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Items: 1 to 50 of 212

1.

Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.

Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ.

Curr Opin Genet Dev. 2019 Jul 6;54:110-117. doi: 10.1016/j.gde.2019.04.005. [Epub ahead of print] Review.

PMID:
31288129
2.

A Fast and Flexible Framework for Network-Assisted Genomic Association.

Carlin DE, Fong SH, Qin Y, Jia T, Huang JK, Bao B, Zhang C, Ideker T.

iScience. 2019 Jun 28;16:155-161. doi: 10.1016/j.isci.2019.05.025. Epub 2019 May 24.

3.

Identifying Epistasis in Cancer Genomes: A Delicate Affair.

van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T.

Cell. 2019 May 30;177(6):1375-1383. doi: 10.1016/j.cell.2019.05.005. Review.

PMID:
31150618
4.

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA.

Nat Commun. 2019 May 29;10(1):2415. doi: 10.1038/s41467-019-10557-7.

5.

Rare variant phasing using paired tumor:normal sequence data.

Buckley AR, Ideker T, Carter H, Schork NJ.

BMC Bioinformatics. 2019 May 27;20(1):265. doi: 10.1186/s12859-019-2753-1.

6.

Transcriptional responses to DNA damage.

Silva E, Ideker T.

DNA Repair (Amst). 2019 Jul;79:40-49. doi: 10.1016/j.dnarep.2019.05.002. Epub 2019 May 7. Review.

PMID:
31102970
7.

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA.

Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Erratum in: Nat Commun. 2019 May 29;10(1):2415.

8.

Strategies for Network GWAS Evaluated Using Classroom Crowd Science.

Fong SH, Carlin DE, Ozturk K; 2018 UCSD Network Biology Class, Ideker T.

Cell Syst. 2019 Apr 24;8(4):275-280. doi: 10.1016/j.cels.2019.03.013.

PMID:
31022372
9.

A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.

Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T.

Cell. 2019 Apr 18;177(3):572-586.e22. doi: 10.1016/j.cell.2019.03.010. Epub 2019 Apr 4.

PMID:
30955884
10.

DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.

Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T.

Cell Syst. 2019 Mar 27;8(3):267-273.e3. doi: 10.1016/j.cels.2019.02.003. Epub 2019 Mar 13.

PMID:
30878356
11.

Classifying tumors by supervised network propagation.

Zhang W, Ma J, Ideker T.

Bioinformatics. 2019 Jul;35(14):2528. doi: 10.1093/bioinformatics/bty1072. Epub 2019 Feb 4. No abstract available.

12.

A Blueprint for Systems Biology.

Ideker T, Hood L.

Clin Chem. 2019 Feb;65(2):342-344. doi: 10.1373/clinchem.2018.291062. Epub 2018 Dec 28. Review. No abstract available.

PMID:
30593465
13.

Typing tumors using pathways selected by somatic evolution.

Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T.

Nat Commun. 2018 Oct 8;9(1):4159. doi: 10.1038/s41467-018-06464-y.

14.

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences.

Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD.

Mol Cell. 2018 Sep 20;71(6):882-895. doi: 10.1016/j.molcel.2018.08.008. Review.

15.

Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas.

Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ.

Genome Med. 2018 Sep 14;10(1):69. doi: 10.1186/s13073-018-0579-5.

16.

Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network.

Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ.

Cancer Discov. 2018 Nov;8(11):1474-1489. doi: 10.1158/2159-8290.CD-17-1018. Epub 2018 Sep 12.

PMID:
30209081
17.

Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism.

van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F.

Nucleic Acids Res. 2018 Nov 30;46(21):11251-11261. doi: 10.1093/nar/gky801.

18.

On entropy and information in gene interaction networks.

Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R.

Bioinformatics. 2019 Mar 1;35(5):815-822. doi: 10.1093/bioinformatics/bty691.

PMID:
30102349
19.

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.

Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ.

Cell. 2018 Jul 26;174(3):505-520. doi: 10.1016/j.cell.2018.06.016. Review.

20.

The Cytoscape Automation app article collection.

Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T.

F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018.

21.

Classifying tumors by supervised network propagation.

Zhang W, Ma J, Ideker T.

Bioinformatics. 2018 Jul 1;34(13):i484-i493. doi: 10.1093/bioinformatics/bty247. Erratum in: Bioinformatics. 2019 Feb 4;35(14):2528.

22.

Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls.

Shen JP, Ideker T.

J Mol Biol. 2018 Sep 14;430(18 Pt A):2900-2912. doi: 10.1016/j.jmb.2018.06.026. Epub 2018 Jun 20. Review.

PMID:
29932943
23.

Visible Machine Learning for Biomedicine.

Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T.

Cell. 2018 Jun 14;173(7):1562-1565. doi: 10.1016/j.cell.2018.05.056.

24.

Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation.

Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T.

Mol Cancer Ther. 2018 Jul;17(7):1585-1594. doi: 10.1158/1535-7163.MCT-17-0937. Epub 2018 Apr 10.

25.

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T.

Nat Genet. 2018 Apr;50(4):613-620. doi: 10.1038/s41588-018-0091-2. Epub 2018 Apr 2.

