Ali Foroughi pour, Te-Chia Wu, Jan Martinek, Santhosh Sivajothi, Paul Robson, Karolina Palucka, Jeffrey H. Chuang. Prediction of Outcome from Spatial Protein Profiling of Triple-Negative Breast Cancers – Biorxiv preprint.
Jill C. Rubinstein, Sergii Domanskyi, Todd B. Sheridan, Brian Sanderson, SungHee Park, Jessica Kaster, Haiyin Li, Olga Anczukow, Meenhard Herlyn, Jeffrey H. Chuang. Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma – Cancer Research (2025) 85 (5): 987–1002.
The CD123 Antibody-Drug Conjugate Pivekimab Sunirine Exerts Profound Activity in Preclinical Models of Pediatric Acute Lymphoblastic Leukemia. In review.
2024
Jared M. Andrews, Michael W. Lloyd, Steven B. Neuhauser, Margaret Bundy, Emily L. Jocoy, Susan D. Airhart, Carol J. Bult, Yvonne A. Evrard, Jeffrey H. Chuang, Suzanne Baker. STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication – Bioinformatics, Volume 40, Issue 12, December 2024, btae713
Malcolm A. Smith, Peter J. Houghton, Richard B. Lock, John M. Maris, Richard Gorlick, Raushan T. Kurmasheva, Xiao-Nan Li, Beverly A. Teicher, Jeffrey H. Chuang, Filemon S. Dela Cruz, Michael A. Dyer, Andrew L. Kung, Michael W. Lloyd, Yael P. Mossé, Timothy M. Stearns, Elizabeth A. Stewart, Carol J. Bult, Stephen W. Erickson. Lessons Learned from 20 Years of Preclinical Testing in Pediatric Cancers – Pharmacology & Therapeutics. Volume 264, December 2024, 108742.
Brittany Angarola , Siddhartha Sharma , Neerja Katiyar , Hyeon Gu Kang , Djamel Nehar-Belaid , SungHee Park , Rachel Gott , Giray Eryilmaz , Mark LaBarge , Karolina Palucka , Jeffrey Chuang , Ron Korstanje , Duygu Ucar, Olga Anczukow. Comprehensive single cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer – Nature Aging (2024). doi.org/10.1038/s43587-024-00751-8
Victor Wang, Zichao Liu, Jan Martinek, Jie Zhou, Hannah Boruchov, Kelly Ray, Karolina Palucka, Jeffrey Chuang. Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironment – Communications Biology volume 7, Article number: 1201 (2024). / JAX News and Insights summary.
Paul Lott, Katherine Chiu, Juanita Elizabeth Quino, April Pangia Vang, Michael W Lloyd, Anuj Srivastava, PDXNet Consortium, Jeffrey H Chuang, Luis G Carvajal-Carmona. Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet Consortium – Cancer Research Communications (2024) 4 (8): 2147–2152.
Funda Meric-Bernstam, Michael W. Lloyd, Soner Koc, Yvonne A. Evrard, Lisa M. McShane, Michael T. Lewis, Kurt W. Evans, Dali Li, Lawrence V. Rubinstein, Alana L. Welm, Dennis A. Dean, Anuj Srivastava, Jeffrey W Grover, Min Jin Ha, Huiqin Chen, Xuelin Huang, Kaushik Varadarajan, Jing Wang, Jack A. Roth, Bryan E. Welm, Ramaswamy Govindan, Ding Li, Salma Kaochar, Nicholas Mitsiades, Luis G Carvajal-Carmona, Meenhard Herlyn, Michael A. Davies, Geoffrey I. Shapiro, Ryan C. Fields, Jose Trevino, J. Chuck Harrell, PDXNet Consortium, Lori Henderson, Tiffany A. Wallace, James H. Doroshow, Jeffrey H. Chuang, and Jeffrey A. Moscow. Assessment of Patient-Derived Xenograft Growth and Antitumor Activity: The NCI PDXNet Consensus Recommendations – Mol Cancer Ther (2024) 23 (7): 924–938.
Brian S White, Xingyi Woo, Soner Koc, Todd Sheridan, Steven B Neuhauser, Shidan Wang, Yvonne A Evrard, John David Landua, R Jay Mashl, Sherri R Davies, Bingliang Fang, Maria Gabriela Raso, Kurt W Evans, Matthew H Bailey, Yeqing Chen, Min Xiao, Jill Rubinstein, Ali Foroughi pour, Lacey Elizabeth Dobrolecki, Maihi Fujita, Junya Fujimoto, Guanghua Xiao, Ryan C Fields, Jacqueline L Mudd, Xiaowei Xu, Melinda G Hollingshead, Shahanawaz Jiwani, PDXNet Consortium, Brandi Davis-Dusenbery, Tiffany A Wallace, Jeffrey A Moscow, James H Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-xian Pan, Moon S Chen Jr., Luis G Carvajal-Carmona, Alana L Welm, Bryan E Welm, Ramaswamy Govindan, Shunqiang Li, Michael A Davies, Jack A Roth, Funda Meric-Bernstam, Yang Xie, Meenhard Herlyn, Li Ding, Michael T Lewis, Carol J Bult, Dennis A Dean II, Jeffrey H Chuang. A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis – Cancer Research. 2024;84:2060–72.
