David Quigley, PhD
Assistant Professor
Urology
School of Medicine

The Quigley Lab studies tumor genomes to understand how urological cancers develop and respond to therapy. Our lab is part of the Department of Urology and the Helen Diller Family Comprehensive Cancer Center at the University of California, San Francisco.

Awards

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• Rob Sutherland Award for Early or Mid-career Investigators, 8th annual PacRim Meeting, 2024
• Outstanding Faculty Mentorship Award, UCSF, 2024
• Young Investigator Award, Prostate Cancer Foundation, 2017-2020

Education & Training

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• PhD Genetics Oslo University 10/2014
• MA Biomedical Informatics Columbia University 06/2006
• BA Computer Science Carleton College 06/1998

Websites

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• Quigley Lab Website (quigleylab.ucsf.edu)
• Quigley Lab Github Repo (github.com)

Grants and Projects

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• Discovering transcriptional drivers of therapy-resistant metastatic prostate cancer, DOD, 2024-2027
• Advancing the Drug Development Process in Metastatic Prostate Cancer through Machine Learning, Prostate Cancer Foundation, 2022-2024

Publications (102)

Top publication keywords:
Quantitative Trait LociDNA MethylationReceptors, AndrogenDrug Resistance, NeoplasmBRCA2 ProteinProstatic NeoplasmsPhenylthiohydantoinCarcinogenesisNeuroendocrine TumorsPoly(ADP-ribose) Polymerase InhibitorsGene Expression Regulation, NeoplasticProstatic Neoplasms, Castration-ResistantHepatocyte Nuclear Factor 3-alphaGenomic Structural VariationAndrogens

• Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
  Cell 2018 Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, …
• Racial Variation in the Advanced Prostate Cancer Genome.
  International Journal of Radiation Oncology • Biology • Physics 2024 E. Feng, J.M.A. Vo-Phamhi, A. Foye, J. Vinson, J.C. Hong, S.J. Freedland, J. Alumkal, H. Beltran, C. Morrissey, P. Nelson, A. Chinnaiyan, C. Sawyers, R. Aggarwal, E. Small, D. Quigley, M. Sjostrom, S.…
• Synthetic Lethal Targeting of Cyclin Dependent Kinase-12-Deficient Prostate Cancer with PARP Inhibitors.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2024 Chou J, Robinson TM, Egusa EA, Lodha R, Zhang M, Badura M, Mikayelyan M, Delavan H, Swinderman J, Wilson C, Zhu J, Das R, Nguyen M, Loehr A, Golsorkhi T, Simmons A, Abida W, Chinnaiyan AM, Arkin MR, …
• An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.
  Cancer research 2024 Shrestha R, Chesner LN, Zhang M, Zhou S, Foye A, Lundberg A, Weinstein AS, Sjöström M, Zhu X, Moreno-Rodriguez T, Li H, SU2C/PCF West Coast Prostate Cancer Dream Team, Alumkal JJ, Aggarwal R, Small EJ…
• Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer.
  The Journal of clinical investigation 2024 Zhu X, Farsh T, Vis D, Yu I, Li H, Liu T, Sjöström M, Shrestha R, Kneppers J, Severson T, Zhang M, Lundberg A, Moreno Rodriguez T, Weinstein AS, Foye A, Mehra N, Aggarwal RR, Bergman AM, Small EJ, …

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• HER2 overexpression in urothelial carcinoma with GATA3 and PPARG copy number gains.
  The oncologist 2024 Zhu X, Chan E, Turski ML, Mendez CE, Hsu SC, Kumar V, Shipp C, Jindal T, Chang K, Onodera C, Devine WP, Grenert JP, Stohr BA, Ding CC, Stachler MD, Quigley DA, Feng FY, Chu CE, Porten SP, Chou J, …
• Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer.
  Nature genetics 2024 Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y, West …
• Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression.
