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Items: 19

1.

Enhancing Next-Generation Sequencing-Guided Cancer Care Through Cognitive Computing.

Patel NM, Michelini VV, Snell JM, Balu S, Hoyle AP, Parker JS, Hayward MC, Eberhard DA, Salazar AH, McNeillie P, Xu J, Huettner CS, Koyama T, Utro F, Rhrissorrakrai K, Norel R, Bilal E, Royyuru A, Parida L, Earp HS, Grilley-Olson JE, Hayes DN, Harvey SJ, Sharpless NE, Kim WY.

Oncologist. 2018 Feb;23(2):179-185. doi: 10.1634/theoncologist.2017-0170. Epub 2017 Nov 20.

PMID:
29158372
2.

Watson for Genomics: Moving Personalized Medicine Forward.

Rhrissorrakrai K, Koyama T, Parida L.

Trends Cancer. 2016 Aug;2(8):392-395. doi: 10.1016/j.trecan.2016.06.008. Epub 2016 Jul 21.

PMID:
28741491
3.

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.

Neurol Genet. 2017 Jul 11;3(4):e164. doi: 10.1212/NXG.0000000000000164. eCollection 2017 Aug.

4.

Erratum to: MINE: Module Identification in Networks.

Rhrissorrakrai K, Gunsalus KC.

BMC Bioinformatics. 2016 Feb 17;17:89. doi: 10.1186/s12859-016-0929-5. No abstract available.

5.

A crowd-sourcing approach for the construction of species-specific cell signaling networks.

Bilal E, Sakellaropoulos T, Melas IN, Messinis DE, Belcastro V, Rhrissorrakrai K, Meyer P, Norel R, Iskandar A, Blaese E, Rice JJ, Peitsch MC, Hoeng J, Stolovitzky G, Alexopoulos LG, Poussin C; Challenge Participants.

Bioinformatics. 2015 Feb 15;31(4):484-91. doi: 10.1093/bioinformatics/btu659. Epub 2014 Oct 7.

6.

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge.

Rhrissorrakrai K, Belcastro V, Bilal E, Norel R, Poussin C, Mathis C, Dulize RH, Ivanov NV, Alexopoulos L, Rice JJ, Peitsch MC, Stolovitzky G, Meyer P, Hoeng J.

Bioinformatics. 2015 Feb 15;31(4):471-83. doi: 10.1093/bioinformatics/btu611. Epub 2014 Sep 17.

7.

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets.

Hormoz S, Bhanot G, Biehl M, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Dayarian A.

Bioinformatics. 2015 Feb 15;31(4):492-500. doi: 10.1093/bioinformatics/btu569. Epub 2014 Aug 24.

8.

Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Hafemeister C, Romero R, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Bonneau R, Tarca AL.

Bioinformatics. 2015 Feb 15;31(4):501-8. doi: 10.1093/bioinformatics/btu570. Epub 2014 Aug 22.

9.

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge.

Dayarian A, Romero R, Wang Z, Biehl M, Bilal E, Hormoz S, Meyer P, Norel R, Rhrissorrakrai K, Bhanot G, Luo F, Tarca AL.

Bioinformatics. 2015 Feb 15;31(4):462-70. doi: 10.1093/bioinformatics/btu490. Epub 2014 Jul 23.

10.

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge.

Biehl M, Sadowski P, Bhanot G, Bilal E, Dayarian A, Meyer P, Norel R, Rhrissorrakrai K, Zeller MD, Hormoz S.

Bioinformatics. 2015 Feb 15;31(4):453-61. doi: 10.1093/bioinformatics/btu407. Epub 2014 Jul 3.

11.

The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.

Poussin C, Mathis C, Alexopoulos LG, Messinis DE, Dulize RH, Belcastro V, Melas IN, Sakellaropoulos T, Rhrissorrakrai K, Bilal E, Meyer P, Talikka M, Boué S, Norel R, Rice JJ, Stolovitzky G, Ivanov NV, Peitsch MC, Hoeng J.

Sci Data. 2014 Jun 10;1:140009. doi: 10.1038/sdata.2014.9. eCollection 2014.

12.

On Crowd-verification of Biological Networks.

sbv IMPROVER project team (in alphabetical order), Ansari S, Binder J, Boue S, Di Fabio A, Hayes W, Hoeng J, Iskandar A, Kleiman R, Norel R, O'Neel B, Peitsch MC, Poussin C, Pratt D, Rhrissorrakrai K, Schlage WK, Stolovitzky G, Talikka M.

Bioinform Biol Insights. 2013 Oct 10;7:307-25. doi: 10.4137/BBI.S12932. eCollection 2013.

13.

Electrical activity can impose time of day on the circadian transcriptome of pacemaker neurons.

Mizrak D, Ruben M, Myers GN, Rhrissorrakrai K, Gunsalus KC, Blau J.

Curr Biol. 2012 Oct 23;22(20):1871-80. doi: 10.1016/j.cub.2012.07.070. Epub 2012 Aug 30.

14.

Networks in Caenorhabditis elegans.

Gunsalus KC, Rhrissorrakrai K.

Curr Opin Genet Dev. 2011 Dec;21(6):787-98. doi: 10.1016/j.gde.2011.10.003. Epub 2011 Nov 4. Review.

PMID:
22054717
15.

MINE: Module Identification in Networks.

Rhrissorrakrai K, Gunsalus KC.

BMC Bioinformatics. 2011 May 23;12:192. doi: 10.1186/1471-2105-12-192. Erratum in: BMC Bioinformatics. 2016;17:89.

16.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

17.

Benzo[a]pyrene diol epoxide stimulates an inflammatory response in normal human lung fibroblasts through a p53 and JNK mediated pathway.

Dreij K, Rhrissorrakrai K, Gunsalus KC, Geacintov NE, Scicchitano DA.

Carcinogenesis. 2010 Jun;31(6):1149-57. doi: 10.1093/carcin/bgq073. Epub 2010 Apr 9.

18.

Mating induces an immune response and developmental switch in the Drosophila oviduct.

Kapelnikov A, Zelinger E, Gottlieb Y, Rhrissorrakrai K, Gunsalus KC, Heifetz Y.

Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13912-7. doi: 10.1073/pnas.0710997105. Epub 2008 Aug 25.

19.

A protein domain-based interactome network for C. elegans early embryogenesis.

Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M.

Cell. 2008 Aug 8;134(3):534-45. doi: 10.1016/j.cell.2008.07.009. Erratum in: Cell. 2012 Dec 21;151(7):1633.

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