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Items: 33

1.

Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer's Disease Not Evident in Mouse Models.

Friedman BA, Srinivasan K, Ayalon G, Meilandt WJ, Lin H, Huntley MA, Cao Y, Lee SH, Haddick PCG, Ngu H, Modrusan Z, Larson JL, Kaminker JS, van der Brug MP, Hansen DV.

Cell Rep. 2018 Jan 16;22(3):832-847. doi: 10.1016/j.celrep.2017.12.066.

2.

Progranulin deficiency causes impairment of autophagy and TDP-43 accumulation.

Chang MC, Srinivasan K, Friedman BA, Suto E, Modrusan Z, Lee WP, Kaminker JS, Hansen DV, Sheng M.

J Exp Med. 2017 Sep 4;214(9):2611-2628. doi: 10.1084/jem.20160999. Epub 2017 Aug 4.

3.

Dual leucine zipper kinase-dependent PERK activation contributes to neuronal degeneration following insult.

Larhammar M, Huntwork-Rodriguez S, Jiang Z, Solanoy H, Sengupta Ghosh A, Wang B, Kaminker JS, Huang K, Eastham-Anderson J, Siu M, Modrusan Z, Farley MM, Tessier-Lavigne M, Lewcock JW, Watkins TA.

Elife. 2017 Apr 25;6. pii: e20725. doi: 10.7554/eLife.20725.

4.

A Common Variant of IL-6R is Associated with Elevated IL-6 Pathway Activity in Alzheimer's Disease Brains.

Haddick PC, Larson JL, Rathore N, Bhangale TR, Phung QT, Srinivasan K, Hansen DV, Lill JR; Alzheimer’s Disease Genetic Consortium (ADGC), Alzheimer’s Disease Neuroimaging Initiative (ADNI), Pericak-Vance MA, Haines J, Farrer LA, Kauwe JS, Schellenberg GD, Cruchaga C, Goate AM, Behrens TW, Watts RJ, Graham RR, Kaminker JS, van der Brug M.

J Alzheimers Dis. 2017;56(3):1037-1054. doi: 10.3233/JAD-160524.

5.

Untangling the brain's neuroinflammatory and neurodegenerative transcriptional responses.

Srinivasan K, Friedman BA, Larson JL, Lauffer BE, Goldstein LD, Appling LL, Borneo J, Poon C, Ho T, Cai F, Steiner P, van der Brug MP, Modrusan Z, Kaminker JS, Hansen DV.

Nat Commun. 2016 Apr 21;7:11295. doi: 10.1038/ncomms11295.

6.

Complex regulation of ADAR-mediated RNA-editing across tissues.

Huntley MA, Lou M, Goldstein LD, Lawrence M, Dijkgraaf GJ, Kaminker JS, Gentleman R.

BMC Genomics. 2016 Jan 15;17:61. doi: 10.1186/s12864-015-2291-9.

7.

A resource for cell line authentication, annotation and quality control.

Yu M, Selvaraj SK, Liang-Chu MM, Aghajani S, Busse M, Yuan J, Lee G, Peale F, Klijn C, Bourgon R, Kaminker JS, Neve RM.

Nature. 2015 Apr 16;520(7547):307-11. doi: 10.1038/nature14397.

PMID:
25877200
8.

Regulation of neuronal gene expression and survival by basal NMDA receptor activity: a role for histone deacetylase 4.

Chen Y, Wang Y, Modrusan Z, Sheng M, Kaminker JS.

J Neurosci. 2014 Nov 12;34(46):15327-39. doi: 10.1523/JNEUROSCI.0569-14.2014.

9.

ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.

Huntley MA, Larson JL, Chaivorapol C, Becker G, Lawrence M, Hackney JA, Kaminker JS.

Bioinformatics. 2013 Dec 15;29(24):3220-1. doi: 10.1093/bioinformatics/btt551. Epub 2013 Sep 29.

10.

Histone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability.

Lauffer BE, Mintzer R, Fong R, Mukund S, Tam C, Zilberleyb I, Flicke B, Ritscher A, Fedorowicz G, Vallero R, Ortwine DF, Gunzner J, Modrusan Z, Neumann L, Koth CM, Lupardus PJ, Kaminker JS, Heise CE, Steiner P.

