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Items: 20

1.

Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies.

O'Brien LL, Guo Q, Bahrami-Samani E, Park JS, Hasso SM, Lee YJ, Fang A, Kim AD, Guo J, Hong TM, Peterson KA, Lozanoff S, Raviram R, Ren B, Fogelgren B, Smith AD, Valouev A, McMahon AP.

PLoS Genet. 2018 Jan 29;14(1):e1007181. doi: 10.1371/journal.pgen.1007181. eCollection 2018 Jan.

2.

Reconstructing genetic history of Siberian and Northeastern European populations.

Wong EH, Khrunin A, Nichols L, Pushkarev D, Khokhrin D, Verbenko D, Evgrafov O, Knowles J, Novembre J, Limborska S, Valouev A.

Genome Res. 2017 Jan;27(1):1-14. doi: 10.1101/gr.202945.115. Epub 2016 Dec 13.

3.

Differential regulation of mouse and human nephron progenitors by the Six family of transcriptional regulators.

O'Brien LL, Guo Q, Lee Y, Tran T, Benazet JD, Whitney PH, Valouev A, McMahon AP.

Development. 2016 Feb 15;143(4):595-608. doi: 10.1242/dev.127175.

4.

Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins.

Peng JC, Valouev A, Liu N, Lin H.

Nat Genet. 2016 Mar;48(3):283-91. doi: 10.1038/ng.3486. Epub 2016 Jan 18.

5.

Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.

Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M.

Dev Cell. 2015 Mar 23;32(6):772-4. doi: 10.1016/j.devcel.2015.03.004.

6.

Copy number variation is a fundamental aspect of the placental genome.

Hannibal RL, Chuong EB, Rivera-Mulia JC, Gilbert DM, Valouev A, Baker JC.

PLoS Genet. 2014 May 1;10(5):e1004290. doi: 10.1371/journal.pgen.1004290. eCollection 2014 May.

7.

Discovery of recurrent structural variants in nasopharyngeal carcinoma.

Valouev A, Weng Z, Sweeney RT, Varma S, Le QT, Kong C, Sidow A, West RB.

Genome Res. 2014 Feb;24(2):300-9. doi: 10.1101/gr.156224.113. Epub 2013 Nov 8.

8.

Next-generation sequencing in hematologic malignancies: what will be the dividends?

Merker JD, Valouev A, Gotlib J.

Ther Adv Hematol. 2012 Dec;3(6):333-9. doi: 10.1177/2040620712458948.

9.

Determinants of nucleosome organization in primary human cells.

Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A.

Nature. 2011 May 22;474(7352):516-20. doi: 10.1038/nature10002.

10.

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates.

Ma Z, Swigut T, Valouev A, Rada-Iglesias A, Wysocka J.

Nat Struct Mol Biol. 2011 Feb;18(2):120-7. doi: 10.1038/nsmb.2000. Epub 2010 Dec 23.

PMID:
21183938
11.

An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo.

Gracey LE, Chen ZY, Maniar JM, Valouev A, Sidow A, Kay MA, Fire AZ.

Epigenetics Chromatin. 2010 Jul 1;3(1):13. doi: 10.1186/1756-8935-3-13.

12.

High-resolution human genome structure by single-molecule analysis.

Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10848-53. doi: 10.1073/pnas.0914638107. Epub 2010 Jun 1.

13.

Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.

Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J.

Cell. 2009 Dec 24;139(7):1290-302. doi: 10.1016/j.cell.2009.12.002.

14.

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.

Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM.

Genome Res. 2009 Jun;19(6):1044-56. doi: 10.1101/gr.088773.108. Epub 2009 Mar 9.

15.

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.

Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.

16.

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM.

Genome Res. 2008 Jul;18(7):1051-63. doi: 10.1101/gr.076463.108. Epub 2008 May 13.

17.

A quantile method for sizing optical maps.

Li H, Valouev A, Schwartz DC, Waterman MS, Li LM.

J Comput Biol. 2007 Apr;14(3):255-66.

PMID:
17563310
18.

An algorithm for assembly of ordered restriction maps from single DNA molecules.

Valouev A, Schwartz DC, Zhou S, Waterman MS.

Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15770-5. Epub 2006 Oct 16.

19.

Alignment of optical maps.

Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, Waterman MS.

J Comput Biol. 2006 Mar;13(2):442-62.

PMID:
16597251
20.

Refinement of optical map assemblies.

Valouev A, Zhang Y, Schwartz DC, Waterman MS.

Bioinformatics. 2006 May 15;22(10):1217-24. Epub 2006 Feb 24.

PMID:
16500933

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