Sergii Domanskyi, Anuj Srivastava, Jessica Kaster, Haiyin Li, Meenhard Herlyn, Jill C Rubinstein, Jeffrey H Chuang. Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples – Cell Reports Methods (2024). Volume 4, Issue 5, 20 May 2024, 100759
Patience Mukashyaka, Todd B. Sheridan, Ali Foroughi pour, Jeffrey H. Chuang. SAMPLER: unsupervised representations for rapid analysis of whole slide tissue images – eBioMedicine (2024). 99:104908
2023
Patience Mukashyaka, Pooja Kumar, David J. Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Olga Anczukow, Edison T. Liu, Jeffrey H. Chuang. High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos – Nature Communications 14, Article number: 8406 (2023)
Wu Y, Chen S, Yang X, Sato K, Lal P, Wang Y, Shinkle AT, Wendl MC, Primeau TM, Zhao Y, Gould A, Sun H, Mudd JL, Hoog J, Mashl RJ, Wyczalkowski MA, Mo CK, Liu R, Herndon JM, Davies SR, Liu D, Ding X, Evrard YA, Welm BE, Lum D, Koh MY, Welm AL, Chuang JH, Moscow JA, Meric-Bernstam F, Govindan R, Li S, Hsieh J, Fields RC, Lim KH, Ma CX, Zhang H, Ding L, Chen F. Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma. – Cancer Res. 2023 Dec 15;83(24):4161-4178. doi: 10.1158/0008-5472.CAN-23-0604. PMID: 38098449; PMCID: PMC10722140.
Myungwoo Nam, Woojung Yang, Hye Sung Kim, Jewel Park, Gahee Park, Sukjun Kim, Sanghoon Song, Chan-Young Ock, Victor G Wang, Jeffrey H Chuang, and Young Kwang Chae. Papillary Thyroid Cancer Immune Phenotypes via Tumor–Infiltrating Lymphocyte Spatial Analysis – Endocrine-Related Cancer, 2023. 30:9 e230110
Keira Hughes, Kathryn Evans, Eric J. Earley, Christopher M. Smith, Stephen W. Erickson, Tim Stearns, Vivek M. Philip, Steven B. Neuhauser, Jeffrey H. Chuang, Emily L. Jocoy, Carol J. Bult, Beverly A. Teicher, Malcolm A. Smith, Richard B. Lock. In Vivo Activity of the Dual SYK/FLT3 Inhibitor TAK-659 Against Pediatric Acute Lymphoblastic Leukemia Xenografts – Pediatric Blood and Cancer, 2023, 70:9, e30503 http://dx.doi.org/10.1002/pbc.30503 .
Spatial mapping of cellular senescence: emerging challenges and opportunities – NIH SenNet Consortium. Nature Aging volume 3, pages 776–790 (2023).
Jie Zhou, Ali Foroughi pour, Hany Deirawan, Fayez Daaboul, Thazin Aung, Rafic Beydoun, Fahad Shabbir Ahmed, Jeffrey H. Chuang. Integrative deep learning analysis improves colon adenocarcinoma patient stratification at risk for mortality – eBioMedicine. 2023. Vol. 94, 104726.
Anczuków O, Airhart S, Chuang JH, Coussens LM, Kuchel GA, Korstanje R, Li S, Lucido AL, McAllister SS, Politi K, Polyak K, Ratliff T, Ren G, Trowbridge JJ, Ucar D, Palucka K. Challenges and opportunities for modeling aging and cancer – Challenges and opportunities for modeling aging and cancer. Cancer Cell. Volume 41, Issue 4, 10 April 2023, Pages 641-645.
2022
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health – NIH SenNet Consortium, Nature Aging, vol. 2, pages 1090–1100 (2022)
Shree Bose, Margarida Barroso, Milan G. Chheda, Hans Clevers, Elena Elez, Salma Kaochar, Scott E. Kopetz, Xiao-Nan Li, Funda Meric-Bernstam, Clifford A. Meyer, Haiwei Mou, Kristen M. Naegle, Martin F. Pera, Zinaida Perova, Katerina A. Politi, Benjamin J.Raphael, Paul Robson, Rosalie C. Sears, Josep Tabernero, David A. Tuveson, Alana L. Welm, Bryan E.Welm, Christopher D. Willey, Konstantin Salnikow, Jeffrey H.Chuang, Xiling Shen. A path to translation: How 3D patient tumor avatars enable next generation precision oncology – Cancer Cell. Volume 40, Issue 12, 12 December 2022, Pages 1448-1453. https://doi.org/10.1016/j.ccell.2022.09.017
Jill C. Rubinstein, Ali Foroughi pour, Jie Zhou, Todd Sheridan, Brian S White, and Jeffrey H. Chuang. Deep Learning Image Analysis Quantifies Tumor Heterogeneity and Identifies Microsatellite Instability in Colon Cancer – 17 October 2022 Journal of Surgical Oncology. https://doi.org/10.1002/jso.27118
Jennifer K Sargent, Mark A Warner, Benjamin E Low, William H Schott, Todd Hoffert, David Coleman, Xing Yi Woo, Todd Sheridan, Sonia Erattupuzha, Philipp P Henrich, Vivek M Philip, Jeffrey H. Chuang, Michael V. Wiles, and Muneer G Hasham. Genetically Diverse Mouse Platform to Xenograft Cancer Cells – Dis Model Mech (2022) 15 (9): dmm049457.
