| Year |
Citation |
Score |
| 2023 |
Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser M, Zhou Y, Guiley KZ, Chan U, ... ... Ideker T, et al. A foundational atlas of autism protein interactions reveals molecular convergence. Biorxiv : the Preprint Server For Biology. PMID 38076945 DOI: 10.1101/2023.12.03.569805 |
0.343 |
|
| 2021 |
Fong SH, Munson BP, Ideker T. Uncovering Tumorigenesis Circuitry with Combinatorial CRISPR. Cancer Research. 81: 6078-6079. PMID 34911780 DOI: 10.1158/0008-5472.CAN-21-3672 |
0.305 |
|
| 2020 |
Silva E, Michaca M, Munson B, Bean GJ, Jaeger PA, Licon K, Winzeler EA, Ideker T. Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. G3 (Bethesda, Md.). PMID 32732306 DOI: 10.1534/G3.120.401417 |
0.745 |
|
| 2020 |
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, ... ... Ideker T, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. PMID 32353859 DOI: 10.1038/S41586-020-2286-9 |
0.336 |
|
| 2020 |
Sun SM, Batté A, Tittel-Elmer M, van der Horst S, van Welsem T, Bean G, Ideker T, van Leeuwen F, van Attikum H. A genetic interaction map centered on cohesin reveals auxiliary factors in sister chromatid cohesion. Journal of Cell Science. PMID 32299836 DOI: 10.1242/Jcs.237628 |
0.443 |
|
| 2020 |
Jia T, Munson B, Lango Allen H, Ideker T, Majithia AR. Thousands of missing variants in the UK Biobank are recoverable by genome realignment. Annals of Human Genetics. 84: 214-220. PMID 32232836 DOI: 10.1111/Ahg.12383 |
0.311 |
|
| 2020 |
Kuenzi BM, Ideker T. A census of pathway maps in cancer systems biology. Nature Reviews. Cancer. PMID 32066900 DOI: 10.1038/S41568-020-0240-7 |
0.355 |
|
| 2020 |
Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, et al. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nature Communications. 11: 781. PMID 32034123 DOI: 10.1038/S41467-020-14500-Z |
0.317 |
|
| 2020 |
Zheng F, Ono K, Silva E, Swaney D, Kim M, Shangguan J, Pratt D, Nan X, Krogan N, Ideker T. Abstract PR14: A multiscale map of recurrently mutated systems in cancer Cancer Research. 80. DOI: 10.1158/1538-7445.Camodels2020-Pr14 |
0.358 |
|
| 2020 |
Kratz A, Zheng F, Kyu M, Krogan N, Ideker T. Abstract PHB03: A hierarchical model of DNA repair inferred from omics-scale genetic interaction data reveals the dynamics of DNA damage induction Cancer Research. 80. DOI: 10.1158/1538-7445.Camodels2020-Phb03 |
0.404 |
|
| 2020 |
Gordan JD, Pitea A, Eckhardt M, Jang G, Turnham RE, Choi ALM, Dollen JV, Lim HC, Thayer EF, Kelley RK, Swaney DL, Zhang W, Theis FJ, Ideker T, Krogan NJ. Abstract 4891: Hepatitis B virus remodels host protein interaction networks to generate distinct cellular dependencies Cancer Research. 80: 4891-4891. DOI: 10.1158/1538-7445.Am2020-4891 |
0.367 |
|
| 2020 |
Kuenzi BM, Park J, Fong S, Sanchez K, Kreisberg J, Ma J, Ideker T. Abstract 1925: DrugCell: A visible neural network to guide personalized medicine Cancer Research. 80: 1925-1925. DOI: 10.1158/1538-7445.Am2020-1925 |
0.358 |
|
| 2020 |
Kreisberg JF, Ideker T, Meric-Bernstam F, Mills G. Prospecting whole cancer genomes Nature Cancer. 1: 273-275. DOI: 10.1038/S43018-020-0045-3 |
0.304 |
|
| 2019 |
Licon K, Shen JP, Munson BP, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. Methods in Molecular Biology (Clifton, N.J.). 2049: 73-85. PMID 31602605 DOI: 10.1007/978-1-4939-9736-7_4 |
0.429 |
|
| 2019 |
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, ... ... Ideker T, et al. Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Cell Reports. 28: 2317-2330.e8. PMID 31461649 DOI: 10.1016/J.Celrep.2019.07.063 |
0.359 |
|
| 2019 |
Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Current Opinion in Genetics & Development. 54: 110-117. PMID 31288129 DOI: 10.1016/J.Gde.2019.04.005 |
0.406 |
|
| 2019 |
Carlin DE, Fong SH, Qin Y, Jia T, Huang JK, Bao B, Zhang C, Ideker T. A Fast and Flexible Framework for Network-Assisted Genomic Association. Iscience. 16: 155-161. PMID 31174177 DOI: 10.1016/J.Isci.2019.05.025 |
0.412 |
|
| 2019 |
van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T. Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell. 177: 1375-1383. PMID 31150618 DOI: 10.1016/J.Cell.2019.05.005 |
0.31 |
|
| 2019 |
Buckley AR, Ideker T, Carter H, Schork NJ. Rare variant phasing using paired tumor:normal sequence data. Bmc Bioinformatics. 20: 265. PMID 31132991 DOI: 10.1186/S12859-019-2753-1 |
0.328 |
|
| 2019 |
Silva E, Ideker T. Transcriptional responses to DNA damage. Dna Repair. 79: 40-49. PMID 31102970 DOI: 10.1016/J.Dnarep.2019.05.002 |
0.302 |
|
| 2019 |
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, ... ... Ideker T, et al. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nature Communications. 10: 2188. PMID 31097695 DOI: 10.1038/S41467-019-09937-W |
0.315 |
|
| 2019 |
Fong SH, Carlin DE, Ideker T. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Systems. 8: 275-280. PMID 31022372 DOI: 10.1016/J.Cels.2019.03.013 |
0.346 |
|
| 2019 |
Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Systems. PMID 30878356 DOI: 10.1016/J.Cels.2019.02.003 |
0.388 |
|
| 2019 |
Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R. On entropy and information in gene interaction networks. Bioinformatics (Oxford, England). 35: 815-822. PMID 30102349 DOI: 10.1093/Bioinformatics/Bty691 |
0.366 |
|
| 2019 |
Kim M, Kim K, Tutuncuoglu B, Soucheray M, Swaney D, Zheng F, Park J, O'Leary P, Coppé J, Veer Lv', Ashworth A, Ideker T, Krogan N. Abstract P6-06-01: Analyzing the physical and functional protein interaction landscape of breast cancer Cancer Research. 79. DOI: 10.1158/1538-7445.Sabcs18-P6-06-01 |
0.436 |
|
| 2019 |
