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Items: 34

1.

Porphyromonas gingivalis in Alzheimer's disease brains: Evidence for disease causation and treatment with small-molecule inhibitors.

Dominy SS, Lynch C, Ermini F, Benedyk M, Marczyk A, Konradi A, Nguyen M, Haditsch U, Raha D, Griffin C, Holsinger LJ, Arastu-Kapur S, Kaba S, Lee A, Ryder MI, Potempa B, Mydel P, Hellvard A, Adamowicz K, Hasturk H, Walker GD, Reynolds EC, Faull RLM, Curtis MA, Dragunow M, Potempa J.

Sci Adv. 2019 Jan 23;5(1):eaau3333. doi: 10.1126/sciadv.aau3333. eCollection 2019 Jan.

2.

The cancer stem cell marker aldehyde dehydrogenase is required to maintain a drug-tolerant tumor cell subpopulation.

Raha D, Wilson TR, Peng J, Peterson D, Yue P, Evangelista M, Wilson C, Merchant M, Settleman J.

Cancer Res. 2014 Jul 1;74(13):3579-90. doi: 10.1158/0008-5472.CAN-13-3456. Epub 2014 May 8.

3.

Central nervous system-immune reconstitution inflammatory syndrome presenting as varicella zoster virus-mediated vasculitis causing stroke.

Teo SY, Raha D, Warren D, Hassan A, Monteiro E.

Int J STD AIDS. 2014 Aug;25(9):683-5. doi: 10.1177/0956462413518501. Epub 2014 Jan 9.

PMID:
24407026
4.

Comparative annotation of functional regions in the human genome using epigenomic data.

Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, Ren B, Wang W.

Nucleic Acids Res. 2013 Apr;41(8):4423-32. doi: 10.1093/nar/gkt143. Epub 2013 Mar 12.

5.

Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.

Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M.

G3 (Bethesda). 2013 Mar;3(3):387-97. doi: 10.1534/g3.112.004812. Epub 2013 Mar 1.

6.

A major epigenetic programming mechanism guided by piRNAs.

Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H.

Dev Cell. 2013 Mar 11;24(5):502-16. doi: 10.1016/j.devcel.2013.01.023. Epub 2013 Feb 21.

7.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

8.

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A.

Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111.

9.

A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells.

Charos AE, Reed BD, Raha D, Szekely AM, Weissman SM, Snyder M.

Genome Res. 2012 Sep;22(9):1668-79. doi: 10.1101/gr.127761.111.

10.

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.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

11.

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y.

Cell. 2012 Jan 20;148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014.

12.

A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster.

Yin H, Sweeney S, Raha D, Snyder M, Lin H.

PLoS Genet. 2011 Dec;7(12):e1002380. doi: 10.1371/journal.pgen.1002380. Epub 2011 Dec 15.

13.

AlleleSeq: analysis of allele-specific expression and binding in a network framework.

Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M.

Mol Syst Biol. 2011 Aug 2;7:522. doi: 10.1038/msb.2011.54.

14.

A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1.

Wontakal SN, Guo X, Will B, Shi M, Raha D, Mahajan MC, Weissman S, Snyder M, Steidl U, Zheng D, Skoultchi AI.

PLoS Genet. 2011 Jun;7(6):e1001392. doi: 10.1371/journal.pgen.1001392. Epub 2011 Jun 9.

15.

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing.

Pérez-Lluch S, Blanco E, Carbonell A, Raha D, Snyder M, Serras F, Corominas M.

Nucleic Acids Res. 2011 Jun;39(11):4628-39. doi: 10.1093/nar/gkq1322. Epub 2011 Feb 9.

16.

ChIP-Seq: a method for global identification of regulatory elements in the genome.

Raha D, Hong M, Snyder M.

Curr Protoc Mol Biol. 2010 Jul;Chapter 21:Unit 21.19.1-14. doi: 10.1002/0471142727.mb2119s91.

PMID:
20583098
17.

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.

Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K.

Nat Struct Mol Biol. 2010 May;17(5):635-40. doi: 10.1038/nsmb.1794. Epub 2010 Apr 25.

18.

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing.

Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M.

Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254-9. doi: 10.1073/pnas.0914114107. Epub 2010 Mar 1.

19.

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.

Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M.