Renfu Shang, Dmitry A. Kretov, Scott I. Adamson, Thomas Treiber, Nora Treiber, Jeffrey Vedanayagam, Jeffrey H. Chuang, Gunter Meister, Daniel Cifuentes and Eric C. Lai. Regulated dicing of pre-mir-144 via reshaping of its terminal loop – Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7637–7654
Ali Foroughi Pour, Brian S. White, Jonghanne Park, Todd B. Sheridan, Jeffrey H. Chuang. Deep Learning Features Encode Interpretable Morphologies within Histological Images – Scientific Reports volume 12, Article number: 9428 (2022)
Joshy George, Yaohui Chen, Nourhan Abdelfattah, Keiko Yamamoto, Thomas D. Gallup, Scott I. Adamson, Brad Rybinski, Anuj Srivastava, Parveen Kumar, Min Gyu Lee, David S. Baskin, Wen Jiang, Jong Min Choi, William Flavahan, Jeffrey H. Chuang, Betty Y.S. Kim, Jiaqiong Xu, Sung Yun Jung, Kyuson Yun. Cancer stem cells, not bulk tumor cells, determine mechanisms of resistance to SMO inhibitors – Cancer Research Communications (2022) 2 (6): 402–416.
Soner Koc, Michael W Lloyd, Jeffrey Grover, Sara Seepo, Sai Lakshmi Subramanian, Manisha Ray, Christian Frech, John DiGiovanna, Phillip Webster, Steven Neuhauser, Anuj Srivastava, Xing Yi Woo, Brian J. Sanderson, Brian White, Paul Lott, PDXNet Consortium, Yvonne A. Evard, Tiffany A. Wallace, Jeffrey A. Moscow, James H. Doroshow, Nicholas Mitsuades, Salma Kaochar, Chong-xian Pan, Moon S. Chen Jr., Luis Carvajal-Carmona, Alana L. Welm, Bryan E. Welm, Michael T. Lewis, Govindan Ramaswarmy, Li Ding, Shunquang Li, Meenherd Herlyn, Mike Davies, Jack Roth, Funda Meric-Bernstam, Peter N. Robinson, Carol J. Bult, Brandi Davis-Dusenbery, Dennis A. Dean II, Jeffrey H. Chuang. PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery – NAR Cancer, Volume 4, Issue 2, June 2022, zcac014
Jan Martinek, Jianan Lin, Kyung In Kim, Victor G.Wang, Te-ChiaWu, Michael Chiorazzi, Hannah Boruchov, Ananya Gulati, Shamreethaa Seeniraj, LiliSun, Florentina Marches, Paul Robson, Anthony Rongvaux, Richard A. Flavell, Joshy George, Jeffrey H. Chuang, Jacques Banchereau, Karolina Palucka. Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function – Cell Reports Medicine. Volume 3, Issue 5, 17 May 2022, 100621
Katrin P. Guillen, Maihi Fujita, Andrew J. Butterfield, Sandra D. Scherer, Matthew H. Bailey, Zhengtao Chu, Yoko S. DeRose, Ling Zhao, Emilio Cortes-Sanchez, Chieh-Hsiang Yang, Jennifer Toner, Guoying Wang, Yi Qiao, Xiaomeng Huang, Jeffery A. Greenland, Jeffery M. Vahrenkamp, David H. Lum, Rachel E. Factor, Edward W. Nelson, Cindy B. Matsen, Jane M. Poretta, Regina Rosenthal, Anna C. Beck, Saundra S. Buys, Christos Vaklavas, John H. Ward, Randy L. Jensen, Kevin B. Jones, Zheqi Li, Steffi Oesterreich, Lacey E. Dobrolecki, Satya S. Pathi, Xing Yi Woo, Kristofer C. Berrett, Mark E. Wadsworth, Jeffrey H. Chuang, Michael T. Lewis, Gabor T. Marth, Jason Gertz, Katherine E. Varley, Bryan E. Welm, Alana L. Welm. A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology – Nature Cancer vol. 3, pages 232–250 (2022)
Saman Farahmand, Aileen Fernandez, Fahad Shabbir Ahmed, David Rimm, Jeffrey H Chuang, Emily Reisenbichler, Kourosh Zarringhalam. Deep learning trained on H&E tumor ROIs predicts HER2 status and Trastuzumab treatment response in HER2+ breast cancer – Modern Pathology 35, pages 44–51 (2022). / Image Data at The Cancer Imaging Archive
2021
Caitlin E. Monaghan, Scott I. Adamson, Mridu Kapur, Jeffrey H. Chuang, and Susan L. Ackerman. The Clp1 R140H mutation alters tRNA metabolism and mRNA 3’ processing in mouse models of pontocerebellar hypoplasia – PNAS (2021) 118 (39) e2110730118.