Kuenzi BM, Park J, Fong S, Kreisberg J, Ideker T. Abstract C006: DrugCell: A visible neural network to guide precision medicine Molecular Cancer Therapeutics. 18. DOI: 10.1158/1535-7163.Targ-19-C006 |
0.376 |
|
| 2018 |
Ideker T, Hood L. A Blueprint for Systems Biology. Clinical Chemistry. PMID 30593465 DOI: 10.1373/Clinchem.2018.291062 |
0.51 |
|
| 2018 |
Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. Typing tumors using pathways selected by somatic evolution. Nature Communications. 9: 4159. PMID 30297789 DOI: 10.1038/S41467-018-06464-Y |
0.39 |
|
| 2018 |
Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ. Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. Genome Medicine. 10: 69. PMID 30217226 DOI: 10.1186/S13073-018-0579-5 |
0.307 |
|
| 2018 |
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, et al. Multiple Routes to Oncogenesis are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discovery. PMID 30209081 DOI: 10.1158/2159-8290.Cd-17-1018 |
0.365 |
|
| 2018 |
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, et al. Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Research. PMID 30203048 DOI: 10.1093/Nar/Gky801 |
0.73 |
|
| 2018 |
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, ... ... Ideker T, et al. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 174: 505-520. PMID 30053424 DOI: 10.1016/J.Cell.2018.06.016 |
0.376 |
|
| 2018 |
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. The Cytoscape Automation app article collection. F1000research. 7: 800. PMID 29983926 DOI: 10.12688/F1000Research.15355.1 |
0.309 |
|
| 2018 |
Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. Journal of Molecular Biology. PMID 29932943 DOI: 10.1016/J.Jmb.2018.06.026 |
0.411 |
|
| 2018 |
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. Disruption of NSD1 in head and neck cancer promotes favorable chemotherapeutic responses linked to hypomethylation. Molecular Cancer Therapeutics. PMID 29636367 DOI: 10.1158/1535-7163.Mct-17-0937 |
0.308 |
|
| 2018 |
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, ... ... Ideker T, et al. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nature Genetics. PMID 29610481 DOI: 10.1038/S41588-018-0091-2 |
0.489 |
|
| 2018 |
Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Systems. PMID 29605183 DOI: 10.1016/J.Cels.2018.03.001 |
0.402 |
|
| 2018 |
Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell. Nature Methods. PMID 29505029 DOI: 10.1038/Nmeth.4627 |
0.344 |
|
| 2018 |
Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Molecular Cell. 69: 915. PMID 29499140 DOI: 10.1016/j.molcel.2018.02.014 |
0.7 |
|
| 2018 |
Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Molecular Cell. 69: 699-708.e7. PMID 29452643 DOI: 10.1016/J.Molcel.2018.01.017 |
0.361 |
|
| 2018 |
Jaeger PA, Ornelas L, McElfresh C, Wong LR, Hampton RY, Ideker T. Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. Molecular Cell. 69: 321-333.e3. PMID 29351850 DOI: 10.1016/J.Molcel.2017.12.016 |
0.768 |
|
| 2018 |
Neal S, Jaeger PA, Duttke SH, Benner CK, Glass C, Ideker T, Hampton R. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Molecular Cell. 69: 306-320.e4. PMID 29351849 DOI: 10.1016/J.Molcel.2017.12.012 |
0.723 |
|
| 2018 |
Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T. Annotating gene sets by mining large literature collections with protein networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 602-613. PMID 29218918 |
0.319 |
|
| 2018 |
Carlin DE, Kim F, Ideker T, Mesirov JP. A unified GenomeSpace recipe to identify essential genes and associated subnetworks from Genome-Scale CRISPR-Cas9 knockout screens F1000research. 7: 1636. DOI: 10.12688/F1000Research.16290.1 |
0.363 |
|
| 2018 |
Ideker T. Abstract PL02-04: Decoding patient genomes through the hierarchical pathway architecture of the cancer cell Cancer Research. 78. DOI: 10.1158/1538-7445.Am2018-Pl02-04 |
0.355 |
|
| 2018 |
Shen JP, Zhao D, Munson B, Birmingham A, Sasik R, Bojorquez-Gomez A, Licon K, Klepper K, Beckett A, Sanchez KS, Mali P, Ideker T. Abstract 3299: High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent Cancer Research. 78: 3299-3299. DOI: 10.1158/1538-7445.Am2018-3299 |
0.443 |
|
| 2018 |
Zheng F, Yu MK, Kim M, Ono K, Flagg M, Kreisberg JF, Krogan N, Ideker T. Abstract 1317: Multi-scale mapping of the physical and functional architecture of the cancer cell Cancer Research. 78: 1317-1317. DOI: 10.1158/1538-7445.Am2018-1317 |
0.367 |
|
| 2018 |
Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. Abstract 1310: Systematic evaluation of gene networks for discovery of disease genes Cancer Research. 78: 1310-1310. DOI: 10.1158/1538-7445.Am2018-1310 |
0.393 |
|
| 2017 |
Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000research. 6: 784. PMID 29487738 DOI: 10.12688/F1000Research.11616.1 |
0.368 |
|
| 2017 |
Shen JP, Ideker T. Correcting CRISPR for copy number. Nature Genetics. 49: 1674-1675. PMID 29186130 DOI: 10.1038/Ng.3994 |
0.329 |
|
| 2017 |
Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Cancer Research. 77: e58-e61. PMID 29092941 DOI: 10.1158/0008-5472.Can-17-0606 |
0.325 |
|
| 2017 |
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, et al. Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. Nature Communications. 8: 1238. PMID 29089570 DOI: 10.1038/S41467-017-01439-X |
0.4 |
|
| 2017 |
Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F. ndexr - an R package to interface with the Network Data Exchange. Bioinformatics (Oxford, England). PMID 29087446 DOI: 10.1093/Bioinformatics/Btx683 |
0.336 |
|
| 2017 |
Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. Plos Computational Biology. 13: e1005598. PMID 29023449 DOI: 10.1371/Journal.Pcbi.1005598 |
