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Items: 1 to 50 of 248

1.

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, Mokrab Y, Newman AM, 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 CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2019 Aug 20;51(2):411-412. doi: 10.1016/j.immuni.2019.08.004. No abstract available.

2.

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts.

Elyada E, Bolisetty M, Laise P, Flynn WF, Courtois ET, Burkhart RA, Teinor JA, Belleau P, Biffi G, Lucito MS, Sivajothi S, Armstrong TD, Engle DD, Yu KH, Hao Y, Wolfgang CL, Park Y, Preall J, Jaffee EM, Califano A, Robson P, Tuveson DA.

Cancer Discov. 2019 Aug;9(8):1102-1123. doi: 10.1158/2159-8290.CD-19-0094. Epub 2019 Jun 13.

PMID:
31197017
3.

Schizotypal personality disorder in individuals with the Attenuated Psychosis Syndrome: Frequent co-occurrence without an increased risk for conversion to threshold psychosis.

Zoghbi AW, Bernanke JA, Gleichman J, Masucci MD, Corcoran CM, Califano A, Segovia J, Colibazzi T, First MB, Brucato G, Girgis RR.

J Psychiatr Res. 2019 Jul;114:88-92. doi: 10.1016/j.jpsychires.2019.04.018. Epub 2019 Apr 21.

PMID:
31054454
4.

Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state.

Echeverria GV, Ge Z, Seth S, Zhang X, Jeter-Jones S, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, Sun Y, Qiu H, Chang Q, Bristow C, Carugo A, Shao J, Ma X, Harris A, Mundi P, Lau R, Ramamoorthy V, Wu Y, Alvarez MJ, Califano A, Moulder SL, Symmans WF, Marszalek JR, Heffernan TP, Chang JT, Piwnica-Worms H.

Sci Transl Med. 2019 Apr 17;11(488). pii: eaav0936. doi: 10.1126/scitranslmed.aav0936.

PMID:
30996079
5.

Physical and chemical stability under environmental stress of microemulsions formulated with fish oil.

Mori Cortés N, Califano AN, Lorenzo G.

Food Res Int. 2019 May;119:283-290. doi: 10.1016/j.foodres.2019.01.067. Epub 2019 Jan 30.

PMID:
30884658
6.

Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-Driven Cancer.

Slotkin EK, Diolaiti D, Shukla NN, Dela Cruz FS, Clark JJ, Gundem G, Yellapantula VD, Levine MF, You D, Ma P, Pachhal S, Ibanez Sanchez G, Benayed R, Jungbluth AA, Smyth LM, Mauguen A, Gushterova I, Ding H, Spraggon L, Darnell R, Califano A, Ladanyi M, Papaemmanuil E, Kung AL, Hyman DM, Roberts SS.

Cancer Discov. 2019 May;9(5):605-616. doi: 10.1158/2159-8290.CD-18-0953. Epub 2019 Mar 15.

PMID:
30877085
7.

Correction: 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. 2019 Mar 1;79(5):1014. doi: 10.1158/0008-5472.CAN-19-0069. No abstract available.

PMID:
30824677
8.

Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes.

Maurer C, Holmstrom SR, He J, Laise P, Su T, Ahmed A, Hibshoosh H, Chabot JA, Oberstein PE, Sepulveda AR, Genkinger JM, Zhang J, Iuga AC, Bansal M, Califano A, Olive KP.

Gut. 2019 Jun;68(6):1034-1043. doi: 10.1136/gutjnl-2018-317706. Epub 2019 Jan 18.

PMID:
30658994
9.

Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis.

Bansal M, He J, Peyton M, Kustagi M, Iyer A, Comb M, White M, Minna JD, Califano A.

PLoS One. 2019 Jan 7;14(1):e0208646. doi: 10.1371/journal.pone.0208646. eCollection 2019.

10.

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.

11.

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

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

Bioinformatics. 2019 Jun 1;35(12):2165-2166. doi: 10.1093/bioinformatics/bty907.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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, Mokrab Y, Newman AM, 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 CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. Erratum in: Immunity. 2019 Aug 20;51(2):411-412.

19.

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.

20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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
34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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. Erratum in: Cancer Res. 2019 Mar 1;79(5):1014.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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
49.

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.

50.

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.

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