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23 results
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TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. BMC Bioinformatics. 2011 Apr 20;12:108. doi: 10.1186/1471-2105-12-108. BMC Bioinformatics. 2011. PMID: 21507242 Free PMC article.
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. BMC Bioinformatics. 2007 Apr 19;8:130. doi: 10.1186/1471-2105-8-130. BMC Bioinformatics. 2007. PMID: 17445273 Free PMC article.
PARTS: probabilistic alignment for RNA joinT secondary structure prediction.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. Nucleic Acids Res. 2008 Apr;36(7):2406-17. doi: 10.1093/nar/gkn043. Epub 2008 Feb 26. Nucleic Acids Res. 2008. PMID: 18304945 Free PMC article.
Stochastic sampling of the RNA structural alignment space.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. Nucleic Acids Res. 2009 Jul;37(12):4063-75. doi: 10.1093/nar/gkp276. Epub 2009 May 8. Nucleic Acids Res. 2009. PMID: 19429694 Free PMC article.
Architecture of the human regulatory network derived from ENCODE data.
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Gerstein MB, et al. Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245. Nature. 2012. PMID: 22955619 Free PMC article.
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. Habegger L, et al. Bioinformatics. 2012 Sep 1;28(17):2267-9. doi: 10.1093/bioinformatics/bts368. Epub 2012 Jun 28. Bioinformatics. 2012. PMID: 22743228 Free PMC article.
Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Gerstein MB, et al. Among authors: harmanci ao. Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424. Nature. 2014. PMID: 25164755 Free PMC article.
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.
Harmanci A, Rozowsky J, Gerstein M. Harmanci A, et al. Genome Biol. 2014;15(10):474. doi: 10.1186/s13059-014-0474-3. Genome Biol. 2014. PMID: 25292436 Free PMC article.
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.
Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Pervouchine DD, et al. Nat Commun. 2015 Jan 13;6:5903. doi: 10.1038/ncomms6903. Nat Commun. 2015. PMID: 25582907 Free PMC article.
Quantification of private information leakage from phenotype-genotype data: linking attacks.
Harmanci A, Gerstein M. Harmanci A, et al. Nat Methods. 2016 Mar;13(3):251-6. doi: 10.1038/nmeth.3746. Epub 2016 Feb 1. Nat Methods. 2016. PMID: 26828419 Free PMC article.
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