Difference between revisions of "Publications"

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In reverse chronological order.
 
In reverse chronological order.
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'''Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis''' <div>
 
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[https://www.biorxiv.org/content/10.1101/790246v1 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. Biorxiv preprint.]
 
  
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'''Pan-cancer classifications of tumor histological images using deep learning''' <div>
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'''STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication'''<div>
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[https://doi.org/10.1101/715656  Javad Noorbakhsh, Saman Farahmand, Mohammad Soltanieh-ha, Sandeep Namburi, Kourosh Zarringhalam, Jeffrey Chuang. Biorxiv preprint]
+
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. In review. <div>
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'''Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma'''<div>
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[https://doi.org/10.1101/2024.02.02.577085  Jill C. Rubinstein, Sergii Domanskyi, Todd B. Sheridan, Brian Sanderson, SungHee Park, Jessica Kaster, Haiyin Li, Olga Anczukow, Meenhard Herlyn, Jeffrey H. Chuang. Biorxiv preprint. In press, Cancer Research] <div>
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'''Lessons Learned from 20 Years of Preclinical Testing in Pediatric Cancers'''<div>
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MA Smith et al, in review. <div>
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'''The CD123 Antibody-Drug Conjugate Pivekimab Sunirine Exerts Profound Activity in Preclinical Models of Pediatric Acute Lymphoblastic Leukemia''' <div>
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In review. <div>
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----
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''2024''
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'''Comprehensive single cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer''' <div>
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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. Nature Aging, in press. <div>
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'''Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments''' <div>
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[https://www.nature.com/articles/s42003-024-06902-2 Victor Wang, Zichao Liu, Jan Martinek, Jie Zhou, Hannah Boruchov, Kelly Ray, Karolina Palucka, Jeffrey Chuang. Communications Biology volume 7, Article number: 1201 (2024).] <div>
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*[https://www.jax.org/news-and-insights/2024/october/a-new-lens-on-cancer-advanced-imaging-to-study-cancer-immune-interactions JAX News and Insights summary.]
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'''Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet Consortium'''<div>
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[https://aacrjournals.org/cancerrescommun/article/doi/10.1158/2767-9764.CRC-23-0417/746712/Development-and-application-of-genetic-ancestry  Paul Lott, Katherine Chiu, Juanita Elizabeth Quino, April Pangia Vang, Michael W Lloyd, Anuj Srivastava, PDXNet Consortium, Jeffrey H Chuang, Luis G Carvajal-Carmona. Cancer Research Communications (2024).] <div>
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'''Assessment of Patient-Derived Xenograft Growth and Antitumor Activity: The NCI PDXNet Consensus Recommendations'''<div>
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[https://aacrjournals.org/mct/article/23/7/924/746063/Assessment-of-Patient-Derived-Xenograft-Growth-and 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. Mol Cancer Ther (2024) 23 (7): 924–938.] <div>
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'''A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis'''<div>
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[https://aacrjournals.org/cancerres/article/84/13/2060/746135/A-Pan-Cancer-Patient-Derived-Xenograft-Histology 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. Cancer Research. 2024;84:2060–72.] <div>
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'''Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples''' <div>
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[https://doi.org/10.1016/j.crmeth.2024.100759 Sergii Domanskyi, Anuj Srivastava, Jessica Kaster, Haiyin Li, Meenhard Herlyn, Jill C Rubinstein, Jeffrey H Chuang. Cell Reports Methods (2024). Volume 4, Issue 5, 20 May 2024, 100759]
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'''SAMPLER: unsupervised representations for rapid analysis of whole slide tissue images'''<div>
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[https://www.sciencedirect.com/science/article/pii/S2352396423004747 Patience Mukashyaka, Todd B. Sheridan, Ali Foroughi pour, Jeffrey H. Chuang. eBioMedicine (2024). 99:104908]
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----
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''2023''
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'''High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos'''<div>
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[https://link.springer.com/article/10.1038/s41467-023-44162-6 Patience Mukashyaka, Pooja Kumar, David J. Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Olga Anczukow, Edison T. Liu, Jeffrey H. Chuang. Nature Communications 14, Article number: 8406 (2023)]
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'''Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma.''' <div>
