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Items: 14

1.

Deep convolutional neural networks for accurate somatic mutation detection.

Sahraeian SME, Liu R, Lau B, Podesta K, Mohiyuddin M, Lam HYK.

Nat Commun. 2019 Mar 4;10(1):1041. doi: 10.1038/s41467-019-09027-x.

2.

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.

Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK.

Nat Commun. 2017 Jul 5;8(1):59. doi: 10.1038/s41467-017-00050-4.

3.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

4.

SIFTER search: a web server for accurate phylogeny-based protein function prediction.

Sahraeian SM, Luo KR, Brenner SE.

Nucleic Acids Res. 2015 Jul 1;43(W1):W141-7. doi: 10.1093/nar/gkv461. Epub 2015 May 15.

5.

PicXAA: a probabilistic scheme for finding the maximum expected accuracy alignment of multiple biological sequences.

Sahraeian SM, Yoon BJ.

Methods Mol Biol. 2014;1079:203-10. doi: 10.1007/978-1-62703-646-7_13.

PMID:
24170404
6.

SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks.

Sahraeian SM, Yoon BJ.

PLoS One. 2013 Jul 12;8(7):e67995. doi: 10.1371/journal.pone.0067995. Print 2013.

7.

Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome.

Morishige DT, Klein PE, Hilley JL, Sahraeian SM, Sharma A, Mullet JE.

BMC Genomics. 2013 Jul 5;14:448. doi: 10.1186/1471-2164-14-448.

8.

Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor.

Wang YH, Upadhyaya HD, Burrell AM, Sahraeian SM, Klein RR, Klein PE.

G3 (Bethesda). 2013 May 20;3(5):783-93. doi: 10.1534/g3.112.004861.

9.

A network synthesis model for generating protein interaction network families.

Sahraeian SM, Yoon BJ.

PLoS One. 2012;7(8):e41474. doi: 10.1371/journal.pone.0041474. Epub 2012 Aug 13.

10.

RESQUE: network reduction using semi-Markov random walk scores for efficient querying of biological networks.

Sahraeian SM, Yoon BJ.

Bioinformatics. 2012 Aug 15;28(16):2129-36. doi: 10.1093/bioinformatics/bts341. Epub 2012 Jun 23.

PMID:
22730436
11.

Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores.

Qian X, Sahraeian SM, Yoon BJ.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S6. doi: 10.1186/1471-2105-12-S10-S6.

12.

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences.

Sahraeian SM, Yoon BJ.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W8-12. doi: 10.1093/nar/gkr244. Epub 2011 Apr 22.

13.

PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach.

Sahraeian SM, Yoon BJ.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S38. doi: 10.1186/1471-2105-12-S1-S38.

14.

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences.

Sahraeian SM, Yoon BJ.

Nucleic Acids Res. 2010 Aug;38(15):4917-28. doi: 10.1093/nar/gkq255. Epub 2010 Apr 22.

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