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Items: 1 to 50 of 235

1.

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
2.

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 Jun 7. doi: 10.1038/s41388-018-0326-9. [Epub ahead of print]

PMID:
29880876
3.

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.

4.

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.

5.

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.

6.

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
7.

Food grade microemulsion systems: Sunflower oil/castor oil derivative-ethanol/water. Rheological and physicochemical analysis.

Mori Cortés N, Lorenzo G, Califano AN.

Food Res Int. 2018 May;107:41-47. doi: 10.1016/j.foodres.2018.01.073. Epub 2018 Jan 31.

PMID:
29580502
8.

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.

9.

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.

10.

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.

11.

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
12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

High-throughput validation of ceRNA regulatory networks.

Chiu HS, Martínez MR, Bansal M, Subramanian A, Golub TR, Yang X, Sumazin P, Califano A.

BMC Genomics. 2017 May 30;18(1):418. doi: 10.1186/s12864-017-3790-7.

19.

Epigenetic Regulation of ZBTB18 Promotes Glioblastoma Progression.

Fedele V, Dai F, Masilamani AP, Heiland DH, Kling E, Gätjens-Sanchez AM, Ferrarese R, Platania L, Soroush D, Kim H, Nelander S, Weyerbrock A, Prinz M, Califano A, Iavarone A, Bredel M, Carro MS.

Mol Cancer Res. 2017 Aug;15(8):998-1011. doi: 10.1158/1541-7786.MCR-16-0494. Epub 2017 May 16.

20.

Kinetic Parameters for the Thermal Inactivation of Peroxidase and Lipoxygenase in Precooked Frozen Brassica Species.

Pérez-Calderón J, Califano A, Santos MV, Zaritzky N.

J Food Sci. 2017 Jun;82(6):1378-1386. doi: 10.1111/1750-3841.13717. Epub 2017 May 4.

PMID:
28471020
21.

A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue.

Talos F, Mitrofanova A, Bergren SK, Califano A, Shen MM.

Nat Commun. 2017 Apr 21;8:14662. doi: 10.1038/ncomms14662.

22.

Erratum to: HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers.

Putcha P, Yu J, Rodriguez-Barrueco R, Saucedo-Cuevas L, Villagrasa P, Murga-Penas E, Quayle SN, Yang M, Castro V, Llobet-Navas D, Birnbaum D, Finetti P, Woodward WA, Bertucci F, Alpaugh ML, Califano A, Silva J.

Breast Cancer Res. 2017 Apr 19;19(1):49. doi: 10.1186/s13058-017-0841-6. No abstract available.

23.

Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer.

Zou M, Toivanen R, Mitrofanova A, Floch N, Hayati S, Sun Y, Le Magnen C, Chester D, Mostaghel EA, Califano A, Rubin MA, Shen MM, Abate-Shen C.

Cancer Discov. 2017 Jul;7(7):736-749. doi: 10.1158/2159-8290.CD-16-1174. Epub 2017 Apr 14.

24.

Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response.

Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Charles Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali G, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U.

Mol Cell Proteomics. 2017 May;16(5):891-910. doi: 10.1074/mcp.M117.067439. Epub 2017 Mar 22.

25.

Synergistic antileukemic therapies in NOTCH1-induced T-ALL.

Sanchez-Martin M, Ambesi-Impiombato A, Qin Y, Herranz D, Bansal M, Girardi T, Paietta E, Tallman MS, Rowe JM, De Keersmaecker K, Califano A, Ferrando AA.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):2006-2011. doi: 10.1073/pnas.1611831114. Epub 2017 Feb 7.

26.

Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases.

Koşaloğlu Z, Zörnig I, Halama N, Kaiser I, Buchhalter I, Grabe N, Eils R, Schlesner M, Califano A, Jäger D.

Oncoimmunology. 2016 Jul 22;5(11):e1213931. doi: 10.1080/2162402X.2016.1213931. eCollection 2016.

27.

The recurrent architecture of tumour initiation, progression and drug sensitivity.

Califano A, Alvarez MJ.

Nat Rev Cancer. 2017 Feb;17(2):116-130. doi: 10.1038/nrc.2016.124. Epub 2016 Dec 15. Review.

