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Items: 19

1.

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism.

Sharifi-Zarchi A, Gerovska D, Adachi K, Totonchi M, Pezeshk H, Taft RJ, Schöler HR, Chitsaz H, Sadeghi M, Baharvand H, Araúzo-Bravo MJ.

BMC Genomics. 2017 Dec 12;18(1):964. doi: 10.1186/s12864-017-4353-7.

2.

Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast.

Al-Husini N, Sharifi A, Mousavi SA, Chitsaz H, Ansari A.

Sci Rep. 2017 Jul 31;7(1):6894. doi: 10.1038/s41598-017-07062-6.

3.

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

Karamzadeh R, Karimi-Jafari MH, Sharifi-Zarchi A, Chitsaz H, Salekdeh GH, Moosavi-Movahedi AA.

Sci Rep. 2017 Jun 16;7(1):3666. doi: 10.1038/s41598-017-03966-5.

4.

SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature.

Bokharaeian B, Diaz A, Taghizadeh N, Chitsaz H, Chavoshinejad R.

J Biomed Semantics. 2017 Apr 7;8(1):14. doi: 10.1186/s13326-017-0116-2.

5.

Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency.

Bokharaeian B, Diaz A, Chitsaz H.

PLoS One. 2016 Oct 3;11(10):e0163480. doi: 10.1371/journal.pone.0163480. eCollection 2016.

6.

Efficient Synergistic Single-Cell Genome Assembly.

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

Front Bioeng Biotechnol. 2016 May 23;4:42. doi: 10.3389/fbioe.2016.00042. eCollection 2016.

7.

Increased robustness of early embryogenesis through collective decision-making by key transcription factors.

Sharifi-Zarchi A, Totonchi M, Khaloughi K, Karamzadeh R, Araúzo-Bravo MJ, Baharvand H, Tusserkani R, Pezeshk H, Chitsaz H, Sadeghi M.

BMC Syst Biol. 2015 Jun 2;9:23. doi: 10.1186/s12918-015-0169-8.

8.

Exact learning of RNA energy parameters from structure.

Chitsaz H, Aminisharifabad M.

J Comput Biol. 2015 Jun;22(6):463-73. doi: 10.1089/cmb.2014.0164. Epub 2015 Mar 10.

PMID:
25756654
9.

HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.

Shariat B, Movahedi NS, Chitsaz H, Boucher C.

BMC Genomics. 2014;15 Suppl 10:S9. doi: 10.1186/1471-2164-15-S10-S9. Epub 2014 Dec 12.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

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