0.368 |
|
| 2017 |
Ideker T, Nussinov R. Network approaches and applications in biology. Plos Computational Biology. 13: e1005771. PMID 29023447 DOI: 10.1371/Journal.Pcbi.1005771 |
0.312 |
|
| 2017 |
Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nature Reviews. Genetics. PMID 28607512 DOI: 10.1038/Nrg.2017.38 |
0.41 |
|
| 2017 |
Farré JC, Kramer M, Ideker T, Subramani S. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy. 0. PMID 28486053 DOI: 10.1080/15548627.2017.1313946 |
0.322 |
|
| 2017 |
Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nature Methods. PMID 28481362 DOI: 10.1038/Nmeth.4286 |
0.442 |
|
| 2017 |
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, ... ... Ideker T, et al. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nature Methods. PMID 28319113 DOI: 10.1038/Nmeth.4225 |
0.426 |
|
| 2017 |
Carter H, Marty R, Hofree M, Gross A, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo G, Gutkind S, ... Ideker T, et al. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discovery. PMID 28188128 DOI: 10.1158/2159-8290.Cd-16-1045 |
0.363 |
|
| 2017 |
Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Molecular Cell. PMID 28132844 DOI: 10.1016/J.Molcel.2016.12.024 |
0.384 |
|
| 2017 |
Shen JP, Bojorquez-Gomez A, Huang J, Hofree M, Kurnit K, Klepper K, Beckett A, Kreisberg JF, Saenz CC, Ideker T. A platinum-resistant subtype of high-grade serous ovarian cancer identified by a network of somatic mutations. Journal of Clinical Oncology. 35: 5561-5561. DOI: 10.1200/Jco.2017.35.15_Suppl.5561 |
0.332 |
|
| 2017 |
Shen JP, Bojorquez-Gomez A, Huang J, Hofree M, Klepper K, Beckett A, Saenz C, Kreisberg J, Ideker T. Abstract AP23: A PLATINUM–RESISTANT SUBTYPE OF HIGH–GRADE SEROUS OVARIAN CANCER IDENTIFIED BY A NETWORK OF SOMATIC MUTATIONS Clinical Cancer Research. 23. DOI: 10.1158/1557-3265.Ovcasymp16-Ap23 |
0.34 |
|
| 2017 |
Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Kreisberg J, Ideker T, Mali P. Abstract PR08: Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Pr08 |
0.42 |
|
| 2017 |
Ideker T. Abstract IA16: Systematic mapping and modeling of genetic interaction networks in cancer cells Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Ia16 |
0.423 |
|
| 2017 |
Shen JP, Zhao D, Sasik R, Luebeck J, Bojorquez-Gomez A, Licon K, Ideker T, Mali P. Abstract 3039: Combinatorial CRISPR-Cas9 gene knockout to enable genetic interaction mapping in human cells Cancer Research. 77: 3039-3039. DOI: 10.1158/1538-7445.Am2017-3039 |
0.388 |
|
| 2016 |
Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proceedings of the National Academy of Sciences of the United States of America. PMID 27638202 DOI: 10.1073/Pnas.1608077113 |
0.34 |
|
| 2016 |
Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, ... ... Ideker T, et al. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Molecular Cell. PMID 27453043 DOI: 10.1016/J.Molcel.2016.06.022 |
0.768 |
|
| 2016 |
Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exome sequencing data. Nature Communications. 7: 12096. PMID 27417679 DOI: 10.1038/Ncomms12096 |
0.55 |
|
| 2016 |
Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hofree M, Huang R, ... ... Ideker T, et al. Erratum to: Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Molecular Neurodegeneration. 11: 42. PMID 27216421 DOI: 10.1186/S13024-016-0105-4 |
0.757 |
|
| 2016 |
Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hoffree M, Huang R, ... ... Ideker T, et al. Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Molecular Neurodegeneration. 11: 31. PMID 27112350 DOI: 10.1186/S13024-016-0095-2 |
0.765 |
|
| 2016 |
Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Molecular Cell. 62: 157-168. PMID 27105112 DOI: 10.1016/J.Molcel.2016.03.019 |
0.708 |
|
| 2016 |
Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. International Journal of Cancer. PMID 26949921 DOI: 10.1002/Ijc.30081 |
0.324 |
|
| 2016 |
Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Systems. 2: 77-88. PMID 26949740 DOI: 10.1016/J.Cels.2016.02.003 |
0.751 |
|
| 2016 |
Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, ... ... Ideker T, et al. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods. PMID 26780094 DOI: 10.1038/Nmeth.3732 |
0.304 |
|
| 2016 |
Shen JP, Srivas R, Yang CC, Sun SM, Li JF, Gross A, Jensen J, Licon K, Bojoquez-Gomez A, Klepper K, Attikum Hv, Aza-Blanc P, Sobol R, Ideker T. Abstract NG02: A network of deeply conserved synthetic-lethal interactions for exploration of precision cancer therapy Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Ng02 |
0.792 |
|
| 2016 |
Zhang W, Ideker T, Pathways. Abstract LB-068: Classification of cancer by synthesis of rare non-coding mutations within recurrent epigenetic and protein networks Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-068 |
0.36 |
|
| 2015 |
Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. Evidence for a common evolutionary rate in metazoan transcriptional networks. Elife. 4. PMID 26682651 DOI: 10.7554/Elife.11615 |
0.558 |
|
| 2015 |
Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobrin R, Braxenthaler M, Kuentzer J, Demchak B, ... Ideker T, et al. NDEx, the Network Data Exchange. Cell Systems. 1: 302-305. PMID 26594663 DOI: 10.1016/J.Cels.2015.10.001 |
0.351 |
|
| 2015 |
Gross AM, Kreisberg JF, Ideker T. Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types. Plos One. 10: e0142618. PMID 26555223 DOI: 10.1371/Journal.Pone.0142618 |
0.34 |
|
| 2015 |
Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, ... ... Ideker T, et al. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. PMID 26437225 DOI: 10.18632/Oncotarget.5928 |