  Nature cell biology 2024 Zhang M, Sjöström M, Cui X, Foye A, Farh K, Shrestha R, Lundberg A, Dang HX, Li H, Febbo PG, Aggarwal R, Alumkal JJ, Small EJ, SU2C/PCF West Coast Prostate Cancer Dream Team, Maher CA, Feng FY, …
• A prostate cancer gastrointestinal transcriptional phenotype may be associated with diminished response to AR-targeted therapy.
  bioRxiv : the preprint server for biology 2024 Subramanian A, Zhang M, Sharifi M, Moreno-Rodriguez T, Feng E, Rydzewski NR, Shrestha R, Zhu X, Zhao SG, Aggarwal R, Small EJ, Ding CC, Quigley DA, Sjöström M
• Development of a machine learning model to predict overall survival results from randomized clinical trials of patients with metastatic prostate cancer.
  Journal of Clinical Oncology 2024 Ali Sabbagh, David Alan Quigley, Nicholas Lillis, Li Zhang, Isabel D Friesner, Adina Bailey, Rahul Raj Aggarwal, Meera Reddy Chappidi, Hari Singhal, Ke Zhang, Joel Greshock, Jinhui Li, Margaret K. Yu,…
• Stem-cell states converge in multistage cutaneous squamous cell carcinoma development.
  Science (New York, N.Y.) 2024 Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A
• Abstract LB196: An atlas of accessible chromatin in advanced prostate cancer.
  Cancer Research 2024 Raunak Shrestha, Lisa N. Chesner, Meng Zhang, Stanley Zhou, Adam Foye, Arian Lundberg, Alana S. Weinstein, Martin Sjöström, Xiaolin Zhu, Thaidy Moreno-Rodriguez, Haolong Li, Joshi J. Alumkal, Rahul …
• Single cell-transcriptomic analysis informs the lncRNA landscape in metastatic castration resistant prostate cancer.
  NPJ genomic medicine 2024 Saha D, Dang HX, Zhang M, Quigley DA, Feng FY, Maher CA
• Advancing the drug development process in metastatic prostate cancer through machine learning.
  Journal of Clinical Oncology 2024 David Alan Quigley, Julian C. Hong, Nicholas Lillis, Ali Sabbagh, Isabel D Friesner, Adina Bailey, Rahul Raj Aggarwal, Li Zhang, Meera Reddy Chappidi, Hari Singhal, Joel Greshock, Ke Zhang, Margaret K…
• Association of a prostate cancer gastrointestinal transcriptional phenotype as found in clinical mCRPC samples with response to AR-targeted therapy.
  Journal of Clinical Oncology 2024 Aishwarya Subramanian, Meng Zhang, Marina Nasrin Sharifi, Thaidy Moreno Rodriguez, Eric Feng, Nicholas Robert Rydzewski, Raunak Shrestha, Xiaolin Zhu, Shuang Zhao, Rahul Raj Aggarwal, Eric J. Small, …
• Somatostatin receptor 1 ( SSTR1 ) expression as a potential predictive biomarker for response to androgen receptor signaling inhibitor (ARSI) therapy in metastatic castration-resistant prostate cancer (mCRPC).
  Journal of Clinical Oncology 2024 Xiaolin Zhu, Daniel J Vis, Martin Sjöström, Raunak Shrestha, Jeroen Kneppers, Tessa Severson, Yanyun Zhu, Haolong Li, Tatyanah Farsh, Meng Zhang, Arian Lundberg, Thaidy Moreno Rodriguez, Adam Foye, …
• The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer.
  Cancer research 2023 Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, …
• AARDVARK: an automated reversion detector for variants affecting resistance kinetics.
  Bioinformatics (Oxford, England) 2023 Moreno T, Magana J, Quigley DA
• Transcriptomic Heterogeneity of Expansile Cribriform and Other Gleason Pattern 4 Prostate Cancer Subtypes.
  European urology oncology 2023 Chappidi MR, Sjöström M, Greenland NY, Cowan JE, Baskin AS, Shee K, Simko JP, Chan E, Stohr BA, Washington SL, Nguyen HG, Quigley DA, Davicioni E, Feng FY, Carroll PR, Cooperberg MR
• Fragmentomic analysis of circulating tumor DNA-targeted cancer panels.