Hua Sun, Song Cao, R. Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael Wendl, Sherri Davies, Matthew Bailey, Tina Primeau, Jeremy Hoog, Jacqueline Mudd, Dennis Dean,II, Rajesh Patidar, Lily Chen, Matthew Wyczalkowski, Reyka Jayasinghe, Fernanda Rodrigues, Nadezhda Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian Van Tine, Cynthia Ma, Rebecca Aft, Katherine Fuh, Julie Schwarz, Jose Zevallos, Sidharth Puram, John DiPersio, The NCI PDXNet Consortium, Brandi Davis-Dusenbery, Matthew Ellis, Michael Lewis, Michael Davies, Meenhard Herlyn, Bingliang Fang, Jack Roth, Alana L Welm, Bryan Welm, Funda Meric-Bernstam, Feng Chen, Ryan Fields, Shunqiang Li, Ramaswamy Govindan, James Doroshow, Jeffrey Moscow, Yvonne Evrard, Jeffrey Chuang, Benjamin Raphael, and Li Ding. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment – Nature Communications. (2021) 12:5086
Markus Terrey, Scott Adamson, Jeffrey Chuang, and Susan Ackerman. Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology – eLife (2021) 10:e66904
Chun Yu, Jan Martinek, Te-Chia Wu, Kyung In Kim, Joshy George, Elaheh Ahmadzadeh, Rick Maser, Florentina Marches, Patrick Metang, Pierre Authie, Vanessa Oliveira, Victor Wang, Jeffrey Chuang, Paul Robson, Jacques Banchereau, and Karolina Palucka. Human KIT+ myeloid cells facilitate visceral metastasis by melanoma – J Exp Med (2021) 218 (6): e20182163.
Xing Yi Woo, Jessica Giordano, Anuj Srivastava, Zi-Ming Zhao, Michael W. Lloyd, Roebi de Bruijn, Yun-Suhk Suh, Rajesh Patidar, Li Chen, Sandra Scherer, Matthew Bailey, Chieh-Hsiang Yang, Emilio Cortes-Sanchez, Yuanxin Xi, Jing Wang, Jayamanna Wickramasinghe, Andrew V. Kossenkov, Vito Rebecca, Hua Sun, R. Jay Mashl, Sherri Davies, Ryan Jeon, Christian Frech, Jelena Randjelovic, Jacqueline Rosains, Francesco Galimi, Andrea Bertotti, Adam Lafferty, Alice C. O’Farrell, Elodie Modave, Diether Lambrechts, Petra ter Brugge, Violeta Serra, Elisabetta Marangoni, Rania El Botty, Hyunsoo Kim, Jong-Il Kim, Han-Kwang Yang, Charles Lee, Dennis A. Dean II, Brandi Davis-Dusenbery, Yvonne A. Evrard, James H. Doroshow, Alana L. Welm, Bryan E. Welm, Michael T. Lewis, Bingliang Fang, Jack A. Roth, Funda Meric-Bernstam, Meenhard Herlyn, Michael Davies, Li Ding, Shunqiang Li, Ramaswamy Govindan, Claudio Isella, Jeffrey A. Moscow, Livio Trusolino, Annette T. Byrne, Jos Jonkers, Carol J. Bult, Enzo Medico, Jeffrey H. Chuang, PDXNET consortium, EurOPDX consortium. Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts – Nature Genetics volume 53, pages 86–99 (2021). /PubMed Central Link – JAX Press Release – NCI news story
2020
Javad Noorbakhsh , Saman Farahmand, Ali Foroughi pour, Sandeep Namburi, Dennis Caruana, David Rimm, Mohammad Soltanieh-ha, Kourosh Zarringhalam, and Jeffrey H Chuang. Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images – Nature Communications 11: 6367 (2020).
JAX press release
Tejal Nair, Ali Foroughi pour, Jeffrey H. Chuang. The effect of blurring on lung cancer subtype classification accuracy of convolutional neural networks. – 2020 IEEE International Conference on Bioinformatics and Biomedicine, conference abstract.
