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Items: 1 to 20 of 202

1.

Classifying tumors by supervised network propagation.

Zhang W, Ma J, Ideker T.

Bioinformatics. 2019 Feb 4. doi: 10.1093/bioinformatics/bty1072. [Epub ahead of print] No abstract available.

PMID:
30726869
2.

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
3.

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.

4.

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.

PMID:
30241605
5.

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.

6.

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
7.

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.

8.

On Entropy and Information in Gene Interaction Networks.

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

Bioinformatics. 2018 Aug 9. doi: 10.1093/bioinformatics/bty691. [Epub ahead of print]

PMID:
30102349
9.

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.

PMID:
30053424
10.

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.

11.

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.

12.

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
13.

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.

PMID:
29906441
14.

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.

PMID:
29636367
15.

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.

16.

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.

PMID:
29608663
17.

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.

PMID:
29605183
18.

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.

19.

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.

PMID:
29499140
20.

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.

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