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Items: 1 to 50 of 218

1.

The great hairball gambit.

Flint J, Ideker T.

PLoS Genet. 2019 Nov 26;15(11):e1008519. doi: 10.1371/journal.pgen.1008519. [Epub ahead of print] No abstract available.

2.

DNA methylation aging clocks: challenges and recommendations.

Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK.

Genome Biol. 2019 Nov 25;20(1):249. doi: 10.1186/s13059-019-1824-y. Review.

3.

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 Oct 23;9(4):414. doi: 10.1016/j.cels.2019.09.001. No abstract available.

PMID:
31647918
4.

Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate.

Licon K, Shen JP, Munson BP, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T.

Methods Mol Biol. 2019;2049:73-85. doi: 10.1007/978-1-4939-9736-7_4.

PMID:
31602605
5.

Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention.

Wiesman AI, Rezich MT, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW.

Cereb Cortex. 2019 Sep 5. pii: bhz162. doi: 10.1093/cercor/bhz162. [Epub ahead of print]

PMID:
31504270
6.

Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers.

Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG.

Cell Rep. 2019 Aug 27;28(9):2317-2330.e8. doi: 10.1016/j.celrep.2019.07.063.

7.

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 Feb;54:110-117. doi: 10.1016/j.gde.2019.04.005. Epub 2019 Jul 6. Review.

PMID:
31288129
8.

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.

9.

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.

10.

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.

11.

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.

12.

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
13.

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.

14.

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. Erratum in: Cell Syst. 2019 Oct 23;9(4):414.

15.

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
16.

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
17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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
25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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
42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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
50.

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.

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