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[https://aacrjournals.org/cancerres/article/83/24/4161/731553/Combining-the-Tyrosine-Kinase-Inhibitor 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. Cancer Res. 2023 Dec 15;83(24):4161-4178. doi: 10.1158/0008-5472.CAN-23-0604. PMID: 38098449; PMCID: PMC10722140.]
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'''Papillary Thyroid Cancer Immune Phenotypes via Tumor–Infiltrating Lymphocyte Spatial Analysis'''<div>
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[https://doi.org/10.1530/ERC-23-0110 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.  Endocrine-Related Cancer, 2023. 30:9 e230110]<div>
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'''In Vivo Activity of the Dual SYK/FLT3 Inhibitor TAK-659 Against Pediatric Acute Lymphoblastic Leukemia Xenografts''' <div>
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[http://doi.org/10.1002/pbc.30503  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. Pediatric Blood and Cancer, 2023, 70:9, e30503 http://dx.doi.org/10.1002/pbc.30503 .] <div>
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'''Spatial mapping of cellular senescence: emerging challenges and opportunities''' <div>
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[https://www.nature.com/articles/s43587-023-00446-6 NIH SenNet Consortium. Nature Aging volume 3, pages 776–790 (2023).] <div>
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'''Integrative deep learning analysis improves colon adenocarcinoma patient stratification at risk for mortality''' <div>
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[https://www.sciencedirect.com/science/article/pii/S2352396423002918 Jie Zhou, Ali Foroughi pour, Hany Deirawan, Fayez Daaboul, Thazin Aung, Rafic Beydoun, Fahad Shabbir Ahmed, Jeffrey H. Chuang. eBioMedicine. 2023. Vol. 94, 104726.] <div>
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'''Challenges and opportunities for modeling aging and cancer''' <div>
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[https://www.sciencedirect.com/science/article/pii/S153561082300079X?via%3Dihub 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. Cancer Cell. Volume 41, Issue 4, 10 April 2023, Pages 641-645.]
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----
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''2022''
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'''NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health''' <div>
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[https://www.nature.com/articles/s43587-022-00326-5 NIH SenNet Consortium, Nature Aging, vol. 2, pages 1090–1100 (2022)] <div>
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'''A path to translation: How 3D patient tumor avatars enable next generation precision oncology''' <div>
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[https://doi.org/10.1016/j.ccell.2022.09.017 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. Cancer Cell. Volume 40, Issue 12, 12 December 2022, Pages 1448-1453. https://doi.org/10.1016/j.ccell.2022.09.017] <div>
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'''Deep Learning Image Analysis Quantifies Tumor Heterogeneity and Identifies Microsatellite Instability in Colon Cancer''' <div>
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[https://onlinelibrary.wiley.com/doi/10.1002/jso.27118 Jill C. Rubinstein, Ali Foroughi pour, Jie Zhou, Todd Sheridan, Brian S White, and Jeffrey H. Chuang. 17 October 2022 Journal of Surgical Oncology. https://doi.org/10.1002/jso.27118] <div>
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'''Genetically Diverse Mouse Platform to Xenograft Cancer Cells''' <div>
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[https://journals.biologists.com/dmm/article/15/9/dmm049457/276456/Genetically-diverse-mouse-platform-to-xenograft 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. Dis Model Mech (2022) 15 (9): dmm049457.] <div>
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'''Regulated dicing of pre-mir-144 via reshaping of its terminal loop''' <div>
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[https://academic.oup.com/nar/article/50/13/7637/6633888 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. Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7637–7654] <div>
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'''Deep Learning Features Encode Interpretable Morphologies within Histological Images''' <div>
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[https://www.nature.com/articles/s41598-022-13541-2 Ali Foroughi Pour, Brian S. White, Jonghanne Park, Todd B. Sheridan, Jeffrey H. Chuang. Scientific Reports volume 12, Article number: 9428 (2022) ]<div>
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'''Cancer stem cells, not bulk tumor cells, determine mechanisms of resistance to SMO inhibitors''' <div>
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[https://doi.org/10.1158/2767-9764.CRC-22-0124 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 Research Communications (2022) 2 (6): 402–416.]<div>
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'''PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery''' <div>
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[https://academic.oup.com/narcancer/article/4/2/zcac014/6572305  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. NAR Cancer, Volume 4, Issue 2, June 2022, zcac014] <div>
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'''Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function'''
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<div>