  Annals of oncology : official journal of the European Society for Medical Oncology 2023 Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM…
• Abstract A029: Whole genome and transcriptome analysis of paired metastatic biopsies identified resistance mechanisms in castration-resistant prostate cancer.
  Cancer Research 2023 Xiaolin Zhu, Daniël Vis, Martin Sjöström, Raunak Shrestha, Jeroen Kneppers, Tesa Severson, Yanyun Zhu, Meng Zhang, Arian Lundberg, Thaidy Moreno Rodriguez, Alana Weinstein, Haolong Li, Adam Foye, …
• Abstract A062: Alternative promoter usage is linked to transcriptional and epigenetic alterations during prostate cancer progression.
  Cancer Research 2023 Meng Zhang, Martin Sjöström, Raunak Shrestha, Arian Lundberg, Thaidy Moreno-Rodriguez, Adam Foye, Ha X. Dang, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Christopher A. Maher, Felix Y. Feng, …
• Abstract B031: Investigation of the ubiquitin ligase RNF31 as a mediator of immune evasion in advanced prostate cancer.
  Cancer Research 2023 Tianyi Liu, Haolong Li, Tony Junjie Hua, Hyunjin Shin, Tanushree Shenoy, Martin Sjoestroem, Arian Lundberg, Luke Gilbert, David Quigley, Alan Ashworth, Lewis Lanier, Felix Feng
• Abstract B041: AR suppresses MHC Class I expression and T-cell response in prostate cancer.
  Cancer Research 2023 Lisa Chesner, Julie Graff, Fanny Polesso, Alexis Smith, Arian Lundberg, Martin Sjoestroem, Zheng Xia, Simon Linder, Andries Bergman, Alan Ashworth, David Quigley, Wilbert Zwart, Luke Gilbert, Amy …
• Abstract PR003: Convergent evolution in DNA repair-deficient mCRPC in response to targeted therapy.
  Cancer Research 2023 Thaidy Moreno, Meng Zhang, Arian Lundberg, Raunak Shrestha, Martin Sjöström, Anu Pasam, Adam Foye, Anna Trigos, Felix Feng, Shahneen Sandhu, David A. Quigley
• Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis.
  bioRxiv : the preprint server for biology 2023 Taylor MA, Kandyba E, Halliwill K, Delrosario R, Koroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam S, Mirzoeva O, Akhurst RJ, Balmain A
• Reversible epigenetic alterations mediate PSMA expression heterogeneity in advanced metastatic prostate cancer.
  JCI insight 2023 Sayar E, Patel RA, Coleman IM, Roudier MP, Zhang A, Mustafi P, Low JY, Hanratty B, Ang LS, Bhatia V, Adil M, Bakbak H, Quigley DA, Schweizer MT, Hawley JE, Kollath L, True LD, Feng FY, Bander NH, …
• Intrinsic Molecular Subtypes of Metastatic Castration-Resistant Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2022 Feng E, Rydzewski NR, Zhang M, Lundberg A, Bootsma M, Helzer KT, Lang JM, Aggarwal R, Small EJ, Quigley DA, Sjöström M, Zhao SG
• Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.
  Cancer research 2022 O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A
• The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
  Cancer research 2022 Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, …
• Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity.
  Nature communications 2022 Westbrook TC, Guan X, Rodansky E, Flores D, Liu CJ, Udager AM, Patel RA, Haffner MC, Hu YM, Sun D, Beer TM, Foye A, Aggarwal R, Quigley DA, Youngren JF, Ryan CJ, Gleave M, Wang Y, Huang J, Coleman I, …
• Why ARNT Prostate Tumors Responding to Enzalutamide?
  Cancer discovery 2022 Zhang M, Moreno-Rodriguez T, Quigley DA
• Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer.
  Nature 2022 Herberts C, Annala M, Sipola J, Ng SWS, Chen XE, Nurminen A, Korhonen OV, Munzur AD, Beja K, Schönlau E, Bernales CQ, Ritch E, Bacon JVW, Lack NA, Nykter M, Aggarwal R, Small EJ, Gleave ME, SU2C/PCF …
• Abstract 3625: Clonal architecture and evolution of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing.