Markus Terrey, Scott I Adamson, Alana L Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H Chuang, Susan L Ackerman. GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis – eLife 2020;9:e62731 doi: 10.7554/eLife.62731
Fatima Zare, Javad Noorbakhsh,Tianyu Wang, Jeffrey H. Chuang, Sheida Nabavi. Integrative Deep Learning for PanCancer Molecular Subtype Classification Using Histopathological Images and RNAseq Data – BCB ’20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. September 2020 Article No.: 8 Pages 1–8
Mridu Kapur, Archan Ganguly, Gabor Nagy, Scott I. Adamson, Jeffrey H. Chuang, Wayne N. Frankel, Susan L. Ackerman. Expression of the Neuronal tRNA n-Tr20 Regulates Synaptic Transmission and Seizure Susceptibility – Neuron 108(1):193-208.e9 (2020)
Yvonne A. Evrard, Anuj Srivastava, Jelena Randjelovic, Sasi Arunachalam, Carol J. Bult, Huiqin Chen, Lily Chen, Michael Davies, Sherri Davies, Brandi Davis-Dusenbery, Jack DiGiovanna, Li Ding, James H. Doroshow, Bingliang Fang, Christian Frech, Ramaswamy Govindan, Min Jin Ha, Meenhard Herlyn, Ryan Jeon, Andrew Kossenkov, Michael T. Lewis, Shunqiang Li, Michael Lloyd, Funda Meric-Bernstam, Nevena Miletic, Jeffrey A. Moscow, Steven Neuhauser, David Nix, Rajesh Patidar, Vito Rebecca, Peter N. Robinson, Jacqueline Rosains, Jack Roth, Isheeta Seth, Tamara Stankovic, Adam Stanojevic, Brian A. Van Tine, Alana L. Welm, Bryan E. Welm, Jayamanna Wickramasinghe, XingYi Woo, Min Xiao, Zi-ming Zhao, Dennis A. Dean II, Jeffrey S. Morris, Jeffrey H. Chuang. Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis – Cancer Res 2020;80:2286–97 / PubMedCentral open access
Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks – Bioinformatics (2020), 36:10, 15 May 2020, Pages 3234–3235 / Biorxiv preprint
Jason A Somarelli, Heather Gardner, Vincent L Cannataro, Ella F Gunady, Amy M Boddy, Norman A Johnson, J Nicholas Fisk, Stephen G Gaffney, Jeffrey H Chuang, Sheng Li, Francesca D Ciccarelli, Anna R Panchenko, Kate Megquier, Sudhir Kumar, Alex Dornburg, James DeGregori, Jeffrey P Townsend. Molecular biology and evolution of cancer: from discovery to action – Mol Biol Evol. 2020 Feb 1;37(2):320-326.
Javad Noorbakhsh, Zi-ming Zhao, James C. Russell, Jeffrey H. Chuang. Treating cancer as an invasive species – Mol. Cancer Res. (2020). 18:20–6 doi:10.1158/1541-7786.MCR-19-0262
Earlier works
Minji Kim, Meizhen Zheng, Simon Zhongyuan Tian, Byoungkoo Lee, Jeffrey H. Chuang, Yijun Ruan. MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms Genome Biology 20:251 (2019).
Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HG, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCW, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JN, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JS, Schuster M, Shaw BL, Short SC, Sillevis Smitt PA, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, de Groot JF, Stead LF, Verhaak RGW, the GLASS Consortium. Longitudinal molecular trajectories of diffuse glioma patients. – Nature, Nature 576:112–120 (2019) doi: 10.1038/s41586-019-1775-1.
Sachdeva R, Wu M, Johnson K, Kim H, Celebre A, Shahzad U, Graham MS, Kessler JA, Chuang JH, Karamchandani J, Bredel M, Verhaak R, Das S. BMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastoma – Sci Rep. 2019 Oct 10;9(1):14569. doi: 10.1038/s41598-019-51270-1
Xing Yi Woo, Anuj Srivastava, Joel H. Graber, Vinod Yadav, Vishal Kumar Sarsani, Al Simons, Glen Beane, Stephen Grubb, Guruprasad Ananda, Rangjiao Liu, Grace Stafford, Jeffrey H. Chuang, Susan D. Airhart, R. Krishna Murthy Karuturi, Joshy George, Carol J. Bult. Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines – BMC Medical Genomics (2019) 12:92
Young Kwang Chae, Pedro Viveiros, Gilberto Lopes, Bhoomika Sukhadia, Muhammad Mubbashir Sheikh, Diana Saravia, Vaia Florou, Ethan S. Sokol, Garrett M. Frampton, Zachary R. Chalmers, Siraj M. Ali, Jeffrey S. Ross, Sangmin Chang, Si Wang, Lauren Chiec, Ashkon Rahbari1, Nisha Mohindra, Victoria Villaflor, Sang Ha Shin, Michael Oh, Jonathan Anker, Lee Chun Park, Victor Wang, Jeffrey Chuang, Wungki Park. The implications of frameshift mutation burden on immune cell landscape and survival outcome in patients with non-small cell lung cancer (NSCLC) – J Thorac Oncol. 2019 Jun 22. pii: S1556-0864(19)30496-4. doi: 10.1016/j.jtho.2019.06.016
Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard Laubenbacher, Jeffrey H. Chuang. Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors – PLoS Computational Biology 15(6): e1007026 (2019). / Education Materials GitHub page
Cho SY, Chae J, Na D, Kang W, Lee A, Min S, Kang J, Choi B, Lee J, Sung CO, Chuang JH, Lee C, Lee WS, Park H, Kim JI. Unstable Genome and Transcriptome Dynamics during Tumor Metastasis Contribute to Therapeutic Heterogeneity in Colorectal Cancers – Clin Cancer Res. 2019 May 1;25(9):2821-2834. doi: 10.1158/1078-0432.CCR-18-3460
Young Kwang Chae, Jonathan Anker , Michael Oh , Preeti Bais , Sandeep Namburi , Sarita Agte , Francis Giles , Jeffrey Chuang. Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinoma – Scientific Reports 9:3235 (2019).