0.748 |
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| 2015 |
Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. Journal of Proteome Research. PMID 26435392 DOI: 10.1021/Acs.Jproteome.5B00827 |
0.48 |
|
| 2015 |
Gross AM, Ideker T. Molecular networks in context. Nature Biotechnology. 33: 720-1. PMID 26154012 DOI: 10.1038/Nbt.3283 |
0.331 |
|
| 2015 |
Till A, Saito R, Merkurjev D, Liu JJ, Syed GH, Kolnik M, Siddiqui A, Glas M, Scheffler B, Ideker T, Subramani S. Evolutionary trends and functional anatomy of the human expanded autophagy network. Autophagy. 0. PMID 26103419 DOI: 10.1080/15548627.2015.1059558 |
0.433 |
|
| 2015 |
Jaeger PA, McElfresh C, Wong LR, Ideker T. Beyond agar: gel substrates for microbial growth experiments with improved optical clarity and drug efficiency and reduced autofluorescence. Applied and Environmental Microbiology. PMID 26070672 DOI: 10.1128/Aem.01327-15 |
0.724 |
|
| 2015 |
Roosing S, Hofree M, Kim S, Scott E, Copeland B, Romani M, Silhavy JL, Rosti RO, Schroth J, Mazza T, Miccinilli E, Zaki MS, Swoboda KJ, Milisa-Drautz J, Dobyns WB, ... ... Ideker T, et al. Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife. 4. PMID 26026149 DOI: 10.7554/Elife.06602 |
0.338 |
|
| 2015 |
Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The Cancer Cell Map Initiative: Defining the Hallmark Networks of Cancer. Molecular Cell. 58: 690-698. PMID 26000852 DOI: 10.1016/J.Molcel.2015.05.008 |
0.379 |
|
| 2015 |
Lau E, Sedy J, Sander C, Shaw MA, Feng Y, Scortegagna M, Claps G, Robinson S, Cheng P, Srivas R, Soonthornvacharin S, Ideker T, Bosenberg M, Gonzalez R, Robinson W, et al. Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy. Oncogene. PMID 25728676 DOI: 10.1038/Onc.2015.22 |
0.72 |
|
| 2015 |
Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM. Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Molecular Cell. 57: 273-89. PMID 25533186 DOI: 10.1016/J.Molcel.2014.11.016 |
0.747 |
|
| 2015 |
Carvunis A, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. Author response: Evidence for a common evolutionary rate in metazoan transcriptional networks Elife. DOI: 10.7554/Elife.11615.062 |
0.544 |
|
| 2015 |
Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Yeerna H, Gross A, Li JF, Sobol R, Ideker T. Abstract 129: RAD17 loss of function is synthetically lethal with the checkpoint kinase inhibitors AZD7762 or MK-1775 Cancer Research. 75: 129-129. DOI: 10.1158/1538-7445.Am2015-129 |
0.744 |
|
| 2015 |
Ideker T. Abstract CN05-01: The Cancer Cell Map Initiative: Mapping molecular networks for tumor stratification and treatment Molecular Cancer Therapeutics. 14. DOI: 10.1158/1535-7163.Targ-15-Cn05-01 |
0.373 |
|
| 2014 |
Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000research. 3: 143. PMID 25520778 DOI: 10.12688/F1000Research.4510.2 |
0.312 |
|
| 2014 |
Lee K, Sung MK, Kim J, Kim K, Byun J, Paik H, Kim B, Huh WK, Ideker T. Proteome-wide remodeling of protein location and function by stress. Proceedings of the National Academy of Sciences of the United States of America. 111: E3157-66. PMID 25028499 DOI: 10.1073/Pnas.1318881111 |
0.378 |
|
| 2014 |
Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics (Oxford, England). 30: i34-42. PMID 24932003 DOI: 10.1093/Bioinformatics/Btu282 |
0.325 |
|
| 2014 |
Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T. An integrated map of HIV-human protein complexes that facilitate viral infection. Plos One. 9: e96687. PMID 24817247 DOI: 10.1371/Journal.Pone.0096687 |
0.364 |
|
| 2014 |
Carvunis AR, Ideker T. Siri of the cell: what biology could learn from the iPhone. Cell. 157: 534-8. PMID 24766803 DOI: 10.1016/J.Cell.2014.03.009 |
0.389 |
|
| 2014 |
Novarino G, Fenstermaker AG, Zaki MS, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel-Salam GM, Karminejad A, ... ... Ideker T, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science (New York, N.Y.). 343: 506-11. PMID 24482476 DOI: 10.1126/Science.1247363 |
0.361 |
|
| 2014 |
Bean GJ, Jaeger PA, Bahr S, Ideker T. Development of ultra-high-density screening tools for microbial "omics". Plos One. 9: e85177. PMID 24465499 DOI: 10.1371/Journal.Pone.0085177 |
0.761 |
|
| 2014 |
Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Research. 42: D1269-74. PMID 24271398 DOI: 10.1093/Nar/Gkt1192 |
0.366 |
|
| 2014 |
Srivas R, Shen JP, Li JF, Licon K, Wang ZZ, Bojoquez-Gomez A, Xu L, Gross A, Bean G, Sobol R, Ideker T. Abstract B34: High-throughput synthetic lethal interaction screening in model organisms as a strategy for the identification of novel therapeutic targets in cancer Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Modorg-B34 |
0.757 |
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| 2014 |
Hofree M, Shen JPY, Ideker T. Abstract 369: Network-based stratification of thyroid cancer Cancer Research. 74: 369-369. DOI: 10.1158/1538-7445.Am2014-369 |
0.362 |
|
| 2013 |
Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T. A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. Cell Reports. 5: 1714-24. PMID 24360959 DOI: 10.1016/J.Celrep.2013.11.035 |
0.768 |
|
| 2013 |
Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Current Opinion in Genetics & Development. 23: 611-21. PMID 24238873 DOI: 10.1016/J.Gde.2013.10.003 |
0.399 |
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| 2013 |
Potts MB, Kim HS, Fisher KW, Hu Y, Carrasco YP, Bulut GB, Ou YH, Herrera-Herrera ML, Cubillos F, Mendiratta S, Xiao G, Hofree M, Ideker T, Xie Y, Huang LJ, et al. Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Science Signaling. 6: ra90. PMID 24129700 DOI: 10.1126/Scisignal.2004657 |