  Cancer Research 2022 Cameron Herberts, Matti Annala, Joonatan Sipola, Sarah W. Ng, Xinyi E. Chen, Anssi Nurminen, Olga Korhonen, Asli D. Munzur, Kevin Beja, Elena Schönlau, Cecily Q. Bernales, Elie Ritch, Jack V. Bacon, …
• Androgen receptor reprogramming demarcates prognostic, context-dependent gene sets in primary and metastatic prostate cancer.
  Clinical epigenetics 2022 Severson T, Qiu X, Alshalalfa M, Sjöström M, Quigley D, Bergman A, Long H, Feng F, Freedman ML, Zwart W, Pomerantz MM
• Clinical and molecular features of low prostate-specific membrane antigen (PSMA) expression in patients (pts) with metastatic castration resistant prostate cancer (mCRPC).
  Journal of Clinical Oncology 2022 Ivan de Kouchkovsky, Li Zhang, Jiaoti Huang, Kai Trepka, Jonathan Chou, Adam Foye, David Shui, Chris Wong, Verena Friedl, Alana Weinstein, Thomas A Hope, David A. Quigley, Josh Stuart, Tomasz M. Beer,…
• Abstract PD15-08: Window of opportunity trial of neoadjuvant olaparib and durvalumab for triple negative or low ER-positive breast cancer.
  Cancer Research 2022 Seock-Ah Im, Kyung-Hun Lee, Ahrum Min, Daewon Lee, Tae Yong Kim, Han Suk Ryu, Jiwon Koh, Gi-Jeong Cheon, Yoon-Jung Shin, Yujin Kim, Hyeong-Gon Moon, Wonshik Han, Han-Byoel Lee, Morgan Diolaiti, David …
• Prognosis Associated With Luminal and Basal Subtypes of Metastatic Prostate Cancer.
  JAMA oncology 2021 Aggarwal R, Rydzewski NR, Zhang L, Foye A, Kim W, Helzer KT, Bakhtiar H, Chang SL, Perry MD, Gleave M, Reiter RE, Huang J, Evans CP, Alumkal JJ, Lang JM, Yu M, Quigley DA, Sjöström M, Small EJ, Feng …
• Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures.
  NPJ genomic medicine 2021 Rydzewski NR, Peterson E, Lang JM, Yu M, Laura Chang S, Sjöström M, Bakhtiar H, Song G, Helzer KT, Bootsma ML, Chen WS, Shrestha RM, Zhang M, Quigley DA, Aggarwal R, Small EJ, Wahl DR, Feng FY, Zhao …
• An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer.
  Nature communications 2021 Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA
• CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer.
  Nature communications 2021 Ahmed M, Soares F, Xia JH, Yang Y, Li J, Guo H, Su P, Tian Y, Lee HJ, Wang M, Akhtar N, Houlahan KE, Bosch A, Zhou S, Mazrooei P, Hua JT, Chen S, Petricca J, Zeng Y, Davies A, Fraser M, Quigley DA, …
• 5-hydroxymethylcytosine as a liquid biopsy biomarker in mCRPC.
  Journal of Clinical Oncology 2021 Martin Sjöström, Shuang Zhao, Eric Jay Small, Yuhong Ning, Corinne Maurice-Dror, Adam Foye, Jun Jie T. Hua, Haolong Li, Tomasz M. Beer, Christopher P. Evans, Matthew Rettig, Kim N. Chi, Joshi J. …
• Genomic characterization of treatment-associated small cell neuroendocrine carcinoma of the prostate.
  Journal of Translational Genetics and Genomics 2021 Ivan de Kouchkovsky, David A. Quigley, Eric J. Small, Rahul Aggarwal
• One of These Things is Not Like the Others: Targeting ATM-mutant Prostate Cancer.
  European urology 2020 Quigley DA
• SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression.
  Scientific reports 2020 Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA
• Autoantibody Landscape in Patients with Advanced Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2020 Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M…
• Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2020 Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, Quigley DA, Foye A, Chen WS, Youngren J, Weinstein AS, Stuart JM, Feng FY, …
• The DNA methylation landscape of advanced prostate cancer.