J Biol Chem. 2013 Sep 13;288(37):26926-43. doi: 10.1074/jbc.M113.490706. Epub 2013 Jul 29.

11.

Identification and analysis of in vivo VEGF downstream markers link VEGF pathway activity with efficacy of anti-VEGF therapies.

Brauer MJ, Zhuang G, Schmidt M, Yao J, Wu X, Kaminker JS, Jurinka SS, Kolumam G, Chung AS, Jubb A, Modrusan Z, Ozawa T, James CD, Phillips H, Haley B, Tam RN, Clermont AC, Cheng JH, Yang SX, Swain SM, Chen D, Scherer SJ, Koeppen H, Yeh RF, Yue P, Stephan JP, Hegde P, Ferrara N, Singh M, Bais C.

Clin Cancer Res. 2013 Jul 1;19(13):3681-92. doi: 10.1158/1078-0432.CCR-12-3635. Epub 2013 May 17.

12.

DLK initiates a transcriptional program that couples apoptotic and regenerative responses to axonal injury.

Watkins TA, Wang B, Huntwork-Rodriguez S, Yang J, Jiang Z, Eastham-Anderson J, Modrusan Z, Kaminker JS, Tessier-Lavigne M, Lewcock JW.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):4039-44. doi: 10.1073/pnas.1211074110. Epub 2013 Feb 19.

13.

Spatially coordinated kinase signaling regulates local axon degeneration.

Chen M, Maloney JA, Kallop DY, Atwal JK, Tam SJ, Baer K, Kissel H, Kaminker JS, Lewcock JW, Weimer RM, Watts RJ.

J Neurosci. 2012 Sep 26;32(39):13439-53.

14.

Death receptors DR6 and TROY regulate brain vascular development.

Tam SJ, Richmond DL, Kaminker JS, Modrusan Z, Martin-McNulty B, Cao TC, Weimer RM, Carano RA, van Bruggen N, Watts RJ.

Dev Cell. 2012 Feb 14;22(2):403-17. doi: 10.1016/j.devcel.2011.11.018.

15.

Sensitivity to antitubulin chemotherapeutics is regulated by MCL1 and FBW7.

Wertz IE, Kusam S, Lam C, Okamoto T, Sandoval W, Anderson DJ, Helgason E, Ernst JA, Eby M, Liu J, Belmont LD, Kaminker JS, O'Rourke KM, Pujara K, Kohli PB, Johnson AR, Chiu ML, Lill JR, Jackson PK, Fairbrother WJ, Seshagiri S, Ludlam MJ, Leong KG, Dueber EC, Maecker H, Huang DC, Dixit VM.

Nature. 2011 Mar 3;471(7336):110-4. doi: 10.1038/nature09779. Erratum in: Nature. 2011 Jul 7;475(7354):122.

PMID:
21368834
16.

Granulocyte-colony stimulating factor promotes lung metastasis through mobilization of Ly6G+Ly6C+ granulocytes.

Kowanetz M, Wu X, Lee J, Tan M, Hagenbeek T, Qu X, Yu L, Ross J, Korsisaari N, Cao T, Bou-Reslan H, Kallop D, Weimer R, Ludlam MJ, Kaminker JS, Modrusan Z, van Bruggen N, Peale FV, Carano R, Meng YG, Ferrara N.

Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21248-55. doi: 10.1073/pnas.1015855107. Epub 2010 Nov 16.

17.

Identification and functional analysis of endothelial tip cell-enriched genes.

del Toro R, Prahst C, Mathivet T, Siegfried G, Kaminker JS, Larrivee B, Breant C, Duarte A, Takakura N, Fukamizu A, Penninger J, Eichmann A.

Blood. 2010 Nov 11;116(19):4025-33. doi: 10.1182/blood-2010-02-270819. Epub 2010 Aug 12.

18.

Diverse somatic mutation patterns and pathway alterations in human cancers.

