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Items: 11

1.

Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia.

Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J, Wang K.

Sci Adv. 2019 Sep 11;5(9):eaau4139. doi: 10.1126/sciadv.aau4139. eCollection 2019 Sep.

2.

Dorsal Amygdala Neurotrophin-3 Decreases Anxious Temperament in Primates.

Fox AS, Souaiaia T, Oler JA, Kovner R, Kim JMH, Nguyen J, French DA, Riedel MK, Fekete EM, Rabska MR, Olsen ME, Brodsky EK, Alexander AL, Block WF, Roseboom PH, Knowles JA, Kalin NH.

Biol Psychiatry. 2019 Dec 15;86(12):881-889. doi: 10.1016/j.biopsych.2019.06.022. Epub 2019 Jul 2.

PMID:
31422797
3.

Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders.

Li J, Zhang W, Yang H, Howrigan DP, Wilkinson B, Souaiaia T, Evgrafov OV, Genovese G, Clementel VA, Tudor JC, Abel T, Knowles JA, Neale BM, Wang K, Sun F, Coba MP.

Nat Neurosci. 2017 Aug;20(8):1150-1161. doi: 10.1038/nn.4594. Epub 2017 Jun 26.

4.

Assessing characteristics of RNA amplification methods for single cell RNA sequencing.

Dueck HR, Ai R, Camarena A, Ding B, Dominguez R, Evgrafov OV, Fan JB, Fisher SA, Herstein JS, Kim TK, Kim JM, Lin MY, Liu R, Mack WJ, McGroty S, Nguyen JD, Salathia N, Shallcross J, Souaiaia T, Spaethling JM, Walker CP, Wang J, Wang K, Wang W, Wildberg A, Zheng L, Chow RH, Eberwine J, Knowles JA, Zhang K, Kim J.

BMC Genomics. 2016 Nov 24;17(1):966.

5.

Non-coding RNAs derived from an alternatively spliced REST transcript (REST-003) regulate breast cancer invasiveness.

Lee NS, Evgrafov OV, Souaiaia T, Bonyad A, Herstein J, Lee JY, Kim J, Ning Y, Sixto M, Weitz AC, Lenz HJ, Wang K, Knowles JA, Press MF, Salvaterra PM, Shung KK, Chow RH.

Sci Rep. 2015 Jun 8;5:11207. doi: 10.1038/srep11207.

6.

Effect of RNA integrity on uniquely mapped reads in RNA-Seq.

Chen EA, Souaiaia T, Herstein JS, Evgrafov OV, Spitsyna VN, Rebolini DF, Knowles JA.

BMC Res Notes. 2014 Oct 23;7:753. doi: 10.1186/1756-0500-7-753.

7.

Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection.

Campo D, Lehmann K, Fjeldsted C, Souaiaia T, Kao J, Nuzhdin SV.

Mol Ecol. 2013 Oct;22(20):5084-97. doi: 10.1111/mec.12468. Epub 2013 Sep 19.

8.

FadE: whole genome methylation analysis for multiple sequencing platforms.

Souaiaia T, Zhang Z, Chen T.

Nucleic Acids Res. 2013 Jan 7;41(1):e14. doi: 10.1093/nar/gks830. Epub 2012 Sep 10.

9.

RseqFlow: workflows for RNA-Seq data analysis.

Wang Y, Mehta G, Mayani R, Lu J, Souaiaia T, Chen Y, Clark A, Yoon HJ, Wan L, Evgrafov OV, Knowles JA, Deelman E, Chen T.

Bioinformatics. 2011 Sep 15;27(18):2598-600. doi: 10.1093/bioinformatics/btr441. Epub 2011 Jul 27.

10.

ComB: SNP calling and mapping analysis for color and nucleotide space platforms.

Souaiaia T, Frazier Z, Chen T.

J Comput Biol. 2011 Jun;18(6):795-807. doi: 10.1089/cmb.2011.0027. Epub 2011 May 12.

11.

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Chen Y, Souaiaia T, Chen T.

Bioinformatics. 2009 Oct 1;25(19):2514-21. doi: 10.1093/bioinformatics/btp486. Epub 2009 Aug 12.

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