  Nature genetics 2020 Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, …
• Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer.
  Urologic oncology 2020 Kwon DH, Zhang L, Quigley DA, Foye A, Chen WS, Wong CK, Feng FY, Bailey A, Huang J, Stuart JM, Friedl V, Weinstein AS, Beer TM, Alumkal JJ, Rettig M, Gleave M, Lara PN, Thomas GV, Li P, Lui A, Small …
• The comprehensive methylation landscape of metastatic castration-resistant prostate cancer (mCRPC) identifies new phenotypic subtypes: Results from the West Coast Prostate Cancer Dream Team (WCDT).
  Journal of Clinical Oncology 2020 Eric Jay Small, Shuang Zhao, William S. Chen, Haolong Li, Adam Foye, Martin Sjöström, Jun Jie Hua, Rahul Raj Aggarwal, Joshi J. Alumkal, Tomasz M. Beer, Martin Gleave, Matthew Rettig, Owen Witte, …
• Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Alumkal JJ, Sun D, Lu E, Beer TM, Thomas GV, Latour E, Aggarwal R, Cetnar J, Ryan CJ, Tabatabaei S, Bailey S, Turina CB, Quigley DA, Guan X, Foye A, Youngren JF, Urrutia J, Huang J, Weinstein AS, …
• An integrated molecular profile of endometrioid ovarian cancer.
  Gynecologic oncology 2020 Pierson WE, Peters PN, Chang MT, Chen LM, Quigley DA, Ashworth A, Chapman JS
• ADRB2 expression in progressive metastatic castration-resistant prostate cancer.
  Journal of Clinical Oncology 2020 Daniel Kwon, Li Zhang, Adam Foye, William S. Chen, Felix Y Feng, Adina Bailey, Jiaoti Huang, David A. Quigley, Josh Stuart, Verena Friedl, Alana Weinstein, Tomasz M. Beer, Joshi J. Alumkal, Matthew …
• Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy.
  Cancer discovery 2020 Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A
• Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2020 Li Y, Yang R, Henzler CM, Ho Y, Passow C, Auch B, Carreira S, Nava Rodrigues D, Bertan C, Hwang TH, Quigley DA, Dang HX, Morrissey C, Fraser M, Plymate SR, Maher CA, Feng FY, de Bono JS, Dehm SM
• Prostate cancer research: The next generation; report from the 2019 Coffey-Holden Prostate Cancer Academy Meeting.
  The Prostate 2019 Miyahira AK, Sharp A, Ellis L, Jones J, Kaochar S, Larman HB, Quigley DA, Ye H, Simons JW, Pienta KJ, Soule HR
• Niche-Specific Factors Dynamically Regulate Sebaceous Gland Stem Cells in the Skin.
  Developmental cell 2019 Veniaminova NA, Grachtchouk M, Doane OJ, Peterson JK, Quigley DA, Lull MV, Pyrozhenko DV, Nair RR, Patrick MT, Balmain A, Dlugosz AA, Tsoi LC, Wong SY
• A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS.
  eLife 2019 McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, Chen B, Quigley DA, Luk JM, Kelley RK, Gordan JD, Gill RM, Blanchard SC, Ruggero D
• DNA-Dependent Protein Kinase Drives Prostate Cancer Progression through Transcriptional Regulation of the Wnt Signaling Pathway.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2019 Kothari V, Goodwin JF, Zhao SG, Drake JM, Yin Y, Chang SL, Evans JR, Wilder-Romans K, Gabbara K, Dylgjeri E, Chou J, Sun G, Tomlins SA, Mehra R, Hege K, Filvaroff EH, Schaeffer EM, Karnes RJ, Quigley …
• Abstract 2291: Single cell capture and molecular analysis of live CTCs using integrated microwells and single cell aspirator.
  Cancer Research 2019 Charlotte N. Stahlfeld, Jake J. Tokar, David Quigley, David Niles, Jamie M. Sperger, Felix Feng, Joshua M. Lang
• Differential cell surface protein expression in response to PARP inhibition in BRCA1 mutant isogenic ovarian and breast cancer cells using a novel proteomic technique.