0.311 |
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| 2013 |
Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nature Reviews. Genetics. 14: 719-32. PMID 24045689 DOI: 10.1038/Nrg3552 |
0.396 |
|
| 2013 |
Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nature Methods. 10: 1108-15. PMID 24037242 DOI: 10.1038/Nmeth.2651 |
0.356 |
|
| 2013 |
Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... Ideker T, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/Elife.00675 |
0.31 |
|
| 2013 |
Fukuyama H, Verdier Y, Guan Y, Makino-Okamura C, Shilova V, Liu X, Maksoud E, Matsubayashi J, Haddad I, Spirohn K, Ono K, Hetru C, Rossier J, Ideker T, Boutros M, et al. Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proceedings of the National Academy of Sciences of the United States of America. 110: 10717-22. PMID 23749869 DOI: 10.1073/Pnas.1304380110 |
0.398 |
|
| 2013 |
Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, Paek SH, Kim H, Shin HY, Ideker T, Lee B. Proteome-wide discovery of mislocated proteins in cancer. Genome Research. 23: 1283-94. PMID 23674306 DOI: 10.1101/Gr.155499.113 |
0.598 |
|
| 2013 |
Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, et al. Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. Journal of Proteome Research. 12: 2805-17. PMID 23647160 DOI: 10.1021/Pr4001527 |
0.496 |
|
| 2013 |
Chen M, Licon K, Otsuka R, Pillus L, Ideker T. Decoupling epigenetic and genetic effects through systematic analysis of gene position. Cell Reports. 3: 128-37. PMID 23291096 DOI: 10.1016/J.Celrep.2012.12.003 |
0.384 |
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| 2013 |
Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H. Dissection of DNA damage responses using multiconditional genetic interaction maps. Molecular Cell. 49: 346-58. PMID 23273983 DOI: 10.1016/J.Molcel.2012.11.023 |
0.765 |
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| 2013 |
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nature Biotechnology. 31: 38-45. PMID 23242164 DOI: 10.1038/Nbt.2463 |
0.4 |
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| 2013 |
Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Molecular Cell. 49: 359-67. PMID 23177740 DOI: 10.1016/J.Molcel.2012.10.016 |
0.761 |
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| 2013 |
Gross A, Choueiri M, Shen JP, Randall JM, Ideker T, Hofree M. Association of methylation of genes in the taurine/hypotaurine pathway with worse prognosis in renal cell carcinoma. Journal of Clinical Oncology. 31. DOI: 10.1200/Jco.2013.31.15_Suppl.E15562 |
0.313 |
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| 2013 |
Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Li JF, Sobol RW, Ideker T. Cross-species synthetic lethal interaction screening as a strategy for the identification of novel therapeutic targets in cancer. Journal of Clinical Oncology. 31: 11105-11105. DOI: 10.1200/Jco.2013.31.15_Suppl.11105 |
0.771 |
|
| 2013 |
Hofree M, Shen JP, Carter H, Gross A, Ideker T. Abstract A14: Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interaction networks to identify clinically relevant subtypes in high grade serous ovarian carcinoma Clinical Cancer Research. 19. DOI: 10.1158/1078-0432.Ovca13-A14 |
0.395 |
|
| 2012 |
Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biology. 13: R123. PMID 23268787 DOI: 10.1186/Gb-2012-13-12-R123 |
0.383 |
|
| 2012 |
Jaeger PA, Doherty C, Ideker T. Modeling transcriptome dynamics in a complex world. Cell. 151: 1161-2. PMID 23217702 DOI: 10.1016/J.Cell.2012.11.031 |
0.738 |
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| 2012 |
Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O'Connor DT, Ma Q, Smoot M, Ideker T, Hook V. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. Plos One. 7: e41134. PMID 22916103 DOI: 10.1371/Journal.Pone.0041134 |
0.35 |
|
| 2012 |
Choi S, Srivas R, Fu KY, Hood BL, Dost B, Gibson GA, Watkins SC, Van Houten B, Bandeira N, Conrads TP, Ideker T, Bakkenist CJ. Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. Journal of Proteome Research. 11: 4983-91. PMID 22909323 DOI: 10.1021/Pr3005524 |
0.756 |
|
| 2012 |
Chuang HY, Rassenti L, Salcedo M, Licon K, Kohlmann A, Haferlach T, Foà R, Ideker T, Kipps TJ. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood. 120: 2639-49. PMID 22837534 DOI: 10.1182/Blood-2012-03-416461 |
0.555 |
|
| 2012 |
Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics. 44: 841-7. PMID 22836096 DOI: 10.1038/Ng.2355 |
0.351 |
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| 2012 |
Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, ... ... Ideker T, et al. Hierarchical modularity and the evolution of genetic interactomes across species. Molecular Cell. 46: 691-704. PMID 22681890 DOI: 10.1016/J.Molcel.2012.05.028 |
0.441 |
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| 2012 |
Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR, Ideker T, Wittenberg C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. The Embo Journal. 31: 1811-22. PMID 22333915 DOI: 10.1038/Emboj.2012.28 |
0.353 |
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| 2012 |
Ideker T, Krogan NJ. Differential network biology. Molecular Systems Biology. 8: 565. PMID 22252388 DOI: 10.1038/Msb.2011.99 |
0.435 |
|
| 2012 |
Zhang L, Lim SL, Du H, Zhang M, Kozak I, Hannum G, Wang X, Ouyang H, Hughes G, Zhao L, Zhu X, Lee C, Su Z, Zhou X, Shaw R, ... ... Ideker T, et al. High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-β family member growth differentiation factor 6. The Journal of Biological Chemistry. 287: 1520-6. PMID 22049084 DOI: 10.1074/Jbc.M111.275990 |