PLoS Genet. 2010 Feb 19;6(2):e1000848. doi: 10.1371/journal.pgen.1000848.

20.

Close association of RNA polymerase II and many transcription factors with Pol III genes.

Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3639-44. doi: 10.1073/pnas.0911315106. Epub 2010 Feb 5.

21.

Evolution of nc-Si network and the control of its growth by He/H2 plasma assistance in SiH4 at PECVD.

Das D, Raha D, Bhattacharya K.

J Nanosci Nanotechnol. 2009 Sep;9(9):5614-21.

PMID:
19928275
22.

Chromatin architecture and transcription factor binding regulate expression of erythrocyte membrane protein genes.

Steiner LA, Maksimova Y, Schulz V, Wong C, Raha D, Mahajan MC, Weissman SM, Gallagher PG.

Mol Cell Biol. 2009 Oct;29(20):5399-412. doi: 10.1128/MCB.00777-09. Epub 2009 Aug 17.

23.

The transcriptional landscape of the yeast genome defined by RNA sequencing.

Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M.

Science. 2008 Jun 6;320(5881):1344-9. doi: 10.1126/science.1158441. Epub 2008 May 1.

24.

IGF-I enhances cortisol secretion from guinea-pig adrenal gland: in vivo and in vitro study.

Raha D, Nehar S, Paswan B, Rebuffat P, Neri G, Naskar R, Kumari K, Raza B, Rao NV, Macchi C, Sen NS, Nussdorfer GG, Ahmad MF.

Int J Mol Med. 2007 Jul;20(1):91-5.

PMID:
17549394
25.

Atrial natriuretic peptide enhances cortisol secretion from guinea-pig adrenal gland: evidence for an indirect paracrine mechanism probably involving the local release of medullary catecholamines.

Raha D, Tortorella C, Neri G, Prasad A, Raza B, Raskar R, Dubey R, Sen NS, Macchi C, Malendowicz LK, Ahmad MF, Nussdorfer GG.

Int J Mol Med. 2006 Apr;17(4):633-6.

PMID:
16525720
26.

Modulation of serum cortisol by substance P in albino rats: evidence of a direct effect on adrenal gland.

Prasad A, Naskar R, Dubey R, Raha D, Ahmed MF.

Indian J Exp Biol. 2006 Feb;44(2):163-4.

PMID:
16480185
27.

Combining RNA interference and kinase inhibitors against cell signalling components involved in cancer.

O'Grady M, Raha D, Hanson BJ, Bunting M, Hanson GT.

BMC Cancer. 2005 Oct 3;5:125.

28.

Posthospital medication discrepancies: prevalence and contributing factors.

Coleman EA, Smith JD, Raha D, Min SJ.

Arch Intern Med. 2005 Sep 12;165(16):1842-7.

PMID:
16157827
29.

Expression profiling using a hexamer-based universal microarray.

Roth ME, Feng L, McConnell KJ, Schaffer PJ, Guerra CE, Affourtit JP, Piper KR, Guccione L, Hariharan J, Ford MJ, Powell SW, Krishnaswamy H, Lane J, Guccione L, Intrieri G, Merkel JS, Perbost C, Valerio A, Zolla B, Graham CD, Hnath J, Michaelson C, Wang R, Ying B, Halling C, Parman CE, Raha D, Orr B, Jedrzkiewicz B, Liao J, Tevelev A, Mattessich MJ, Kranz DM, Lacey M, Kaufman JC, Kim J, Latimer DR, Lizardi PM.

Nat Biotechnol. 2004 Apr;22(4):418-26. Epub 2004 Mar 14.

PMID:
15024387
30.
31.

Requirement for a phospholipase C in odor response: overlap between olfaction and vision in Drosophila.

Riesgo-Escovar J, Raha D, Carlson JR.

Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2864-8.

32.

OS9: a novel olfactory gene of Drosophila expressed in two olfactory organs.

Raha D, Carlson J.

J Neurobiol. 1994 Feb;25(2):169-84.

PMID:
8021646
33.
34.

cDNA cloning of β-tubulin gene and organization of tubulin genes in Vigna radiata (mung bean) genome.

Raha D, Sen K, Biswas BB.

Plant Mol Biol. 1987 Nov;9(6):565-71. doi: 10.1007/BF00020533.

PMID:
24277193

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