  Gynecologic Oncology 2019 A. Freeman, S. Bakker, A. Weeks, M.E. Diolaiti, D. Quigley, J.S. Chapman, L.M. Chen, A. Ashworth
• Novel RB1-Loss Transcriptomic Signature Is Associated with Poor Clinical Outcomes across Cancer Types.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2019 Chen WS, Alshalalfa M, Zhao SG, Liu Y, Mahal BA, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL, Feng FY
• Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer.
  European urology 2019 Chen WS, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley DA, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, …
• Whole-Genome and Transcriptional Analysis of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer Demonstrates Intraclass Heterogeneity.
  Molecular cancer research : MCR 2019 Aggarwal RR, Quigley DA, Huang J, Zhang L, Beer TM, Rettig MB, Reiter RE, Gleave ME, Thomas GV, Foye A, Playdle D, Lloyd P, Chi KN, Evans CP, Lara PN, Feng FY, Alumkal JJ, Small EJ
• High density is a property of slow-cycling and treatment-resistant human glioblastoma cells.
  Experimental cell research 2019 Sabelström H, Quigley DA, Fenster T, Foster DJ, Fuchshuber CAM, Saxena S, Yuan E, Li N, Paterno F, Phillips JJ, James CD, Norling B, Berger MS, Persson AI
• Genomic drivers of poor prognosis and enzalutamide resistance in metastatic castration-resistant prostate cancer.
  Journal of Clinical Oncology 2019 William S. Chen, Rahul Raj Aggarwal, Li Zhang, Shuang Zhao, Tomasz M. Beer, David A Quigley, Adam Foye, Denise Playdle, Paul Lloyd, Matthew Rettig, Martin Gleave, Christopher P. Evans, Primo Lara, …
• Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2018 Zhao SG, Chen WS, Das R, Chang SL, Tomlins SA, Chou J, Quigley DA, Dang HX, Barnard TJ, Mahal BA, Gibb EA, Liu Y, Davicioni E, Duska LR, Posadas EM, Jolly S, Spratt DE, Nguyen PL, Maher CA, Small EJ, …
• Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
  Cell 2018 Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, …
• DNA Repair Gene Alterations and PARP Inhibitor Response in Patients With Metastatic Castration-Resistant Prostate Cancer.
  Journal of the National Comprehensive Cancer Network : JNCCN 2018 Lu E, Thomas GV, Chen Y, Wyatt AW, Lloyd P, Youngren J, Quigley D, Bergan R, Bailey S, Beer TM, Feng FY, Small EJ, Alumkal JJ
• Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry.
  Cell reports 2018 Gonzalez VD, Samusik N, Chen TJ, Savig ES, Aghaeepour N, Quigley DA, Huang YW, Giangarrà V, Borowsky AD, Hubbard NE, Chen SY, Han G, Ashworth A, Kipps TJ, Berek JS, Nolan GP, Fantl WJ
• Antisecretory Factor-Mediated Inhibition of Cell Volume Dynamics Produces Antitumor Activity in Glioblastoma.
  Molecular cancer research : MCR 2018 Ilkhanizadeh S, Sabelström H, Miroshnikova YA, Frantz A, Zhu W, Idilli A, Lakins JN, Schmidt C, Quigley DA, Fenster T, Yuan E, Trzeciak JR, Saxena S, Lindberg OR, Mouw JK, Burdick JA, Magnitsky S, …
• EXTH-23. ANTISECRETORY FACTOR-MEDIATED LOWERING OF INTERSTITIAL FLUID PRESSURE PRODUCES ANTI-TUMOR ACTIVITY IN GLIOBLASTOMA.
  Neuro-Oncology 2017 Hanna Sabelstrom, Shirin IIkhanizadeh, Yekaterina A Miroshnikova, Aaron Frantz, Wen Zhu, Aurora Idilli, David Quigley, Trenten Fenster, Edith Yuan, Supna Saxena, Janna K Mouw, Jason A Burdick, Sergey …
• Age, estrogen, and immune response in breast adenocarcinoma and adjacent normal tissue.