0.776 |
|
| 2011 |
Atwood A, DeConde R, Wang SS, Mockler TC, Sabir JS, Ideker T, Kay SA. Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proceedings of the National Academy of Sciences of the United States of America. 108: 18560-5. PMID 22042857 DOI: 10.1073/Pnas.1115753108 |
0.321 |
|
| 2011 |
Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. Plos Computational Biology. 7: e1002180. PMID 21980275 DOI: 10.1371/Journal.Pcbi.1002180 |
0.394 |
|
| 2011 |
Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nature Protocols. 6: 1308-23. PMID 21886098 DOI: 10.1038/Nprot.2011.368 |
0.8 |
|
| 2011 |
Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. 144: 860-3. PMID 21414478 DOI: 10.1016/J.Cell.2011.03.007 |
0.435 |
|
| 2011 |
Smoot M, Ono K, Ideker T, Maere S. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics (Oxford, England). 27: 1030-1. PMID 21278188 DOI: 10.1093/Bioinformatics/Btr045 |
0.374 |
|
| 2011 |
Califano A, Butte A, Friend S, Ideker T, Schadt EE. Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era Nature Precedings. DOI: 10.1038/Npre.2011.5732.1 |
0.503 |
|
| 2010 |
Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, ... ... Ideker T, et al. Rewiring of genetic networks in response to DNA damage. Science (New York, N.Y.). 330: 1385-9. PMID 21127252 DOI: 10.1126/Science.1195618 |
0.609 |
|
| 2010 |
Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Research. 20: 1672-8. PMID 20978140 DOI: 10.1101/Gr.111765.110 |
0.642 |
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| 2010 |
Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nature Methods. 7: 801-5. PMID 20936779 DOI: 10.1038/Nmeth.1506 |
0.592 |
|
| 2010 |
Pentchev K, Ono K, Herwig R, Ideker T, Kamburov A. Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics (Oxford, England). 26: 2796-7. PMID 20847220 DOI: 10.1093/Bioinformatics/Btq522 |
0.415 |
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| 2010 |
Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biology. 11: R77. PMID 20653936 DOI: 10.1186/Gb-2010-11-7-R77 |
0.474 |
|
| 2010 |
Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annual Review of Cell and Developmental Biology. 26: 721-44. PMID 20604711 DOI: 10.1146/Annurev-Cellbio-100109-104122 |
0.571 |
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| 2010 |
Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nature Immunology. 11: 635-43. PMID 20543837 DOI: 10.1038/Ni.1891 |
0.319 |
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| 2010 |
Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, Ideker T, Aza-Blanc P, Gleeson JG. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature. 464: 1048-51. PMID 20393563 DOI: 10.1038/Nature08895 |
0.363 |
|
| 2010 |
Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T. Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. The Plant Cell. 22: 997-1005. PMID 20371643 DOI: 10.1105/Tpc.109.072736 |
0.382 |
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| 2010 |
Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, ... ... Ideker T, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140: 744-52. PMID 20211142 DOI: 10.1016/J.Cell.2010.01.044 |
0.566 |
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| 2010 |
König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, ... ... Ideker T, et al. Human host factors required for influenza virus replication. Nature. 463: 813-7. PMID 20027183 DOI: 10.1038/Nature08699 |
0.511 |
|
| 2010 |
van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Research. 20: 190-200. PMID 20007327 DOI: 10.1101/Gr.098822.109 |
0.439 |
|
| 2009 |
Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. Plos Genetics. 5: e1000782. PMID 20041197 DOI: 10.1371/Journal.Pgen.1000782 |
0.805 |
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| 2009 |
Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS. An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 29: 12467-76. PMID 19812322 DOI: 10.1523/Jneurosci.3180-09.2009 |
0.361 |
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| 2009 |
Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, ... ... Ideker T, et al. Evolutionarily conserved herpesviral protein interaction networks. Plos Pathogens. 5: e1000570. PMID 19730696 DOI: 10.1371/Journal.Ppat.1000570 |
0.804 |
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| 2009 |
Kelley R, Ideker T. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. Plos Genetics. 5: e1000488. PMID 19503593 DOI: 10.1371/Journal.Pgen.1000488 |
0.585 |
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| 2009 |
Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, et al. Host cell factors in HIV replication: meta-analysis of genome-wide studies. Plos Pathogens. 5: e1000437. PMID 19478882 DOI: 10.1371/Journal.Ppat.1000437 |
0.553 |
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| 2009 |
Mak HC, Pillus L, Ideker T. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Research. 19: 1014-25. PMID 19372386 DOI: 10.1101/Gr.084178.108 |
0.719 |
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| 2009 |
Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proceedings of the National Academy of Sciences of the United States of America. 106: 6477-82. PMID 19346491 DOI: 10.1073/Pnas.0811091106 |
0.395 |
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| 2009 |
Schwartz AS, Yu J, Gardenour KR, Finley RL, Ideker T. Cost-effective strategies for completing the interactome. Nature Methods. 6: 55-61. PMID 19079254 DOI: 10.1038/Nmeth.1283 |
0.325 |
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| 2009 |