Kan Z, Jaiswal BS, Stinson J, Janakiraman V, Bhatt D, Stern HM, Yue P, Haverty PM, Bourgon R, Zheng J, Moorhead M, Chaudhuri S, Tomsho LP, Peters BA, Pujara K, Cordes S, Davis DP, Carlton VE, Yuan W, Li L, Wang W, Eigenbrot C, Kaminker JS, Eberhard DA, Waring P, Schuster SC, Modrusan Z, Zhang Z, Stokoe D, de Sauvage FJ, Faham M, Seshagiri S.

Nature. 2010 Aug 12;466(7308):869-73. doi: 10.1038/nature09208. Epub 2010 Jul 28.

PMID:
20668451
19.

Microarray analysis of retinal endothelial tip cells identifies CXCR4 as a mediator of tip cell morphology and branching.

Strasser GA, Kaminker JS, Tessier-Lavigne M.

Blood. 2010 Jun 17;115(24):5102-10. doi: 10.1182/blood-2009-07-230284. Epub 2010 Feb 12.

20.

Inferring the functional effects of mutation through clusters of mutations in homologous proteins.

Yue P, Forrest WF, Kaminker JS, Lohr S, Zhang Z, Cavet G.

Hum Mutat. 2010 Mar;31(3):264-71. doi: 10.1002/humu.21194.

PMID:
20052764
21.

Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation.

Jaiswal BS, Janakiraman V, Kljavin NM, Chaudhuri S, Stern HM, Wang W, Kan Z, Dbouk HA, Peters BA, Waring P, Dela Vega T, Kenski DM, Bowman KK, Lorenzo M, Li H, Wu J, Modrusan Z, Stinson J, Eby M, Yue P, Kaminker JS, de Sauvage FJ, Backer JM, Seshagiri S.

Cancer Cell. 2009 Dec 8;16(6):463-74. doi: 10.1016/j.ccr.2009.10.016.

22.

High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors.

Haverty PM, Hon LS, Kaminker JS, Chant J, Zhang Z.

BMC Med Genomics. 2009 May 6;2:21. doi: 10.1186/1755-8794-2-21.

23.

Computational prediction of the functional effects of amino acid substitutions in signal peptides using a model-based approach.

Hon LS, Zhang Y, Kaminker JS, Zhang Z.

Hum Mutat. 2009 Jan;30(1):99-106. doi: 10.1002/humu.20798.

PMID:
18570327
24.

The genomic landscapes of human breast and colorectal cancers.

Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B.

Science. 2007 Nov 16;318(5853):1108-13. Epub 2007 Oct 11.

25.

CanPredict: a computational tool for predicting cancer-associated missense mutations.

Kaminker JS, Zhang Y, Watanabe C, Zhang Z.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W595-8. Epub 2007 May 30.

26.

Distinguishing cancer-associated missense mutations from common polymorphisms.

Kaminker JS, Zhang Y, Waugh A, Haverty PM, Peters B, Sebisanovic D, Stinson J, Forrest WF, Bazan JF, Seshagiri S, Zhang Z.

Cancer Res. 2007 Jan 15;67(2):465-73.

27.

Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.

Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker SE, Rubin GM, Karpen GH.

Genome Biol. 2002;3(12):RESEARCH0085. Epub 2002 Dec 31.

28.

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE.

Genome Biol. 2002;3(12):RESEARCH0084. Epub 2002 Dec 23.

29.

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE.

Genome Biol. 2002;3(12):RESEARCH0083. Epub 2002 Dec 31. Review.

30.

Apollo: a sequence annotation editor.

Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME.

Genome Biol. 2002;3(12):RESEARCH0082. Epub 2002 Dec 23. Review.

31.

An integrated computational pipeline and database to support whole-genome sequence annotation.

Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE.

Genome Biol. 2002;3(12):RESEARCH0081. Epub 2002 Dec 23. Review.

32.

Control of photoreceptor axon target choice by transcriptional repression of Runt.

Kaminker JS, Canon J, Salecker I, Banerjee U.

Nat Neurosci. 2002 Aug;5(8):746-50.

PMID:
12118258
33.

Redundant function of Runt Domain binding partners, Big brother and Brother, during Drosophila development.

Kaminker JS, Singh R, Lebestky T, Yan H, Banerjee U.

Development. 2001 Jul;128(14):2639-48.

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