  Oncoimmunology 2017 Quigley DA, Tahiri A, Lüders T, Riis MH, Balmain A, Børresen-Dale AL, Bukholm I, Kristensen V
• Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors.
  Cancer discovery 2017 Quigley D, Alumkal JJ, Wyatt AW, Kothari V, Foye A, Lloyd P, Aggarwal R, Kim W, Lu E, Schwartzman J, Beja K, Annala M, Das R, Diolaiti M, Pritchard C, Thomas G, Tomlins S, Knudsen K, Lord CJ, Ryan C, …
• Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer.
  Genome medicine 2016 Halliwill KD, Quigley DA, Kang HC, Del Rosario R, Ginzinger D, Balmain A
• Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer.
  Cell reports 2016 Quigley DA, Kandyba E, Huang P, Halliwill KD, Sjölund J, Pelorosso F, Wong CE, Hirst GL, Wu D, Delrosario R, Kumar A, Balmain A
• Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines.
  Cell reports 2016 Campbell J, Ryan CJ, Brough R, Bajrami I, Pemberton HN, Chong IY, Costa-Cabral S, Frankum J, Gulati A, Holme H, Miller R, Postel-Vinay S, Rafiq R, Wei W, Williamson CT, Quigley DA, Tym J, Al-Lazikani …
• Abstract P6-08-05: Protein tyrosine kinase activity and miRNA expression profiling reveals differences according to progesterone-receptor-status in HER-2 negative breast cancer.
  Poster Session Abstracts 2016 A Tahiri, SV Satheesh, R de Wijn, T Lders, MR Aure, DA Quigley, IR Bukholm, A Hurtado, VN Kristensen, J Geisler
• Abstract B59: Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue.
  Tumor Microenvironment and Immunotherapy 2016 David A. Quigley, Andliena Tahiri, Torben Lüders, Margit H. Riis, Allan Balmain, Anne-Lise Børresen-Dale, Ida R. Bukholm, Vessela Kristensen
• ATPS-63OSMOTIC SWELLING REGULATES TUMOR GROWTH AND DRUG UPTAKE IN HUMAN GLIOBLASTOMA.
  Neuro-Oncology 2015 Shirin Iikhanizadeh, Yekaterina Miroshnikova, Aaron Frantz, Wen Zhu, Aurora Idilli, David Quigley, John Lakins, Sergey Magnitsky, Joanna Phillips, David James, Mitchel Berger, Daniele Arosio, Dandan …
• Predicting prognosis and therapeutic response from interactions between lymphocytes and tumor cells.
  Molecular oncology 2015 Quigley DA, Kristensen V
• Equalizer reduces SNP bias in Affymetrix microarrays.
  BMC bioinformatics 2015 Quigley D
• The genetics of splicing in neuroblastoma.
  Cancer discovery 2015 Chen J, Hackett CS, Zhang S, Song YK, Bell RJ, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA
• The mutational landscapes of genetic and chemical models of Kras-driven lung cancer.
  Nature 2014 Westcott PM, Halliwill KD, To MD, Rashid M, Rust AG, Keane TM, Delrosario R, Jen KY, Gurley KE, Kemp CJ, Fredlund E, Quigley DA, Adams DJ, Balmain A
• Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.
  Molecular cancer research : MCR 2014 Quigley D, Silwal-Pandit L, Dannenfelser R, Langerød A, Vollan HK, Vaske C, Siegel JU, Troyanskaya O, Chin SF, Caldas C, Balmain A, Børresen-Dale AL, Kristensen V
• Expression quantitative trait loci and receptor pharmacology implicate Arg1 and the GABA-A receptor as therapeutic targets in neuroblastoma.
  Cell reports 2014 Hackett CS, Quigley DA, Wong RA, Chen J, Cheng C, Song YK, Wei JS, Pawlikowska L, Bao Y, Goldenberg DD, Nguyen K, Gustafson WC, Rallapalli SK, Cho YJ, Cook JM, Kozlov S, Mao JH, Van Dyke T, Kwok PY, …
• TP53 mutation spectrum in breast cancer is subtype specific and has distinct prognostic relevance.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2014 Silwal-Pandit L, Vollan HK, Chin SF, Rueda OM, McKinney S, Osako T, Quigley DA, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Langerød A
• Identification of Hipk2 as an essential regulator of white fat development.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Sjölund J, Pelorosso FG, Quigley DA, DelRosario R, Balmain A
• The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors.
