.141903. No abstract available.

17.

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM.

PLoS One. 2014 Nov 19;9(11):e112963. doi: 10.1371/journal.pone.0112963. eCollection 2014.

18.

Evolution of invasion in a diverse set of Fusobacterium species.

Manson McGuire A, Cochrane K, Griggs AD, Haas BJ, Abeel T, Zeng Q, Nice JB, MacDonald H, Birren BW, Berger BW, Allen-Vercoe E, Earl AM.

MBio. 2014 Nov 4;5(6):e01864. doi: 10.1128/mBio.01864-14.

19.

The upside of failure: how regional student groups learn from their mistakes.

Mishra T, Parra RG, Abeel T.

PLoS Comput Biol. 2014 Aug 7;10(8):e1003768. doi: 10.1371/journal.pcbi.1003768. eCollection 2014 Aug.

20.

Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction.

Gomes AL, Abeel T, Peterson M, Azizi E, Lyubetskaya A, Carvalho L, Galagan J.

Genome Res. 2014 Oct;24(10):1686-97. doi: 10.1101/gr.161711.113. Epub 2014 Jul 14.

21.

Soft skills: an important asset acquired from organizing regional student group activities.

de Ridder J, Meysman P, Oluwagbemi O, Abeel T.

PLoS Comput Biol. 2014 Jul 3;10(7):e1003708. doi: 10.1371/journal.pcbi.1003708. eCollection 2014 Jul.

22.

A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification.

Verkest A, Abeel T, Heyndrickx KS, Van Leene J, Lanz C, Van De Slijke E, De Winne N, Eeckhout D, Persiau G, Van Breusegem F, Inzé D, Vandepoele K, De Jaeger G.

Plant Physiol. 2014 Mar;164(3):1122-33. doi: 10.1104/pp.113.229617. Epub 2014 Jan 22.

23.

ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development.

Vercruyssen L, Verkest A, Gonzalez N, Heyndrickx KS, Eeckhout D, Han SK, Jégu T, Archacki R, Van Leene J, Andriankaja M, De Bodt S, Abeel T, Coppens F, Dhondt S, De Milde L, Vermeersch M, Maleux K, Gevaert K, Jerzmanowski A, Benhamed M, Wagner D, Vandepoele K, De Jaeger G, Inzé D.

Plant Cell. 2014 Jan;26(1):210-29. doi: 10.1105/tpc.113.115907. Epub 2014 Jan 17.

24.

The spirit of competition: to win or not to win.

Szczepinska T, Iwasaki W, Abeel T.

PLoS Comput Biol. 2013;9(12):e1003413. doi: 10.1371/journal.pcbi.1003413. Epub 2013 Dec 26.

25.

Ten simple rules for starting a regional student group.

Shanmugam AK, Macintyre G, Michaut M, Abeel T.

PLoS Comput Biol. 2013;9(11):e1003340. doi: 10.1371/journal.pcbi.1003340. Epub 2013 Nov 21. No abstract available.

26.

The regional student group program of the ISCB student council: stories from the road.

Macintyre G, Michaut M, Abeel T.

PLoS Comput Biol. 2013;9(9):e1003241. doi: 10.1371/journal.pcbi.1003241. Epub 2013 Sep 26.

27.

ISCB computational biology Wikipedia competition.

Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B.

PLoS Comput Biol. 2013;9(9):e1003242. doi: 10.1371/journal.pcbi.1003242. Epub 2013 Sep 19. No abstract available.

28.

The Mycobacterium tuberculosis regulatory network and hypoxia.

Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, Gomes A, Rustad T, Dolganov G, Glotova I, Abeel T, Mahwinney C, Kennedy AD, Allard R, Brabant W, Krueger A, Jaini S, Honda B, Yu WH, Hickey MJ, Zucker J, Garay C, Weiner B, Sisk P, Stolte C, Winkler JK, Van de Peer Y, Iazzetti P, Camacho D, Dreyfuss J, Liu Y, Dorhoi A, Mollenkopf HJ, Drogaris P, Lamontagne J, Zhou Y, Piquenot J, Park ST, Raman S, Kaufmann SH, Mohney RP, Chelsky D, Moody DB, Sherman DR, Schoolnik GK.

Nature. 2013 Jul 11;499(7457):178-83. doi: 10.1038/nature12337. Epub 2013 Jul 3.

29.

ORCAE: online resource for community annotation of eukaryotes.

Sterck L, Billiau K, Abeel T, Rouzé P, Van de Peer Y.

Nat Methods. 2012 Nov;9(11):1041. doi: 10.1038/nmeth.2242. No abstract available.

PMID:
23132114
30.

Semantically linking molecular entities in literature through entity relationships.

Van Landeghem S, Björne J, Abeel T, De Baets B, Salakoski T, Van de Peer Y.

BMC Bioinformatics. 2012 Jun 26;13 Suppl 11:S6. doi: 10.1186/1471-2105-13-S11-S6.

31.

Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

McGuire AM, Weiner B, Park ST, Wapinski I, Raman S, Dolganov G, Peterson M, Riley R, Zucker J, Abeel T, White J, Sisk P, Stolte C, Koehrsen M, Yamamoto RT, Iacobelli-Martinez M, Kidd MJ, Maer AM, Schoolnik GK, Regev A, Galagan J.

BMC Genomics. 2012 Mar 28;13:120. doi: 10.1186/1471-2164-13-120.

32.

GenomeView: a next-generation genome browser.

Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y.

Nucleic Acids Res. 2012 Jan;40(2):e12. doi: 10.1093/nar/gkr995. Epub 2011 Nov 18.

33.

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.

Holder JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J, Zeng Q, Leach AL, Ghiviriga I, Dancel C, Abeel T, Gevers D, Kodira CD, Desany B, Affourtit JP, Birren BW, Sinskey AJ.

PLoS Genet. 2011 Sep;7(9):e1002219. doi: 10.1371/journal.pgen.1002219. Epub 2011 Sep 8.

34.

Discriminative and informative features for biomolecular text mining with ensemble feature selection.

Van Landeghem S, Abeel T, Saeys Y, Van de Peer Y.

Bioinformatics. 2010 Sep 15;26(18):i554-60. doi: 10.1093/bioinformatics/btq381.

35.

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods.

Abeel T, Helleputte T, Van de Peer Y, Dupont P, Saeys Y.

Bioinformatics. 2010 Feb 1;26(3):392-8. doi: 10.1093/bioinformatics/btp630. Epub 2009 Nov 25.

PMID:
19942583
37.

Toward a gold standard for promoter prediction evaluation.

Abeel T, Van de Peer Y, Saeys Y.

Bioinformatics. 2009 Jun 15;25(12):i313-20. doi: 10.1093/bioinformatics/btp191.

38.

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles.

Abeel T, Saeys Y, Rouzé P, Van de Peer Y.

Bioinformatics. 2008 Jul 1;24(13):i24-31. doi: 10.1093/bioinformatics/btn172.

39.

Generic eukaryotic core promoter prediction using structural features of DNA.

Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y.

Genome Res. 2008 Feb;18(2):310-23. Epub 2007 Dec 20.

40.

Translation initiation site prediction on a genomic scale: beauty in simplicity.

Saeys Y, Abeel T, Degroeve S, Van de Peer Y.

Bioinformatics. 2007 Jul 1;23(13):i418-23.

PMID:
17646326

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