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Results: 10

1.

ARYANA: Aligning Reads by Yet Another Approach.

Gholami M, Arbabi A, Sharifi-Zarchi A, Chitsaz H, Sadeghi M.

BMC Bioinformatics. 2014;15 Suppl 9:S12. doi: 10.1186/1471-2105-15-S9-S12. Epub 2014 Sep 10.

PMID:
25252881
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.

Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K.

ISME J. 2014 Apr;8(4):757-67. doi: 10.1038/ismej.2013.187. Epub 2013 Oct 24.

PMID:
24152715
[PubMed - indexed for MEDLINE]
3.

Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.

Taghavi Z, Movahedi NS, Draghici S, Chitsaz H.

Bioinformatics. 2013 Oct 1;29(19):2395-401. doi: 10.1093/bioinformatics/btt420. Epub 2013 Aug 5.

PMID:
23918251
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

PMID:
23870653
[PubMed]
Free PMC Article
5.

An efficient algorithm for upper bound on the partition function of nucleic acids.

Chitsaz H, Forouzmand E, Haffari G.

J Comput Biol. 2013 Jul;20(7):486-94. doi: 10.1089/cmb.2013.0003. Epub 2013 Apr 15.

PMID:
23829650
[PubMed - indexed for MEDLINE]
6.

The RNA Newton polytope and learnability of energy parameters.

Forouzmand E, Chitsaz H.

Bioinformatics. 2013 Jul 1;29(13):i300-7. doi: 10.1093/bioinformatics/btt226.

PMID:
23812998
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.

McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10.

PMID:
23754396
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

SEQuel: improving the accuracy of genome assemblies.

Ronen R, Boucher C, Chitsaz H, Pevzner P.

Bioinformatics. 2012 Jun 15;28(12):i188-96. doi: 10.1093/bioinformatics/bts219.

PMID:
22689760
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.

Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS.

Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966.

PMID:
21926975
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A partition function algorithm for interacting nucleic acid strands.

Chitsaz H, Salari R, Sahinalp SC, Backofen R.

Bioinformatics. 2009 Jun 15;25(12):i365-73. doi: 10.1093/bioinformatics/btp212.

PMID:
19478011
[PubMed - indexed for MEDLINE]
Free PMC Article

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