Zi-Ming Zhao, Susan E. Yost, Katherine E. Hutchinson, Sierra Min Li, Yate-Ching Yuan, Javad Noorbakhsh, Zheng Liu, Charles Warden, Xiwei Wu, Jeffrey Chuang, Yuan Yuan. CCNE1 Amplification Is Associated with Poor Prognosis in Patients with Triple Negative Breast Cancer – BMC Cancer (2019) 19:96.
Victor G. Wang, Hyunsoo Kim, Jeffrey H. Chuang. Whole-exome sequencing capture kit biases yield false negative mutation calls in TCGA cohorts – PLoS ONE 13(10): e0204912. (2018).
Hyunsoo Kim, Pooja Kumar, Francesca Menghi, Javad Noorbakhsh, Eliza Cerveira, Mallory Ryan, Qihui Zhu, Guruprasad Ananda, Joshy George, Henry Chen, Susan Mockus, Chengsheng Zhang, Yan Yang, James Keck, R. Krishna Murthy Karuturi, Carol J Bult, Charles Lee, Edison T Liu, Jeffrey H Chuang. High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts – Scientific Reports 8: 17937 (2018). / Biorxiv version.
Javad Noorbakhsh, Hyunsoo Kim, Sandeep Namburi, Jeffrey Chuang. Distribution-based measures of tumor heterogeneity are sensitive to mutation calling and lack strong clinical predictive power – Scientific Reports 8:11445 DOI:10.1038/s41598-018-29154-7 (2018). / Biorxiv version.
Ivan Dotu, Scott Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras, and Jeffrey H Chuang. SARNAclust: Semi-Automatic Detection Of RNA Protein Binding Motifs From Immunoprecipitation Data – PLoS Comput Biol 14 (3): e1006078. (2018)
Sung-Yup Cho, Chang Ohk Sung, Jeesoo Chae, Jieun Lee, Deukchae Na, Wonyoung Kang, Jinjoo Kang, Seoyeon Min, Ahra Lee, Eunhye Kwak, Jooyoung Kim, Boram Choi, Hyunsoo Kim, Jeffrey H. Chuang, Hyo-Kyung Pak, Chan-Sik Park, Sanghui Park, Young Hyeh Ko, Dakeun Lee, Jin Roh, Min-Sun Cho, Seongyeol Park, Young Seok Ju, Yun-Suhk Suh, Seong-Ho Kong, Hyuk-Joon Lee, James Keck, Jacques Banchereau, Edison T. Liu, Woo-Ho Kim, Hansoo Park, Han-Kwang Yang, Jong-Il Kim and Charles Lee. Alterations in the Rho pathway contribute to Epstein-Barr virus-induced lymphomagenesis in immunosuppressed environments – Blood 131:1931-1941 (2018).
Young Kwang Chae, Jonathan F. Anker, Preeti Bais, Sandeep Namburi, Francis J. Giles and Jeffrey H. Chuang. Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma – Oncotarget. 9:7949-7960 (2018)
Javad Noorbakhsh and Jeffrey H Chuang, Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures – Nature Genetics 49, 1288–1289 doi:10.1038/ng.3876 (2017).
Preeti Bais, Sandeep Namburi, Daniel M. Gatti, Xinyu Zhang, Jeffrey H. Chuang. CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens – Bioinformatics, 33:3110-3112 (2017)
Ryuta Ishimura, Gabor Nagy, Ivan Dotu, Jeffrey H Chuang, and Susan Ackerman. Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation – eLife 10.7554/eLife.14295. (2016)
Francesca Menghi, Koichiro Inaki, XingYi Woo, Pooja A. Kumar, Krzysztof R. Grzeda, Ankit Malhotra, Hyunsoo Kim, Eladio J. Marquez, Duygu Ucar, Phung T. Shreckengast, Joel P. Wagner, R. Krishna Murthy Karuturi, James Keck, Jeffrey H. Chuang, and Edison T. Liu. The Tandem Duplicator Phenotype as a Distinct Genomic Configuration in Cancer – PNAS 113:17 E2373-E2382 (2016).