28.

Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity.

Udyavar AR, Wooten DJ, Hoeksema M, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V.

Cancer Res. 2017 Mar 1;77(5):1063-1074. doi: 10.1158/0008-5472.CAN-16-1467. Epub 2016 Dec 8.

29.

A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma.

Dela Cruz FS, Diolaiti D, Turk AT, Rainey AR, Ambesi-Impiombato A, Andrews SJ, Mansukhani MM, Nagy PL, Alvarez MJ, Califano A, Forouhar F, Modzelewski B, Mitchell CM, Yamashiro DJ, Marks LJ, Glade Bender JL, Kung AL.

Genome Med. 2016 Oct 31;8(1):116. doi: 10.1186/s13073-016-0366-0.

30.

Correction: Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information.

Giorgi FM, Lopez G, Woo JH, Bisikirska B, Califano A, Bansal M.

PLoS One. 2016 Sep 15;11(9):e0163402. doi: 10.1371/journal.pone.0163402. eCollection 2016.

31.

HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma.

Tavana O, Li D, Dai C, Lopez G, Banerjee D, Kon N, Chen C, Califano A, Yamashiro DJ, Sun H, Gu W.

Nat Med. 2016 Oct;22(10):1180-1186. doi: 10.1038/nm.4180. Epub 2016 Sep 12.

32.

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks.

Chen JC, Alvarez MJ, Talos F, Dhruv H, Rieckhof GE, Iyer A, Diefes KL, Aldape K, Berens M, Shen MM, Califano A.

Cell. 2016 Aug 11;166(4):1055. doi: 10.1016/j.cell.2016.07.036. No abstract available.

33.

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.

Dutta A, Le Magnen C, Mitrofanova A, Ouyang X, Califano A, Abate-Shen C.

Science. 2016 Jun 24;352(6293):1576-80. doi: 10.1126/science.aad9512.

34.

Functional characterization of somatic mutations in cancer using network-based inference of protein activity.

Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A.

Nat Genet. 2016 Aug;48(8):838-47. doi: 10.1038/ng.3593. Epub 2016 Jun 20.

35.

Detection and removal of spatial bias in multiwell assays.

Lachmann A, Giorgi FM, Alvarez MJ, Califano A.

Bioinformatics. 2016 Jul 1;32(13):1959-65. doi: 10.1093/bioinformatics/btw092. Epub 2016 Feb 28.

PMID:
27153732
36.

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.

Lachmann A, Giorgi FM, Lopez G, Califano A.

Bioinformatics. 2016 Jul 15;32(14):2233-5. doi: 10.1093/bioinformatics/btw216. Epub 2016 Apr 23.

37.

Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification.

Kushwaha R, Jagadish N, Kustagi M, Mendiratta G, Seandel M, Soni R, Korkola JE, Thodima V, Califano A, Bosl GJ, Chaganti RSK.

Stem Cell Reports. 2016 May 10;6(5):772-783. doi: 10.1016/j.stemcr.2016.04.002. Epub 2016 Apr 28.

38.

Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis.

Westphalen CB, Takemoto Y, Tanaka T, Macchini M, Jiang Z, Renz BW, Chen X, Ormanns S, Nagar K, Tailor Y, May R, Cho Y, Asfaha S, Worthley DL, Hayakawa Y, Urbanska AM, Quante M, Reichert M, Broyde J, Subramaniam PS, Remotti H, Su GH, Rustgi AK, Friedman RA, Honig B, Califano A, Houchen CW, Olive KP, Wang TC.

Cell Stem Cell. 2016 Apr 7;18(4):441-55. doi: 10.1016/j.stem.2016.03.016.

39.

High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing.

Sepulveda JL, Gutierrez-Pajares JL, Luna A, Yao Y, Tobias JW, Thomas S, Woo Y, Giorgi F, Komissarova EV, Califano A, Wang TC, Sepulveda AR.

Mod Pathol. 2016 Feb;29(2):182-93. doi: 10.1038/modpathol.2015.144. Epub 2016 Jan 15.

40.

An ID2-dependent mechanism for VHL inactivation in cancer.