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[https://www.sciencedirect.com/science/article/pii/S2666379122001380 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. Cell Reports Medicine. Volume 3, Issue 5, 17 May 2022, 100621] <div>
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'''A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology''' <div>
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[https://www.nature.com/articles/s43018-022-00337-6 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. Nature Cancer vol. 3, pages 232–250 (2022)] <div>
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'''Deep learning trained on H&E tumor ROIs predicts HER2 status and Trastuzumab treatment response in HER2+ breast cancer''' <div>
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[https://www.nature.com/articles/s41379-021-00911-w Saman Farahmand, Aileen Fernandez, Fahad Shabbir Ahmed, David Rimm, Jeffrey H Chuang, Emily Reisenbichler, Kourosh Zarringhalam.  Modern Pathology 35, pages 44–51 (2022).] <div>
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[https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=119702524 Image Data at The Cancer Imaging Archive]
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<div>
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----
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''2021''
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'''The Clp1 R140H mutation alters tRNA metabolism and mRNA 3’ processing in mouse models of pontocerebellar hypoplasia'''<div>
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[https://www.pnas.org/content/118/39/e2110730118 Caitlin E. Monaghan, Scott I. Adamson, Mridu Kapur, Jeffrey H. Chuang, and Susan L. Ackerman. PNAS (2021) 118 (39) e2110730118.] <div>
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'''Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment''' <div>
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[https://www.nature.com/articles/s41467-021-25177-3 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. Nature Communications. (2021) 12:5086] <div>
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'''Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology''' <div>
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[https://elifesciences.org/articles/66904 Markus Terrey, Scott Adamson, Jeffrey Chuang, and Susan Ackerman.  eLife (2021) 10:e66904] <div>
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'''Human KIT+ myeloid cells facilitate visceral metastasis by melanoma''' <div>
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[https://doi.org/10.1084/jem.20182163 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. J Exp Med (2021) 218 (6): e20182163.] <div>
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'''Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts''' <div>
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[https://www.nature.com/articles/s41588-020-00750-6 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.  Nature Genetics volume 53, pages 86–99 (2021).] <div>
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* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7808565 PubMed Central Link] <div>
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* [https://www.jax.org/news-and-insights/2021/january/connecting-cancer-research-to-clinical-trials JAX Press Release] <div>
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* [https://www.cancer.gov/news-events/cancer-currents-blog/2021/cancer-pdx-mouse-models-retain-genetics-human-tumor NCI news story] <div>
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----
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''2020''
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'''Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images''' <div>
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[https://doi.org/10.1038/s41467-020-20030-5 Javad Noorbakhsh , Saman Farahmand, Ali Foroughi pour, Sandeep Namburi, Dennis Caruana, David Rimm, Mohammad Soltanieh-ha, Kourosh Zarringhalam, and Jeffrey H Chuang. Nature Communications 11: 6367 (2020).] <br>
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[https://www.jax.org/news-and-insights/2020/december/unlocking-cancer-image-data JAX press release]
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'''The effect of blurring on lung cancer subtype classification accuracy of convolutional neural networks. '''<div>
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Tejal Nair, Ali Foroughi pour, Jeffrey H. Chuang. 2020 IEEE International Conference on Bioinformatics and Biomedicine, conference abstract.
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[http://chuanglabwiki.jax.org/images/e/ef/BIBM_NairForoughipour.pdf PDF]
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'''GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis''' <div>
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[https://elifesciences.org/articles/62731  Markus Terrey, Scott I Adamson, Alana L Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H Chuang, Susan L Ackerman eLife 2020;9:e62731 doi: 10.7554/eLife.62731]
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'''Integrative Deep Learning for PanCancer Molecular Subtype Classification Using Histopathological Images and RNAseq Data''' <div>
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[https://doi.org/10.1145/3388440.3412414 Fatima Zare, Javad Noorbakhsh,Tianyu Wang, Jeffrey H. Chuang, Sheida Nabavi. BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. September 2020 Article No.: 8 Pages 1–8] <div>
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[http://chuanglabwiki.jax.org/images/3/3e/Zare2020.pdf PDF]
  
