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Items: 34

1.

A Molecular Signature in Blood Reveals a Role for p53 in Regulating Malaria-Induced Inflammation.

Tran TM, Guha R, Portugal S, Skinner J, Ongoiba A, Bhardwaj J, Jones M, Moebius J, Venepally P, Doumbo S, DeRiso EA, Li S, Vijayan K, Anzick SL, Hart GT, O'Connell EM, Doumbo OK, Kaushansky A, Alter G, Felgner PL, Lorenzi H, Kayentao K, Traore B, Kirkness EF, Crompton PD.

Immunity. 2019 Oct 15;51(4):750-765.e10. doi: 10.1016/j.immuni.2019.08.009. Epub 2019 Sep 3.

PMID:
31492649
2.

Whole-blood transcriptomic signatures induced during immunization by chloroquine prophylaxis and Plasmodium falciparum sporozoites.

Tran TM, Bijker EM, Haks MC, Ottenhoff THM, Visser L, Schats R, Venepally P, Lorenzi H, Crompton PD, Sauerwein RW.

Sci Rep. 2019 Jun 10;9(1):8386. doi: 10.1038/s41598-019-44924-7.

3.

Rapid Replacement of Acinetobacter baumannii Strains Accompanied by Changes in Lipooligosaccharide Loci and Resistance Gene Repertoire.

Adams MD, Wright MS, Karichu JK, Venepally P, Fouts DE, Chan AP, Richter SS, Jacobs MR, Bonomo RA.

MBio. 2019 Mar 26;10(2). pii: e00356-19. doi: 10.1128/mBio.00356-19.

4.

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type.

Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Close JL, Diez-Fuertes F, Ding SL, Faragó N, Kocsis ÁK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G.

Nat Neurosci. 2018 Sep;21(9):1185-1195. doi: 10.1038/s41593-018-0205-2. Epub 2018 Aug 27.

5.

Draft Genome Sequence and Annotation of the Apicomplexan Parasite Besnoitia besnoiti.

Schares G, Venepally P, Lorenzi HA.

Genome Announc. 2017 Nov 16;5(46). pii: e01200-17. doi: 10.1128/genomeA.01200-17.

6.

Corrected Genome Sequence of Acinetobacter baumannii Strain AB0057, an Antibiotic-Resistant Isolate from Lineage 1 of Global Clone 1.

Hamidian M, Venepally P, Hall RM, Adams MD.

Genome Announc. 2017 Aug 31;5(35). pii: e00836-17. doi: 10.1128/genomeA.00836-17.

7.

Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH.

Nat Commun. 2017 Mar 17;8:15047. doi: 10.1038/ncomms15047. No abstract available.

8.

LOCUST: a custom sequence locus typer for classifying microbial isolates.

Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G.

Bioinformatics. 2017 Jun 1;33(11):1725-1726. doi: 10.1093/bioinformatics/btx045.

9.

PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX.

Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken RS, Lein ED, Schork N, Scheuermann RH.

Pac Symp Biocomput. 2017;22:564-575. doi: 10.1142/9789813207813_0052.

10.

Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria.

Tran TM, Jones MB, Ongoiba A, Bijker EM, Schats R, Venepally P, Skinner J, Doumbo S, Quinten E, Visser LG, Whalen E, Presnell S, O'Connell EM, Kayentao K, Doumbo OK, Chaussabel D, Lorenzi H, Nutman TB, Ottenhoff TH, Haks MC, Traore B, Kirkness EF, Sauerwein RW, Crompton PD.

Sci Rep. 2016 Aug 10;6:31291. doi: 10.1038/srep31291.

11.

Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH.

Nat Commun. 2016 Jun 14;7:12020. doi: 10.1038/ncomms12020. No abstract available.

12.

Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJE, Parylak SL, Paquola ACM, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH.

Nat Commun. 2016 Apr 19;7:11022. doi: 10.1038/ncomms11022. Erratum in: Nat Commun. 2016 Jun 14;7:12020. Nat Commun. 2017 Mar 17;8:15047.

13.

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons.

Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS.

Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18.

14.

Genetic Analysis Using an Isogenic Mating Pair of Aspergillus fumigatus Identifies Azole Resistance Genes and Lack of MAT Locus's Role in Virulence.

Losada L, Sugui JA, Eckhaus MA, Chang YC, Mounaud S, Figat A, Joardar V, Pakala SB, Pakala S, Venepally P, Fedorova N, Nierman WC, Kwon-Chung KJ.

PLoS Pathog. 2015 Apr 24;11(4):e1004834. doi: 10.1371/journal.ppat.1004834. eCollection 2015 Apr.

15.

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA.

BMC Bioinformatics. 2014 Nov 19;15:357. doi: 10.1186/s12859-014-0357-3.

16.

PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.

Tovchigrechko A, Venepally P, Payne SH.

Bioinformatics. 2014 May 15;30(10):1469-70. doi: 10.1093/bioinformatics/btu051. Epub 2014 Jan 27.