  Molecular oncology 2013 Quigley DA, Fiorito E, Nord S, Van Loo P, Alnæs GG, Fleischer T, Tost J, Moen Vollan HK, Tramm T, Overgaard J, Bukholm IR, Hurtado A, Balmain A, Børresen-Dale AL, Kristensen V
• Inflammation and Hras signaling control epithelial-mesenchymal transition during skin tumor progression.
  Genes & development 2013 Wong CE, Yu JS, Quigley DA, To MD, Jen KY, Huang PY, Del Rosario R, Balmain A
• Rewiring of human lung cell lineage and mitotic networks in lung adenocarcinomas.
  Nature communications 2013 Kim IJ, Quigley D, To MD, Pham P, Lin K, Jo B, Jen KY, Raz D, Kim J, Mao JH, Jablons D, Balmain A
• Abstract P5-05-03: The 5p12 breast cancer susceptibility locus is associated with MRPS30 expression in estrogen receptor - positive tumors.
  Poster Session Abstracts 2012 DA Quigley, P Van Loo, GG Alnæs, J Tost, D Zelenika, A Balmain, A-L Børresen-Dale, VN Kristensen
• Mouse and human strategies identify PTPN14 as a modifier of angiogenesis and hereditary haemorrhagic telangiectasia.
  Nature communications 2012 Benzinou M, Clermont FF, Letteboer TG, Kim JH, Espejel S, Harradine KA, Arbelaez J, Luu MT, Roy R, Quigley D, Higgins MN, Zaid M, Aouizerat BE, van Amstel JK, Giraud S, Dupuis-Girod S, Lesca G, …
• Erratum: Mouse and human strategies identify PTPN14 as a modifier of angiogenesis and hereditary haemorrhagic telangiectasia.
  Nature Communications 2012 Michael Benzinou, Frederic F. Clermont, Tom G W. Letteboer, Jai-hyun Kim, Silvia Espejel, Kelly A. Harradine, Juan Arbelaez, Minh Thu Luu, Ritu Roy, David Quigley, Mamie Nakayama Higgins, Musa Zaid, …
• Progressive genomic instability in the FVB/Kras(LA2) mouse model of lung cancer.
  Molecular cancer research : MCR 2011 To MD, Quigley DA, Mao JH, Del Rosario R, Hsu J, Hodgson G, Jacks T, Balmain A
• Outgrowth of drug-resistant carcinomas expressing markers of tumor aggression after long-term TβRI/II kinase inhibition with LY2109761.
  Cancer research 2011 Connolly EC, Saunier EF, Quigley D, Luu MT, De Sapio A, Hann B, Yingling JM, Akhurst RJ
• Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility.
  Genome biology 2011 Quigley DA, To MD, Kim IJ, Lin KK, Albertson DG, Sjolund J, Pérez-Losada J, Balmain A
• Deletion of the PER3 gene on chromosome 1p36 in recurrent ER-positive breast cancer.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2010 Climent J, Perez-Losada J, Quigley DA, Kim IJ, Delrosario R, Jen KY, Bosch A, Lluch A, Mao JH, Balmain A
• 606 Evolution of genetic and gene expression networks during tumour development.
  European Journal of Cancer Supplements 2010 M. To, D. Quigley, J. Sjolund, A. Balmain
• Systems genetics analysis of cancer susceptibility: from mouse models to humans.
  Nature reviews. Genetics 2009 Quigley D, Balmain A
• Genetic architecture of mouse skin inflammation and tumour susceptibility.
  Nature 2009 Quigley DA, To MD, Pérez-Losada J, Pelorosso FG, Mao JH, Nagase H, Ginzinger DG, Balmain A
• On the origin of lateral asymmetry.
  Chromosoma 1996 Goodwin EH, Meyne J, Bailey SM, Quigley D