Rocke DM, Ideker T, Troyanskaya O, Quackenbush J, Dopazo J. Papers on normalization, variable selection, classification or clustering of microarray data Bioinformatics. 25: 701-702. DOI: 10.1093/Bioinformatics/Btp038 |
0.301 |
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| 2008 |
Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Molecular Cell. 32: 735-46. PMID 19061648 DOI: 10.1016/J.Molcel.2008.11.012 |
0.557 |
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| 2008 |
Lee E, Chuang HY, Kim JW, Ideker T, Lee D. Inferring pathway activity toward precise disease classification. Plos Computational Biology. 4: e1000217. PMID 18989396 DOI: 10.1371/Journal.Pcbi.1000217 |
0.601 |
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| 2008 |
König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, ... ... Ideker T, et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 135: 49-60. PMID 18854154 DOI: 10.1016/J.Cell.2008.07.032 |
0.539 |
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| 2008 |
Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Research. 36: e136. PMID 18836191 DOI: 10.1093/Nar/Gkn619 |
0.668 |
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| 2008 |
Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science (New York, N.Y.). 322: 405-10. PMID 18818364 DOI: 10.1126/Science.1162609 |
0.588 |
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| 2008 |
Ideker T. Forging new ties between E. coli genes. Cell. 133: 1135-7. PMID 18585345 DOI: 10.1016/J.Cell.2008.06.003 |
0.336 |
|
| 2008 |
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. Plos Computational Biology. 4: e1000065. PMID 18421374 DOI: 10.1371/Journal.Pcbi.1000065 |
0.727 |
|
| 2008 |
Ideker T, Sharan R. Protein networks in disease. Genome Research. 18: 644-52. PMID 18381899 DOI: 10.1101/Gr.071852.107 |
0.392 |
|
| 2008 |
Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. eQED: an efficient method for interpreting eQTL associations using protein networks. Molecular Systems Biology. 4: 162. PMID 18319721 DOI: 10.1038/Msb.2008.4 |
0.818 |
|
| 2008 |
Tan K, Feizi H, Luo C, Fan SH, Ravasi T, Ideker TG. A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proceedings of the National Academy of Sciences of the United States of America. 105: 2934-9. PMID 18287073 DOI: 10.1073/Pnas.0708670105 |
0.493 |
|
| 2008 |
Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. Bioinformatics (Oxford, England). 24: 594-6. PMID 18174180 DOI: 10.1093/Bioinformatics/Btm630 |
0.399 |
|
| 2008 |
Kelley R, Feizi H, Ideker T. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics (Oxford, England). 24: 71-7. PMID 17623705 DOI: 10.1093/Bioinformatics/Btm347 |
0.583 |
|
| 2008 |
Chuang H, Rassenti L, Ideker T, Kipps TJ. Interactome-Based Molecular Prognosis of Chronic Lymphocytic Leukemia Blood. 112: 545-545. DOI: 10.1182/Blood.V112.11.545.545 |
0.63 |
|
| 2007 |
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, ... ... Ideker T, et al. Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. 2: 2366-82. PMID 17947979 DOI: 10.1038/Nprot.2007.324 |
0.77 |
|
| 2007 |
Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Molecular Systems Biology. 3: 140. PMID 17940530 DOI: 10.1038/Msb4100180 |
0.628 |
|
| 2007 |
Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nature Reviews. Genetics. 8: 699-710. PMID 17703239 DOI: 10.1038/Nrg2144 |
0.685 |
|
| 2007 |
Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (Oxford, England). 23: i359-66. PMID 17646318 DOI: 10.1093/bioinformatics/btm170 |
0.338 |
|
| 2007 |
Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, DiRita VJ, Ideker T, Andrews P, Finley RL. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biology. 8: R130. PMID 17615063 DOI: 10.1186/Gb-2007-8-7-R130 |
0.437 |
|
| 2007 |
Ideker TE. Network genomics. Ernst Schering Research Foundation Workshop. 89-115. PMID 17249498 |
0.334 |
|
| 2007 |
Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. Transcriptional regulation of protein complexes within and across species. Proceedings of the National Academy of Sciences of the United States of America. 104: 1283-8. PMID 17227853 DOI: 10.1073/Pnas.0606914104 |
0.587 |
|
| 2007 |
Mak HC, Daly M, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Research. 35: D538-45. PMID 17135207 DOI: 10.1093/Nar/Gkl937 |
0.731 |
|
| 2007 |
Beyer A, Suthram S, Ideker T. Uncovering regulatory pathways with expression quantitative trait loci Gensips'07 - 5th Ieee International Workshop On Genomic Signal Processing and Statistics. DOI: 10.1109/GENSIPS.2007.4365837 |
0.762 |
|
| 2007 |
WARNER G, ADELEYE Y, IDEKER T, WORKMAN C, SCOTT D. Development of a systems approach for the analysis of toxicogenomic data Toxicology. 231: 109-110. DOI: 10.1016/J.Tox.2006.11.034 |
0.517 |
|
| 2007 |
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. Comparison of protein-protein interaction confidence assignment schemes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4023: 39-50. |
0.729 |
|
| 2006 |
Bandyopadhyay S, Kelley R, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 354-66. PMID 17094252 |
0.634 |
|
| 2006 |
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. Bmc Bioinformatics. 7: 360. PMID 16872496 DOI: 10.1186/1471-2105-7-360 |
0.749 |
|
| 2006 |
Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T. Integrated assessment and prediction of transcription factor binding. Plos Computational Biology. 2: e70. PMID 16789814 DOI: 10.1371/Journal.Pcbi.0020070 |
0.747 |
|
| 2006 |
Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, ... ... Ideker T, et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of Biology. 5: 11. PMID 16762047 DOI: 10.1186/Jbiol36 |
0.464 |
|
| 2006 |
Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Molecular Systems Biology. 2: 2006.0004. PMID 16738551 DOI: 10.1038/Msb4100046 |
0.314 |
|
| 2006 |
Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways. Science (New York, N.Y.). 312: 1054-9. PMID 16709784 DOI: 10.1126/Science.1122088 |
0.773 |
|
| 2006 |
Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nature Biotechnology. 24: 427-33. PMID 16601728 DOI: 10.1038/Nbt1196 |
0.385 |
|
| 2006 |
Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting signaling pathways in protein interaction networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 133-44. PMID 16597231 DOI: 10.1089/Cmb.2006.13.133 |
0.382 |
|
| 2006 |
Warner GJ, Adeleye YA, Ideker T. Interactome networks: the state of the science. Genome Biology. 7: 301. PMID 16515723 DOI: 10.1186/Gb-2006-7-1-301 |
0.412 |
|
| 2006 |
Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Research. 16: 428-35. PMID 16510899 DOI: 10.1101/Gr.4526006 |
0.585 |
|
| 2006 |
Ideker T, Winslow LR, Lauffenburger AD. Bioengineering and systems biology. Annals of Biomedical Engineering. 34: 257-64. PMID 16474915 DOI: 10.1007/S10439-005-9047-7 |
0.334 |
|
| 2005 |
Suthram S, Sittler T, Ideker T. The Plasmodium protein network diverges from those of other eukaryotes. Nature. 438: 108-12. PMID 16267557 DOI: 10.1038/Nature04135 |
0.779 |
|
| 2005 |
Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 835-46. PMID 16108720 DOI: 10.1089/Cmb.2005.12.835 |
0.354 |
|
| 2005 |
Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biology. 6: R62. PMID 15998451 DOI: 10.1186/Gb-2005-6-7-R62 |
0.784 |
|
| 2005 |
Hsiao A, Ideker T, Olefsky JM, Subramaniam S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Research. 33: W627-32. PMID 15980550 DOI: 10.1093/Nar/Gki443 |
0.379 |
|
| 2005 |
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Research. 33: W389-92. PMID 15980495 DOI: 10.1093/Nar/Gki439 |
0.518 |
|
| 2005 |
Kelley R, Ideker T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology. 23: 561-6. PMID 15877074 DOI: 10.1038/Nbt1096 |
0.664 |
|
| 2005 |
Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America. 102: 1974-9. PMID 15687504 DOI: 10.1073/Pnas.0409522102 |
0.813 |
|
| 2004 |
Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biology. 5: R95. PMID 15575969 DOI: 10.1186/Gb-2004-5-12-R95 |
0.643 |
|
| 2004 |
Begley TJ, Rosenbach AS, Ideker T, Samson LD. Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Molecular Cell. 16: 117-25. PMID 15469827 DOI: 10.1016/J.Molcel.2004.09.005 |
0.381 |
|
| 2004 |
Yeang CH, Ideker T, Jaakkola T. Physical network models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 243-62. PMID 15285891 DOI: 10.1089/1066527041410382 |
0.417 |
|
| 2004 |
Ideker T. A systems approach to discovering signaling and regulatory pathways--or, how to digest large interaction networks into relevant pieces. Advances in Experimental Medicine and Biology. 547: 21-30. PMID 15230090 DOI: 10.1007/978-1-4419-8861-4_3 |
0.477 |
|
| 2004 |
Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Research. 32: W83-8. PMID 15215356 DOI: 10.1093/Nar/Gkh411 |
0.432 |
|
| 2003 |
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 13: 2498-504. PMID 14597658 DOI: 10.1101/Gr.1239303 |
0.47 |
|
| 2003 |
Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proceedings of the National Academy of Sciences of the United States of America. 100: 11394-9. PMID 14504397 DOI: 10.1073/Pnas.1534710100 |
0.434 |
|
| 2003 |
Ideker T, Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends in Biotechnology. 21: 255-62. PMID 12788545 DOI: 10.1016/S0167-7799(03)00115-X |
0.324 |
|
| 2003 |
Ozier O, Amin N, Ideker T. Global architecture of genetic interactions on the protein network. Nature Biotechnology. 21: 490-1. PMID 12721566 DOI: 10.1038/Nbt0503-490 |
0.412 |
|
| 2003 |
Young ET, Dombek KM, Tachibana C, Ideker T. Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. The Journal of Biological Chemistry. 278: 26146-58. PMID 12676948 DOI: 10.1074/Jbc.M301981200 |
0.371 |
|
| 2002 |
Begley TJ, Rosenbach AS, Ideker T, Samson LD. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping Molecular Cancer Research. 1: 103-112. PMID 12496357 |
0.35 |
|
| 2002 |
Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD. Transcriptome profiling to identify genes involved in peroxisome assembly and function. The Journal of Cell Biology. 158: 259-71. PMID 12135984 DOI: 10.1083/Jcb.200204059 |
0.369 |
|
| 2002 |
Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. 1: 323-33. PMID 12096114 DOI: 10.1074/Mcp.M200001-Mcp200 |
0.535 |
|
| 2001 |
Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annual Review of Genomics and Human Genetics. 2: 343-72. PMID 11701654 DOI: 10.1146/Annurev.Genom.2.1.343 |
0.489 |
|
| 2001 |
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (New York, N.Y.). 292: 929-34. PMID 11340206 DOI: 10.1126/Science.292.5518.929 |
0.562 |
|
| 2000 |
Ideker T, Thorsson V, Siegel AF, Hood LE. Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 805-17. PMID 11382363 DOI: 10.1089/10665270050514945 |
0.506 |
|
| 2000 |
Ideker TE, Thorsson V, Karp RM. Discovery of regulatory interactions through perturbation: inference and experimental design. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 305-16. PMID 10902179 DOI: 10.1142/9789814447331_0029 |
0.306 |
|
| 1999 |
Nelson PS, Hawkins V, Schummer M, Bumgarner R, Ng WL, Ideker T, Ferguson C, Hood L. Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays. Genetic Analysis : Biomolecular Engineering. 15: 209-15. PMID 10609756 DOI: 10.1016/S1050-3862(99)00006-6 |
0.501 |
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