17.

RNA-sequencing from single nuclei.

Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, O'Shaughnessy AL, Lambert GM, Araúzo-Bravo MJ, Lee J, Fishman M, Robbins GE, Lin X, Venepally P, Badger JH, Galbraith DW, Gage FH, Lasken RS.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19802-7. doi: 10.1073/pnas.1319700110. Epub 2013 Nov 18.

18.

Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.

Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA 3rd.

Nucleic Acids Res. 2012 Nov 1;40(20):10375-83. doi: 10.1093/nar/gks823. Epub 2012 Aug 31.

19.

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium.

Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN.

BMC Genomics. 2011 Aug 25;12:433. doi: 10.1186/1471-2164-12-433.

20.

Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains.

Pandya GA, McEllistrem MC, Venepally P, Holmes MH, Jarrahi B, Sanka R, Liu J, Karamycheva SA, Bai Y, Fleischmann RD, Peterson SN.

PLoS One. 2011 Jan 10;6(1):e15950. doi: 10.1371/journal.pone.0015950.

21.

A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform.

Pandya GA, Holmes MH, Sunkara S, Sparks A, Bai Y, Verratti K, Saeed K, Venepally P, Jarrahi B, Fleischmann RD, Peterson SN.

Nucleic Acids Res. 2007;35(21):e148. Epub 2007 Nov 15.

22.

Molecular dissection of DNA sequences and factors involved in slow muscle-specific transcription.

Calvo S, Vullhorst D, Venepally P, Cheng J, Karavanova I, Buonanno A.

Mol Cell Biol. 2001 Dec;21(24):8490-503.

23.

Fiber-type-specific transcription of the troponin I slow gene is regulated by multiple elements.

Calvo S, Venepally P, Cheng J, Buonanno A.

Mol Cell Biol. 1999 Jan;19(1):515-25.

24.

Activity-dependent regulation of muscle genes: repressive and stimulatory effects of innervation.

Buonanno A, Cheng J, Venepally P, Weis J, Calvo S.

Acta Physiol Scand. 1998 Jul;163(3):S17-26. Review. No abstract available.

PMID:
9715746
25.

Conformationally defined retinoic acid analogues. 4. Potential new agents for acute promyelocytic and juvenile myelomonocytic leukemias.

Muccio DD, Brouillette WJ, Breitman TR, Taimi M, Emanuel PD, Zhang X, Chen G, Sani BP, Venepally P, Reddy L, Alam M, Simpson-Herren L, Hill DL.

J Med Chem. 1998 May 7;41(10):1679-87.

PMID:
9572893
26.

Analysis of homo- and heterodimerization of retinoid receptors in solution.

Venepally P, Reddy LG, Sani BP.

Arch Biochem Biophys. 1997 Jul 15;343(2):234-42.

PMID:
9224735
27.

Didehydroretinoic acid: retinoid receptor-mediated transcriptional activation and binding properties.

Sani BP, Venepally PR, Levin AA.

Biochem Pharmacol. 1997 Apr 4;53(7):1049-53.

PMID:
9174119
28.

Characterization of cellular retinoic acid-binding protein I from chick embryo and its ligand binding properties.

Venepally P, Reddy LG, Sani BP.

Arch Biochem Biophys. 1996 Dec 15;336(2):231-9.

PMID:
8954570
29.

Conformationally defined 6-s-trans-retinoic acid analogs. 3. Structure-activity relationships for nuclear receptor binding, transcriptional activity, and cancer chemopreventive activity.

Muccio DD, Brouillette WJ, Alam M, Vaezi MF, Sani BP, Venepally P, Reddy L, Li E, Norris AW, Simpson-Herren L, Hill DL.

J Med Chem. 1996 Sep 13;39(19):3625-35.

PMID:
8809153
30.

Analysis of the effects of CRABP I expression on the RA-induced transcription mediated by retinoid receptors.

Venepally P, Reddy LG, Sani BP.

Biochemistry. 1996 Aug 6;35(31):9974-82.

PMID:
8756459
31.

Biochemical characteristics and differentiating activity of 4-oxo analogs of retinoic acid.

Sani BP, Venepally P, Zhang XK, Hill DL, Shealy YF.

Anticancer Res. 1996 May-Jun;16(3A):1177-81.

PMID:
8702232
33.

Conformationally defined 6-s-trans-retinoic acid analogs. 2. Selective agonists for nuclear receptor binding and transcriptional activity.

Alam M, Zhestkov V, Sani BP, Venepally P, Levin AA, Kazmer S, Li E, Norris AW, Zhang XK, Lee MO, et al.

J Med Chem. 1995 Jun 23;38(13):2302-10.

PMID:
7608895
34.

Transcriptional regulatory elements for basal expression of cytochrome P450IIC genes.

Venepally P, Chen D, Kemper B.

J Biol Chem. 1992 Aug 25;267(24):17333-8.

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