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Results: 1 to 20 of 182

1.

Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks.

Repunte-Canonigo V, Shin W, Vendruscolo LF, Lefebvre C, van der Stap L, Kawamura T, Schlosburg JE, Alvarez M, Koob GF, Califano A, Sanna PP.

Genome Biol. 2015 Feb 2;16(1):68. [Epub ahead of print]

PMID:
25886852
2.

Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue.

Califano A, Kellis M, Stolovitzky G.

J Comput Biol. 2015 Apr;22(4):251-2. doi: 10.1089/cmb.2015.020P. No abstract available.

PMID:
25844665
3.

Assembly and interrogation of Alzheimer's disease genetic networks reveal novel regulators of progression.

Aubry S, Shin W, Crary JF, Lefort R, Qureshi YH, Lefebvre C, Califano A, Shelanski ML.

PLoS One. 2015 Mar 17;10(3):e0120352. doi: 10.1371/journal.pone.0120352. eCollection 2015.

4.

Sodium-reduced lean sausages with fish oil optimized by a mixture design approach.

Marchetti L, Argel N, Andrés SC, Califano AN.

Meat Sci. 2015 Jun;104:67-77. doi: 10.1016/j.meatsci.2015.02.005. Epub 2015 Feb 20.

PMID:
25725284
5.

Development of an ionic-liquid-based dispersive liquid-liquid microextraction method for the determination of antichagasic drugs in human breast milk. Optimization by central composite design.

Padró JM, Vidal RB, Echevarria RN, Califano AN, Reta MR.

J Sep Sci. 2015 Feb 24. doi: 10.1002/jssc.201401367. [Epub ahead of print]

PMID:
25711461
6.

A systems approach to drug discovery in Alzheimer's disease.

Shelanski M, Shin W, Aubry S, Sims P, Alvarez MJ, Califano A.

Neurotherapeutics. 2015 Jan;12(1):126-31. doi: 10.1007/s13311-014-0335-5.

PMID:
25608936
7.

The Cyni framework for network inference in Cytoscape.

Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B.

Bioinformatics. 2014 Dec 18. pii: btu812. [Epub ahead of print]

PMID:
25527096
8.

Mechanical and optical characterization of gelled matrices during storage.

Lorenzo G, Zaritzky N, Califano A.

Carbohydr Polym. 2015 Mar 6;117:825-35. doi: 10.1016/j.carbpol.2014.10.040. Epub 2014 Oct 24.

PMID:
25498706
9.
10.

A community computational challenge to predict the activity of pairs of compounds.

Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community.

Nat Biotechnol. 2014 Dec;32(12):1213-22. doi: 10.1038/nbt.3052. Epub 2014 Nov 17.

11.

Predicting protein networks in cancer.

Califano A.

Nat Genet. 2014 Dec;46(12):1252-3. doi: 10.1038/ng.3156.

PMID:
25418743
12.

Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A, Kim HR, Seviour EG, Luo Z, Sehgal V, Moss T, Lu Y, Ram P, Silva J, Mills GB, Califano A, Sumazin P.

Genome Res. 2015 Feb;25(2):257-67. doi: 10.1101/gr.178194.114. Epub 2014 Nov 5.

PMID:
25378249
13.

Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.

Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C, Villagrasa-Gonzalez P, Viale A, Korkola JE, Houldsworth J, Feldman DR, Bosl GJ, Califano A, Chaganti RS.

Stem Cells. 2015 Feb;33(2):367-77. doi: 10.1002/stem.1870.

PMID:
25336442
14.

Toward better benchmarking: challenge-based methods assessment in cancer genomics.

Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G.

Genome Biol. 2014 Sep 17;15(9):462. doi: 10.1186/s13059-014-0462-7.

15.

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. 2014 Oct 14;9(10):e109569. doi: 10.1371/journal.pone.0109569. eCollection 2014.

16.

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. 2014 Oct 9;159(2):402-14. doi: 10.1016/j.cell.2014.09.021.

PMID:
25303533
17.

Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats.

Repunte-Canonigo V, Lefebvre C, George O, Kawamura T, Morales M, Koob GF, Califano A, Masliah E, Sanna PP.

Mol Neurodegener. 2014 Jul 1;9:26. doi: 10.1186/1750-1326-9-26.

18.

Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.

Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, Eastham JA, Gopalan A, Pienta KJ, Shen MM, Califano A, Abate-Shen C.

Cancer Cell. 2014 May 12;25(5):638-51. doi: 10.1016/j.ccr.2014.03.017.

PMID:
24823640
19.

RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue.

Califano A, Kellis M, Stolovitzky G.

J Comput Biol. 2014 May;21(5):371-2. doi: 10.1089/cmb.2014.009p. No abstract available.

PMID:
24784777
20.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

PMID:
24670764
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