Tongjun Gu, Daniel M. Gatti, Anuj Srivastava, Elizabeth M. Snyder, Narayanan Raghupathy, Petr Simecek, Karen L. Svenson, Ivan Dotu, Jeffrey H. Chuang, Mark P. Keller, Alan D. Attie, Robert E. Braun, and Gary A. Churchill. Genetic Architectures of Quantitative Variation in RNA Editing Pathways – Genetics 202:798 (2016).
Rajani Rajbhandari, Braden McFarland, Ashish Patel, G Gray, Samuel Fehling, Markus Bredel, Nicolas Berbari, Hyunsoo Kim, Margaret Marks, Gordon Meares, Tanvi Sinha, Jeffrey Chuang, Etty Benveniste, and Susan Nozell. Loss of Tumor Suppressive MicroRNA-31 Enhances TRADD/NF-κB Signaling in Glioblastoma – Oncotarget 6:17805 (2015).
Hyunsoo Kim, Markus Bredel, Haesun Park, Jeffrey H Chuang. Identification of Tumor Subtypes of Endometrial Carcinoma by Integration of Heterogeneous Datasets – J Med Diagn Meth 4:189 (2015).
Krzysztof R Grzeda, Beryl Royer-Bertrand, Koichiro Inaki, Hyunsoo Kim, Axel M Hillmer, Edison T Liu, Jeffrey H Chuang. Functional chromatin features are associated with structural mutations in cancer – BMC Genomics 15:1013 (2014).
Ryuta Ishimura, Gabor Nagy, Ivan Dotu, Huihao Zhou, Xiang-Lei Yang, Paul Schimmel, Satoru Senju, Yasuharu Nishimura, Jeffrey H. Chuang, and Susan L. Ackerman. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration – Science 345, 455–459 (2014). / Science Perspective / News Summary in The Scientist
Lu Zhang, Norberto Díaz–Díaz, Kourosh Zarringhalam, Martin Hermansson, Pentti Somerharju, and Jeffrey Chuang. Dynamics of the ethanolamine glycerophospholipid remodeling network – PLoS ONE 7(12): e50858 (2012). doi:10.1371/journal.pone.0050858. / Software website
Kourosh Zarringhalam, Michelle Meyer, Ivan Dotu, Jeffrey H Chuang, and Peter Clote. Integrating chemical footprinting data into RNA secondary structure prediction -PLoS ONE 7(10): e45160. (2012) doi:10.1371/journal.pone.0045160
Kourosh Zarringhalam, Lu Zhang, Michael A Kiebish, Kui Yang, Xianlin Han, Richard W Gross, and Jeffrey H Chuang. Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition – PLoS ONE 7(5): e37293. (2012) doi:10.1371/journal.pone.0037293.
Deborah I Ritter, Zhiqiang dong, Su Guo, Jeffrey H Chuang, Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes – PLoS ONE 7(5): e35202 (2012). doi:10.1371/journal.pone.0035202.
Yang Ding, William A Lorenz and Jeffrey H Chuang. CodingMotif: Exact Determination of Overrepresented Nucleotide Motifs in Coding Sequences – BMC Bioinformatics. 13:32 (2012).
Busby MA, Gray JM, Costa AM, Stewart C, Stromberg MP, Barnett D, Chuang JH, Springer M, Marth GT. Expression divergence measured by transcriptome sequencing of four yeast species – BMC Genomics. 12:635 (2011).
Lu Zhang, Robert J. A. Bell, Michael A. Kiebish, Thomas N. Seyfried, Xianlin Han, Richard W. Gross, Jeffrey H. Chuang A Mathematical Model for the Determination of Steady-State Cardiolipin Remodeling Mechanisms Using Lipidomic Data – PLoS ONE 6:e21170 (2011)
Dong Cai, Lu Ren, Huaizhou Zhao, Chenjia Xu, Lu Zhang, Ying Yu, Hengzhi Wang, Yucheng Lan, Mary F. Roberts, Jeffrey H. Chuang, Michael J. Naughton, Zhifeng Ren and Thomas C. Chiles. A molecular-imprint nanosensor for ultrasensitive detection of proteins– Nature Nanotechnology 5:597 (2010). / Highlight on Nature Chemistry / Highlight on Nature Methods
Deborah I. Ritter, Qiang Li, Dennis Kostka, Katherine S Pollard, Su Guo, Jeffrey H Chuang. The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity – Mol Biol Evol. 27(10): 2322–2332. (2010).
Michael A. Kiebish, Rob Bell, Kui Yang, Toan Phan, Zhongdan Zhao, William Ames, Thomas N. Seyfried, Richard W. Gross, Jeffrey H. Chuang, and Xianlin Han. Dynamic simulation of cardiolipin remodeling: Greasing the wheels for an interpretative approach to lipidomics – J. Lipid Res. 51:2153 (2010).
