Below is a complete list of research published by the Ideker Lab in chronological order. Cover articles, reviews, and book chapters are noted accordingly. Where applicable, associated datasets and press are linked. Visit our Research pages to learn more about our current projects and go here to view select Publication Highlights

Additionally, publications may also be viewed at –

2022

  • Schantell M, Taylor BK, Spooner RK, May PE, O’Neill J, Morsey BM, Wang T, Ideker T, Bares SH, Fox HS, Wilson TW. Epigenetic aging is associated with aberrant neural oscillatory dynamics serving visuospatial processing in people with HIV. Aging (Albany NY). 2022 Dec 15;14(24):9818-9831. doi: 10.18632/aging.204437. Epub 2022 Dec 15. PMID: 36534452 [PDF] [PubMed]

  • Van Oss SB, Parikh SB, Castilho Coelho N, Wacholder A, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR. On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w. J Biol Chem. 2022 Dec;298(12):102697. doi: 10.1016/j.jbc.2022.102697. Epub 2022 Nov 13. PMID: 36379252 [PDF] [PubMed]

  • Li A, Koch Z, Ideker T. Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging. J Intern Med. 2022 Nov;292(5):733-744. doi: 10.1111/joim.13533. Epub 2022 Jun 20. PMID: 35726002 [PDF] [PubMed] (Review)

  • Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. Understudied proteins: opportunities and challenges for functional proteomics. Nat Methods. 2022 Jul;19(7):774-779. doi: 10.1038/s41592-022-01454-x. PMID: 35534633 [PDF] [PubMed]

  • Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. An open invitation to the Understudied Proteins Initiative. Nat Biotechnol. 2022 Jun;40(6):815-817. doi: 10.1038/s41587-022-01316-z. PMID: 35534555  [PDF] [PubMed]

  • Ottilie S, Luth MR, Hellemann E, Goldgof GM, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, Abraham M, Tarsio M, LeBlanc E, Whitesell L, Schenken J, Gunawan F, Patel R, Smith J, Love MS, Williams RM, McNamara CW, Gerwick WH, Ideker T, Suzuki Y, Wirth DF, Lukens AK, Kane PM, Cowen LE, Durrant JD, Winzeler EA. Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol. 2022 Feb 11;5(1):128. doi: 10.1038/s42003-022-03076-7. PMID: 35149760 [PubMed] [PDF]

  • Konno N, Kijima Y, Watano K, Ishiguro S, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W, Yachie N. Deep distributed computing to reconstruct extremely large lineage trees. Nat Biotechnol. 2022 Apr;40(4):566-575. doi: 10.1038/s41587-021-01111-2. Epub 2022 Jan 6. PMID: 34992246 [PubMed] [PDF]

2021

  • Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O’Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T†, Krogan NJ†. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science. 2021 Oct;374(6563):eabf2911. doi: 10.1126/science.abf2911. Epub 2021 Oct 1. PMID: 34591642 †Co-Corresponding Authors [PubMed] [PDF

2020

2019

2018

  • Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls.* Journal of Molecular Biology. Volume 430, Issue 18, Part A, Pages 2900–2912 (14 September 2018).  [Epub ahead of print: 2018 Jun 19] doi: 10.1016/j.jmb.2018.06.026. PMID: 29932943 [PDF] [PubMed] (Review)

    • *Special Issue, Edited by Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass.
    • *Cover art by Kivilcim Ozturk, Michelle Dow and Hannah Carter. 

2017

2016

2015

2014

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 Rep 5(6):1714-24 (2013) [PDF] [PubMed]

2012

2011

2010

2009

2008

2007

2006

2005

2004 and prior