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Items: 1 to 20 of 118

1.

NSD2 is a conserved driver of metastatic prostate cancer progression.

Aytes A, Giacobbe A, Mitrofanova A, Ruggero K, Cyrta J, Arriaga J, Palomero L, Farran-Matas S, Rubin MA, Shen MM, Califano A, Abate-Shen C.

Nat Commun. 2018 Dec 5;9(1):5201. doi: 10.1038/s41467-018-07511-4.

PMID:
30518758
2.

SJARACNe: a scalable software tool for gene network reverse engineering from big data.

Khatamian A, Paull EO, Califano A, Yu J.

Bioinformatics. 2018 Nov 2. doi: 10.1093/bioinformatics/bty907. [Epub ahead of print]

PMID:
30388204
3.

Cooperation of loss of NKX3.1 and inflammation in prostate cancer initiation.

Le Magnen C, Virk RK, Dutta A, Kim JY, Panja S, Lopez-Bujanda ZA, Califano A, Drake CG, Mitrofanova A, Abate-Shen C.

Dis Model Mech. 2018 Nov 16;11(11). pii: dmm035139. doi: 10.1242/dmm.035139.

4.

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.

Risom T, Langer EM, Chapman MP, Rantala J, Fields AJ, Boniface C, Alvarez MJ, Kendsersky ND, Pelz CR, Johnson-Camacho K, Dobrolecki LE, Chin K, Aswani AJ, Wang NJ, Califano A, Lewis MT, Tomlin CJ, Spellman PT, Adey A, Gray JW, Sears RC.

Nat Commun. 2018 Sep 19;9(1):3815. doi: 10.1038/s41467-018-05729-w.

5.

A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors.

Alvarez MJ, Subramaniam PS, Tang LH, Grunn A, Aburi M, Rieckhof G, Komissarova EV, Hagan EA, Bodei L, Clemons PA, Dela Cruz FS, Dhall D, Diolaiti D, Fraker DA, Ghavami A, Kaemmerer D, Karan C, Kidd M, Kim KM, Kim HC, Kunju LP, Langel Ü, Li Z, Lee J, Li H, LiVolsi V, Pfragner R, Rainey AR, Realubit RB, Remotti H, Regberg J, Roses R, Rustgi A, Sepulveda AR, Serra S, Shi C, Yuan X, Barberis M, Bergamaschi R, Chinnaiyan AM, Detre T, Ezzat S, Frilling A, Hommann M, Jaeger D, Kim MK, Knudsen BS, Kung AL, Leahy E, Metz DC, Milsom JW, Park YS, Reidy-Lagunes D, Schreiber S, Washington K, Wiedenmann B, Modlin I, Califano A.

Nat Genet. 2018 Jul;50(7):979-989. doi: 10.1038/s41588-018-0138-4. Epub 2018 Jun 18.

PMID:
29915428
6.

Transcription factor activating protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma.

Boboila S, Lopez G, Yu J, Banerjee D, Kadenhe-Chiweshe A, Connolly EP, Kandel JJ, Rajbhandari P, Silva JM, Califano A, Yamashiro DJ.

Oncogene. 2018 Oct;37(40):5451-5465. doi: 10.1038/s41388-018-0326-9. Epub 2018 Jun 7.

7.

The number of titrated microRNA species dictates ceRNA regulation.

Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A.

Nucleic Acids Res. 2018 May 18;46(9):4354-4369. doi: 10.1093/nar/gky286.

8.

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.

Ding H, Douglass EF Jr, Sonabend AM, Mela A, Bose S, Gonzalez C, Canoll PD, Sims PA, Alvarez MJ, Califano A.

Nat Commun. 2018 Apr 16;9(1):1471. doi: 10.1038/s41467-018-03843-3.

9.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

10.

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ.

Cell Stem Cell. 2018 Apr 5;22(4):575-588.e7. doi: 10.1016/j.stem.2018.03.012.

PMID:
29625070
11.

iterClust: a statistical framework for iterative clustering analysis.

Ding H, Wang W, Califano A.

Bioinformatics. 2018 Aug 15;34(16):2865-2866. doi: 10.1093/bioinformatics/bty176.

12.

Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.

Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A.

Cancer Discov. 2018 May;8(5):582-599. doi: 10.1158/2159-8290.CD-16-0861. Epub 2018 Mar 6.

13.

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network.

Aksoy BA, Dancík V, Smith K, Mazerik JN, Ji Z, Gross B, Nikolova O, Jaber N, Califano A, Schreiber SL, Gerhard DS, Hermida LC, Jagu S, Sander C, Floratos A, Clemons PA.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax054.

14.

Bone Marrow Myeloid Cells Regulate Myeloid-Biased Hematopoietic Stem Cells via a Histamine-Dependent Feedback Loop.

Chen X, Deng H, Churchill MJ, Luchsinger LL, Du X, Chu TH, Friedman RA, Middelhoff M, Ding H, Tailor YH, Wang ALE, Liu H, Niu Z, Wang H, Jiang Z, Renders S, Ho SH, Shah SV, Tishchenko P, Chang W, Swayne TC, Munteanu L, Califano A, Takahashi R, Nagar KK, Renz BW, Worthley DL, Westphalen CB, Hayakawa Y, Asfaha S, Borot F, Lin CS, Snoeck HW, Mukherjee S, Wang TC.

Cell Stem Cell. 2017 Dec 7;21(6):747-760.e7. doi: 10.1016/j.stem.2017.11.003. Epub 2017 Nov 30.

PMID:
29198940
15.

ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.

Tomljanovic Z, Patel M, Shin W, Califano A, Teich AF.

Bioinformatics. 2018 Feb 1;34(3):367-371. doi: 10.1093/bioinformatics/btx608.

PMID:
29028963
16.

Systematic, network-based characterization of therapeutic target inhibitors.

Shen Y, Alvarez MJ, Bisikirska B, Lachmann A, Realubit R, Pampou S, Coku J, Karan C, Califano A.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005599. doi: 10.1371/journal.pcbi.1005599. eCollection 2017 Oct.

17.

Accelerated parallel algorithm for gene network reverse engineering.

He J, Zhou Z, Reed M, Califano A.

BMC Syst Biol. 2017 Sep 21;11(Suppl 4):83. doi: 10.1186/s12918-017-0458-5.

18.

An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.

Walsh LA, Alvarez MJ, Sabio EY, Reyngold M, Makarov V, Mukherjee S, Lee KW, Desrichard A, Turcan Ş, Dalin MG, Rajasekhar VK, Chen S, Vahdat LT, Califano A, Chan TA.

Cell Rep. 2017 Aug 15;20(7):1623-1640. doi: 10.1016/j.celrep.2017.07.052.

19.

PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.

Bush EC, Ray F, Alvarez MJ, Realubit R, Li H, Karan C, Califano A, Sims PA.

Nat Commun. 2017 Jul 24;8(1):105. doi: 10.1038/s41467-017-00136-z.

20.

PI3Kγ/δ and NOTCH1 Cross-Regulate Pathways That Define the T-cell Acute Lymphoblastic Leukemia Disease Signature.

Efimenko E, Davé UP, Lebedeva IV, Shen Y, Sanchez-Quintero MJ, Diolaiti D, Kung A, Lannutti BJ, Chen J, Realubit R, Niatsetskaya Z, Ten V, Karan C, Chen X, Califano A, Diacovo TG.

Mol Cancer Ther. 2017 Oct;16(10):2069-2082. doi: 10.1158/1535-7163.MCT-17-0141. Epub 2017 Jul 17.

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