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Items: 29

1.

Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network.

Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ.

Cancer Discov. 2018 Nov;8(11):1474-1489. doi: 10.1158/2159-8290.CD-17-1018. Epub 2018 Sep 12.

PMID:
30209081
2.

Theory and Application of Network Biology Toward Precision Medicine.

Demchak B, Kreisberg JF, Fuxman Bass JI.

J Mol Biol. 2018 Sep 14;430(18 Pt A):2873-2874. doi: 10.1016/j.jmb.2018.07.019. Epub 2018 Jul 18. No abstract available.

PMID:
30030027
3.

Visible Machine Learning for Biomedicine.

Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T.

Cell. 2018 Jun 14;173(7):1562-1565. doi: 10.1016/j.cell.2018.05.056.

4.

Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation.

Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T.

Mol Cancer Ther. 2018 Jul;17(7):1585-1594. doi: 10.1158/1535-7163.MCT-17-0937. Epub 2018 Apr 10.

PMID:
29636367
5.

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T.

Nat Genet. 2018 Apr;50(4):613-620. doi: 10.1038/s41588-018-0091-2. Epub 2018 Apr 2.

6.

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes.

Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T.

Cell Syst. 2018 Apr 25;6(4):484-495.e5. doi: 10.1016/j.cels.2018.03.001. Epub 2018 Mar 28.

7.

Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment.

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T.

Genome Biol. 2017 Mar 28;18(1):57. doi: 10.1186/s13059-017-1186-2.

8.

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P.

Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225. Epub 2017 Mar 20.

9.

Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.

Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T.

Cancer Discov. 2017 Apr;7(4):410-423. doi: 10.1158/2159-8290.CD-16-1045. Epub 2017 Feb 10.

10.

Challenges in identifying cancer genes by analysis of exome sequencing data.

Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T.

Nat Commun. 2016 Jul 15;7:12096. doi: 10.1038/ncomms12096.

11.

Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA.

Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T.

Mol Cell. 2016 Apr 21;62(2):157-168. doi: 10.1016/j.molcel.2016.03.019.

12.

Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces.

Engin HB, Kreisberg JF, Carter H.

PLoS One. 2016 Apr 4;11(4):e0152929. doi: 10.1371/journal.pone.0152929. eCollection 2016.

13.

Evidence for a common evolutionary rate in metazoan transcriptional networks.

Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T.

Elife. 2015 Dec 18;4. pii: e11615. doi: 10.7554/eLife.11615.

14.

Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types.

Gross AM, Kreisberg JF, Ideker T.

PLoS One. 2015 Nov 10;10(11):e0142618. doi: 10.1371/journal.pone.0142618. eCollection 2015.

15.

Establishment of a novel whole animal HTS technology platform for melioidosis drug discovery.

Lakshmanan U, Yap A, Fulwood J, Yichun L, Hoon SS, Lim J, Ting A, Sem XH, Kreisberg JF, Tan P, Tan G, Flotow H.

Comb Chem High Throughput Screen. 2014;17(9):790-803.

PMID:
25329838
16.

The condition-dependent transcriptional landscape of Burkholderia pseudomallei.

Ooi WF, Ong C, Nandi T, Kreisberg JF, Chua HH, Sun G, Chen Y, Mueller C, Conejero L, Eshaghi M, Ang RM, Liu J, Sobral BW, Korbsrisate S, Gan YH, Titball RW, Bancroft GJ, Valade E, Tan P.

PLoS Genet. 2013;9(9):e1003795. doi: 10.1371/journal.pgen.1003795. Epub 2013 Sep 12.

17.

Growth inhibition of pathogenic bacteria by sulfonylurea herbicides.

Kreisberg JF, Ong NT, Krishna A, Joseph TL, Wang J, Ong C, Ooi HA, Sung JC, Siew CC, Chang GC, Biot F, Cuccui J, Wren BW, Chan J, Sivalingam SP, Zhang LH, Verma C, Tan P.

Antimicrob Agents Chemother. 2013 Mar;57(3):1513-7. doi: 10.1128/AAC.02327-12. Epub 2012 Dec 21.

18.

Modulation of Caenorhabditis elegans infection sensitivity by the LIN-7 cell junction protein.

Sem X, Kreisberg JF, Kawli T, Tan MW, Rhen M, Tan P.

Cell Microbiol. 2012 Oct;14(10):1584-99. doi: 10.1111/j.1462-5822.2012.01824.x. Epub 2012 Jun 21.

19.

A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence.

Nandi T, Ong C, Singh AP, Boddey J, Atkins T, Sarkar-Tyson M, Essex-Lopresti AE, Chua HH, Pearson T, Kreisberg JF, Nilsson C, Ariyaratne P, Ronning C, Losada L, Ruan Y, Sung WK, Woods D, Titball RW, Beacham I, Peak I, Keim P, Nierman WC, Tan P.

PLoS Pathog. 2010 Apr 1;6(4):e1000845. doi: 10.1371/journal.ppat.1000845.

20.

In vitro derived dendritic cells trans-infect CD4 T cells primarily with surface-bound HIV-1 virions.

Cavrois M, Neidleman J, Kreisberg JF, Greene WC.

PLoS Pathog. 2007 Jan;3(1):e4.

21.
22.

Human immunodeficiency virus fusion to dendritic cells declines as cells mature.

Cavrois M, Neidleman J, Kreisberg JF, Fenard D, Callebaut C, Greene WC.

J Virol. 2006 Feb;80(4):1992-9.

23.

Cellular APOBEC3G restricts HIV-1 infection in resting CD4+ T cells.

Chiu YL, Soros VB, Kreisberg JF, Stopak K, Yonemoto W, Greene WC.

Nature. 2005 May 5;435(7038):108-14. Epub 2005 Apr 13. Retraction in: Nature. 2010 Jul 8;466(7303):276.

PMID:
15829920
24.

HIV-1 Vpr displays natural protein-transducing properties: implications for viral pathogenesis.

Sherman MP, Schubert U, Williams SA, de Noronha CM, Kreisberg JF, Henklein P, Greene WC.

Virology. 2002 Oct 10;302(1):95-105.

25.

The interdigitated beta-helix domain of the P22 tailspike protein acts as a molecular clamp in trimer stabilization.

Kreisberg JF, Betts SD, Haase-Pettingell C, King J.

Protein Sci. 2002 Apr;11(4):820-30.

26.

HIV-1 actively replicates in naive CD4(+) T cells residing within human lymphoid tissues.

Eckstein DA, Penn ML, Korin YD, Scripture-Adams DD, Zack JA, Kreisberg JF, Roederer M, Sherman MP, Chin PS, Goldsmith MA.

Immunity. 2001 Oct;15(4):671-82.

27.

Cytopathicity of human immunodeficiency virus type 1 primary isolates depends on coreceptor usage and not patient disease status.

Kreisberg JF, Kwa D, Schramm B, Trautner V, Connor R, Schuitemaker H, Mullins JI, van't Wout AB, Goldsmith MA.

J Virol. 2001 Sep;75(18):8842-7.

28.

Folate receptor-alpha is a cofactor for cellular entry by Marburg and Ebola viruses.

Chan SY, Empig CJ, Welte FJ, Speck RF, Schmaljohn A, Kreisberg JF, Goldsmith MA.

Cell. 2001 Jul 13;106(1):117-26.

29.

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