26.

pyNBS: a Python implementation for network-based stratification of tumor mutations.

Huang JK, Jia T, Carlin DE, Ideker T.

Bioinformatics. 2018 Aug 15;34(16):2859-2861. doi: 10.1093/bioinformatics/bty186.

27.

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes.

Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T.

Cell Syst. 2018 Apr 25;6(4):484-495.e5. doi: 10.1016/j.cels.2018.03.001. Epub 2018 Mar 28.

28.

Using deep learning to model the hierarchical structure and function of a cell.

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T.

Nat Methods. 2018 Apr;15(4):290-298. doi: 10.1038/nmeth.4627. Epub 2018 Mar 5.

29.

The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins.

Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY.

Mol Cell. 2018 Mar 1;69(5):915. doi: 10.1016/j.molcel.2018.02.014. No abstract available.

30.

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression.

Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J.

Version 2. F1000Res. 2017 Jun 6 [revised 2018 Jan 1];6:784. doi: 10.12688/f1000research.11616.2. eCollection 2017.

31.

Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis.

Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P.

Mol Cell. 2018 Feb 15;69(4):699-708.e7. doi: 10.1016/j.molcel.2018.01.017.

32.

Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping.

Jaeger PA, Ornelas L, McElfresh C, Wong LR, Hampton RY, Ideker T.

Mol Cell. 2018 Jan 18;69(2):321-333.e3. doi: 10.1016/j.molcel.2017.12.016.

33.

The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins.

Neal S, Jaeger PA, Duttke SH, Benner C, K Glass C, Ideker T, Hampton RY.

Mol Cell. 2018 Jan 18;69(2):306-320.e4. doi: 10.1016/j.molcel.2017.12.012. Erratum in: Mol Cell. 2018 Mar 1;69(5):915.

34.

Annotating gene sets by mining large literature collections with protein networks.

Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T.

Pac Symp Biocomput. 2018;23:602-613.

35.

Correcting CRISPR for copy number.

Shen JP, Ideker T.

Nat Genet. 2017 Nov 29;49(12):1674-1675. doi: 10.1038/ng.3994.

PMID:
29186130
36.

MHC-I Genotype Restricts the Oncogenic Mutational Landscape.

Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H.

Cell. 2017 Nov 30;171(6):1272-1283.e15. doi: 10.1016/j.cell.2017.09.050. Epub 2017 Oct 26.

37.

NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T.

Cancer Res. 2017 Nov 1;77(21):e58-e61. doi: 10.1158/0008-5472.CAN-17-0606.

38.

Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia.

Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI.

Nat Commun. 2017 Nov 1;8(1):1238. doi: 10.1038/s41467-017-01439-x.

39.

ndexr-an R package to interface with the network data exchange.

Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F.

Bioinformatics. 2018 Feb 15;34(4):716-717. doi: 10.1093/bioinformatics/btx683.

40.

Network propagation in the cytoscape cyberinfrastructure.

Carlin DE, Demchak B, Pratt D, Sage E, Ideker T.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005598. doi: 10.1371/journal.pcbi.1005598. eCollection 2017 Oct.

41.

Network approaches and applications in biology.

Ideker T, Nussinov R.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005771. doi: 10.1371/journal.pcbi.1005771. eCollection 2017 Oct. No abstract available.

42.

Common genetic variation in the germline influences where and how tumors develop.

Carter H, Ideker T.

Mol Cell Oncol. 2017 Mar 10;4(3):e1302905. doi: 10.1080/23723556.2017.1302905. eCollection 2017.

43.

Network propagation: a universal amplifier of genetic associations.

Cowen L, Ideker T, Raphael BJ, Sharan R.

Nat Rev Genet. 2017 Sep;18(9):551-562. doi: 10.1038/nrg.2017.38. Epub 2017 Jun 12. Review.

PMID:
28607512
44.

Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ.

BMC Genomics. 2017 Jun 12;18(1):458. doi: 10.1186/s12864-017-3770-y.

45.

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

Farré JC, Kramer M, Ideker T, Subramani S.

Autophagy. 2017 Jul 3;13(7):1248-1249. doi: 10.1080/15548627.2017.1313946. Epub 2017 May 9.

46.

Genetic interaction mapping in mammalian cells using CRISPR interference.

Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ.

Nat Methods. 2017 Jun;14(6):577-580. doi: 10.1038/nmeth.4286. Epub 2017 May 8.

47.

Systems biology guided by XCMS Online metabolomics.

Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G.

Nat Methods. 2017 Apr 27;14(5):461-462. doi: 10.1038/nmeth.4260. No abstract available.

48.

Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment.

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T.

Genome Biol. 2017 Mar 28;18(1):57. doi: 10.1186/s13059-017-1186-2.

49.

Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions.

Cole JJ, Robertson NA, Rather MI, Thomson JP, McBryan T, Sproul D, Wang T, Brock C, Clark W, Ideker T, Meehan RR, Miller RA, Brown-Borg HM, Adams PD.

Genome Biol. 2017 Mar 28;18(1):58. doi: 10.1186/s13059-017-1185-3.

50.

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P.

Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225. Epub 2017 Mar 20.

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