Lee SB, Frattini V, Bansal M, Castano AM, Sherman D, Hutchinson K, Bruce JN, Califano A, Liu G, Cardozo T, Iavarone A, Lasorella A.

Nature. 2016 Jan 14;529(7585):172-7. doi: 10.1038/nature16475. Epub 2016 Jan 6.

41.

HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers.

Putcha P, Yu J, Rodriguez-Barrueco R, Saucedo-Cuevas L, Villagrasa P, Murga-Penas E, Quayle SN, Yang M, Castro V, Llobet-Navas D, Birnbaum D, Finetti P, Woodward WA, Bertucci F, Alpaugh ML, Califano A, Silva J.

Breast Cancer Res. 2015 Dec 8;17(1):149. doi: 10.1186/s13058-015-0658-0. Erratum in: Breast Cancer Res. 2017 Apr 19;19(1):49.

42.

Elucidation and Pharmacological Targeting of Novel Molecular Drivers of Follicular Lymphoma Progression.

Bisikirska B, Bansal M, Shen Y, Teruya-Feldstein J, Chaganti R, Califano A.

Cancer Res. 2016 Feb 1;76(3):664-74. doi: 10.1158/0008-5472.CAN-15-0828. Epub 2015 Nov 20.

43.

TOpic: Rare and Special Cases, The Real "Strange Cases".

Teoh A, Chan S, Yip H, Chiu P, Ng E, Sekmen U, Paksoy M, Sahoo M, Tonizzo CA, Lauretta A, Kosuta M, Pinciroli L, Infantino A, Khetan M, Bhatia P, Kalhan S, John S, Bindal V, Hansske B, Axer S, Ertem M, Gök H, Ozveri E, Cavallaro G, Iorio O, Palleschi G, Pastore AL, Silvestri L, Autieri D, Ripoli A, Leto A, Silecchia G, Rizzello M, Carbone A, Bertoglio C, Carnevali P, Magistro C, DeMartini P, Forgione A, Di Lernia S, Ferrari G, Pugliese R, Ureña MA, Monclús JL, Panizzo V, Califano A, Marini M, Basilico G, Micheletto G.

Hernia. 2015 Apr;19 Suppl 1:S371-4. doi: 10.1007/BF03355402. No abstract available.

PMID:
26518857
44.

ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling.

Yu J, Silva J, Califano A.

Bioinformatics. 2016 Jan 15;32(2):260-7. doi: 10.1093/bioinformatics/btv556. Epub 2015 Sep 28.

45.

Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models.

Mitrofanova A, Aytes A, Zou M, Shen MM, Abate-Shen C, Califano A.

Cell Rep. 2015 Sep 29;12(12):2060-71. doi: 10.1016/j.celrep.2015.08.051. Epub 2015 Sep 17.

46.

DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.

Alvarez MJ, Chen JC, Califano A.

Bioinformatics. 2015 Dec 15;31(24):4032-4. doi: 10.1093/bioinformatics/btv499. Epub 2015 Sep 2.

47.

Toward understanding and exploiting tumor heterogeneity.

Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J.

Nat Med. 2015 Aug;21(8):846-53. doi: 10.1038/nm.3915.

48.

Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers.

Rodriguez-Barrueco R, Yu J, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M, Alvarez M, Cordon-Cardo C, Kalinsky K, Maurer M, Califano A, Silva JM.

Genes Dev. 2015 Aug 1;29(15):1631-48. doi: 10.1101/gad.262642.115. Epub 2015 Jul 30.

49.

Identification of neurodegenerative factors using translatome-regulatory network analysis.

Brichta L, Shin W, Jackson-Lewis V, Blesa J, Yap EL, Walker Z, Zhang J, Roussarie JP, Alvarez MJ, Califano A, Przedborski S, Greengard P.

Nat Neurosci. 2015 Sep;18(9):1325-33. doi: 10.1038/nn.4070. Epub 2015 Jul 27.

50.

Elucidating Compound Mechanism of Action by Network Perturbation Analysis.

Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A.

Cell. 2015 Jul 16;162(2):441-451. doi: 10.1016/j.cell.2015.05.056.

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