Qiang Li, Deborah Ritter, Nan Yang, Zhiqiang Dong, Hao Li, Jeffrey H. Chuang, Su Guo. A systematic approach to identify functional motifs within vertebrate developmental enhancers – Developmental Biology 337:484 (2010).
Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, and Jeffrey H. Chuang. COMIT: Identification of Noncoding Motifs under Selection in Coding Sequences – Genome Biology 10:R133 (2009).
Merrick CJ, Dzikowski R, Imamura H, Chuang J, Deitsch K, Duraisingh MT. The effect of Plasmodium falciparum Sir2a histone deacetylase on clonal and longitudinal variation in expression of the var family of virulence genes – Int J Parasitol. 40:35 (2009).
Hideo Imamura, John E Karro and Jeffrey H. Chuang. Weak preservation of local neutral mutation rates across mammalian genomes – BMC Evolutionary Biology (2009), 9:89
Michael A. Kiebish, Xianlin Han, Hua Cheng, Jeffrey H. Chuang and Thomas N. Seyfried. Cardiolipin and electron transport chain abnormalities in mouse brain tumor mitochondria: Lipidomic evidence supporting the Warburg theory of cancer – Journal of Lipid Research, Vol. 49, 2545-2556 (2008)
Persampieri, D. I. Ritter, D. Lees, J. Lehoczky, Q. Li, S. Guo, and Jeffrey H. Chuang. cneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene Regulation – Bioinformatics, 24:2418-2419 (2008).
M.A. Kiebish, X. Han, H. Cheng, Jeffrey H. Chuang, and T.N. Seyfried. Brain Mitochondrial Lipid Abnormalities in Mice Susceptible to Spontaneous Gliomas – Lipids 43, 951-9 (2008).
A.K. Fox, B.B. Tuch, and Jeffrey H. Chuang. Measuring the Prevalence of Regional Mutation Rates: An Analysis of Silent Substitutions in Mammals, Fungi, and Insects – BMC: Evolutionary Biology, 8, 186 (2008).
M.A. Kiebish, X. Han, H. Cheng, A. Lunford, C.F. Clarke, H. Moon, Jeffrey H. Chuang, and T.N. Seyfried. Lipidomic Analysis and Electron Transport Chain Activities in C57BL/6J Mouse Brain Mitochondria – Journal of Neurochemistry 106, 299–312(2008).
Jeffrey H. Chuang and H. Li. Similarity of Synonymous Substitutions Rates Across Mammalian Genomes – Journal of Molecular Evolution, 65, 236 (2007).
Imamura, J. Persampieri, and Jeffrey H. Chuang. Sequences Conserved by Selection across Mouse and Human Malaria Species – BMC: Genomics, 8, 372 (2007).
Alvarez-Lorenzo, A. Concheiro, Jeffrey Chuang and A. Yu. Grosberg. Smart Polymers: Applications in Biotechnology and Biomedicine, Second Edition. Chapter title: Imprinting Using Smart Polymers – CRC Press: Boca Raton (2007).
C.S. Chin, Jeffrey H. Chuang, and H. Li. Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence. – Genome Research, 15, 205 (2005). / Supplementary Materials Website
Jeffrey Chuang and H. Li, Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome – PLOS Biology, 2, 0253, doi:10.1371/journal.pbio (2004).
Ito, J. Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Multiple Contact Adsorption of Target Molecules by Heteropolymer Gels – Macromolecular Symposia 207, 1 (2004).
Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Multiple point adsorption in a Heteropolymer Gel and the Tanaka Approach To Imprinting: Experiment and Theory – Grosberg, Progress in Polymer Science, 28, 1489 (2003).
Jeffrey Chuang, Y. Kantor, and M. Kardar, Anomalous Dynamics of Translocation – Physical Review E, 65, 011802 (2001).
Hiratani, C. Alvarez-Lorenzo, Jeffrey Chuang, O. Guney, A. Yu.Grosberg, and T. Tanaka, Effect of Reversible Cross-linker, N,N’-Bis(acryloyl)-cystamine, on Calcium Ion Adsorption by Imprinted Gels – Langmuir, 17, 4431 (2001).
Jeffrey Chuang, A. Yu. Grosberg, and M. Kardar. Free Energy Self-Averaging in Protein-Sized Heteropolymers – Physical Review Letters, 87, 078104 (2001).
Enoki, Jeffrey Chuang, T. Tanaka, A. Yu. Grosberg, et al., Frustrations in Polymer Gels and Their Minimization through Molecular Imprinting – Physical Review Letters, 85, 5000 (2000).
Jeffrey Chuang, A. Yu. Grosberg, and T. Tanaka. Topological Repulsion between Polymer Globules – Journal of Chemical Physics 112, 6434 (2000).