Publications

2011

Global landscape of HIV-human protein complexes.

Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ.

Nature. 2011 Dec 21;481(7381):365-70. doi: 10.1038/nature10719.

PMID: 22190034 Free PMC article.

Tumor suppressor protein (p)53, is a regulator of NF-kappaB repression by the glucocorticoid receptor.

Murphy SH, Suzuki K, Downes M, Welch GL, De Jesus P, Miraglia LJ, Orth AP, Chanda SK, Evans RM, Verma IM.

Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):17117-22. doi: 10.1073/pnas.1114420108. Epub 2011 Sep 26.

PMID: 21949408 Free PMC article.

GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.

Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ.

BMC Bioinformatics. 2011 Jul 22;12:298. doi: 10.1186/1471-2105-12-298.

PMID: 21777475 Free PMC article.

HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2.

Ocwieja KE, Brady TL, Ronen K, Huegel A, Roth SL, Schaller T, James LC, Towers GJ, Young JA, Chanda SK, König R, Malani N, Berry CC, Bushman FD.

PLoS Pathog. 2011 Mar;7(3):e1001313. doi: 10.1371/journal.ppat.1001313. Epub 2011 Mar 10.

PMID: 21423673 Free PMC article.

In silico gene prioritization by integrating multiple data sources.

Chen Y, Wang W, Zhou Y, Shields R, Chanda SK, Elston RC, Li J.

PLoS One. 2011;6(6):e21137. doi: 10.1371/journal.pone.0021137. Epub 2011 Jun 24.

PMID: 21731658 Free PMC article.

Identifying HIV-1 host cell factors by genome-scale RNAi screening.

Pache L, König R, Chanda SK.

Methods. 2011 Jan;53(1):3-12. doi: 10.1016/j.ymeth.2010.07.009. Epub 2010 Jul 21.

PMID: 20654720 Review.

2010

A human MAP kinase interactome.

Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T.

Nat Methods. 2010 Oct;7(10):801-5. doi: 10.1038/nmeth.1506.

PMID: 20936779 Free PMC article.

Gene expression and transcription factor profiling reveal inhibition of transcription factor cAMP-response element-binding protein by gamma-herpesvirus replication and transcription activator.

Brown HJ, Peng L, Harada JN, Walker JR, Cole S, Lin SF, Zack JA, Chanda SK, Sun R.

J Biol Chem. 2010 Aug 13;285(33):25139-53. doi: 10.1074/jbc.M110.137737. Epub 2010 Jun 1.

PMID: 20516076 Free PMC article.

Telomere-independent Rap1 is an IKK adaptor and regulates NF-kappaB-dependent gene expression.

Teo H, Ghosh S, Luesch H, Ghosh A, Wong ET, Malik N, Orth A, de Jesus P, Perry AS, Oliver JD, Tran NL, Speiser LJ, Wong M, Saez E, Schultz P, Chanda SK, Verma IM, Tergaonkar V.

Nat Cell Biol. 2010 Aug;12(8):758-67. doi: 10.1038/ncb2080. Epub 2010 Jul 11.

PMID: 20622870

Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns.

Peng T, Bonamy GM, Glory-Afshar E, Rines DR, Chanda SK, Murphy RF.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2944-9. doi: 10.1073/pnas.0912090107. Epub 2010 Feb 1.

PMID: 20133616 Free PMC article.

Human host factors required for influenza virus replication.

König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, García-Sastre A, Young JA, Palese P, Shaw ML, Chanda SK.

Nature. 2010 Feb 11;463(7282):813-7. doi: 10.1038/nature08699.

PMID: 20027183 Free PMC article.

2009

Host cell factors in HIV replication: meta-analysis of genome-wide studies.

Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK.

PLoS Pathog. 2009 May;5(5):e1000437. doi: 10.1371/journal.ppat.1000437. Epub 2009 May 29.

PMID: 19478882 Free PMC article. Review.

A functional screen for regulators of CKDN2A reveals MEOX2 as a transcriptional activator of INK4a.

Irelan JT, Gutierrez Del Arroyo A, Gutierrez A, Peters G, Quon KC, Miraglia L, Chanda SK.

PLoS One. 2009;4(4):e5067. doi: 10.1371/journal.pone.0005067. Epub 2009 Apr 2.

PMID: 19340300 Free PMC article.

2008

Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication.

König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK.

Cell. 2008 Oct 3;135(1):49-60. doi: 10.1016/j.cell.2008.07.032.

PMID: 18854154 Free PMC article.

Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling.

Li W, Bengtson MH, Ulbrich A, Matsuda A, Reddy VA, Orth A, Chanda SK, Batalov S, Joazeiro CA.

PLoS One. 2008 Jan 23;3(1):e1487. doi: 10.1371/journal.pone.0001487.

PMID: 18213395 Free PMC article.

Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells.

Rines DR, Gomez-Ferreria MA, Zhou Y, DeJesus P, Grob S, Batalov S, Labow M, Huesken D, Mickanin C, Hall J, Reinhardt M, Natt F, Lange J, Sharp DJ, Chanda SK, Caldwell JS.

Genome Biol. 2008;9(2):R44. doi: 10.1186/gb-2008-9-2-r44. Epub 2008 Feb 26.

PMID: 18302737 Free PMC article.