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'''pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks''' <div>
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'''Expression of the Neuronal tRNA n-Tr20 Regulates Synaptic Transmission and Seizure Susceptibility''' <div>
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[https://www.biorxiv.org/content/10.1101/709683v1 Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. Biorxiv preprint]
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[https://doi.org/10.1016/j.neuron.2020.07.023  Mridu Kapur, Archan Ganguly, Gabor Nagy, Scott I. Adamson, Jeffrey H. Chuang, Wayne N. Frankel, Susan L. Ackerman. Neuron 108(1):193-208.e9 (2020)]
  
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'''MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms''' <div>
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'''Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis''' <div>
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Minji Kim; Meizhen Zheng; Simon Zhongyuan Tian; Byoungkoo Lee; Jeffrey H. Chuang; Yijun Ruan. In press, Genome Biology.  
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[https://cancerres.aacrjournals.org/content/80/11/2286.abstract 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.  Cancer Res 2020;80:2286–97]
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[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272270/ PubMedCentral open access]
  
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'''Longitudinal molecular trajectories of diffuse glioma patients.''' <div>
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'''pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks''' <div>
−
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. Nature, Nov 20 2019. doi: 10.1038/s41586-019-1775-1.
+
[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa061/5733724 Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan.  Bioinformatics (2020), 36:10, 15 May 2020, Pages 3234–3235 ] <div>
 +
[https://www.biorxiv.org/content/10.1101/709683v1  Biorxiv preprint]
  
 
'''Molecular biology and evolution of cancer: from discovery to action''' <div>
 
'''Molecular biology and evolution of cancer: from discovery to action''' <div>
−
[https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz242/5603308 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, https://doi.org/10.1093/molbev/msz242 23 October 2019]  
+
[https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz242/5603308 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. Mol Biol Evol. 2020 Feb 1;37(2):320-326.]  
  
 
'''Treating cancer as an invasive species'''<div>
 
'''Treating cancer as an invasive species'''<div>
−
[https://mcr.aacrjournals.org/content/early/2019/09/14/1541-7786.MCR-19-0262 Javad Noorbakhsh, Zi-ming Zhao, James C. Russell, Jeffrey H. Chuang. In press, Molecular Cancer Research. 10.1158/1541-7786.MCR-19-0262]
+
[https://mcr.aacrjournals.org/content/18/1/20 Javad Noorbakhsh, Zi-ming Zhao, James C. Russell, Jeffrey H. Chuang. Mol. Cancer Res. (2020). 18:20–6 doi:10.1158/1541-7786.MCR-19-0262]
 +
 
 +
----
 +
''Earlier works''
 +
 
 +
'''MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms''' <div>
 +
[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1868-z Minji Kim; Meizhen Zheng; Simon Zhongyuan Tian; Byoungkoo Lee; Jeffrey H. Chuang; Yijun Ruan. Genome Biology 20:251 (2019).]
 +
 
 +
'''Longitudinal molecular trajectories of diffuse glioma patients.''' <div>
 +
[https://www.nature.com/articles/s41586-019-1775-1 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.  Nature, Nature 576:112–120 (2019) doi: 10.1038/s41586-019-1775-1.]
  
 
'''BMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastoma'''<div>
 
'''BMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastoma'''<div>
Line 173: Line 318:
  
 
'''Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence.'''<div>
 
'''Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence.'''<div>
−
C.S. Chin, Jeffrey H. Chuang, and H. Li. Genome Research, 15, 205 (2005). <div>
+
[https://genome.cshlp.org/content/15/2/205.long C.S. Chin, Jeffrey H. Chuang, and H. Li. Genome Research, 15, 205 (2005).] <div>
−
*[http://chuanglabapps.jax.org/chuanglab/Papers/yeastreg.pdf PDF] <div>
 
 
*[http://genome.ucsf.edu/YeastReg/ Supplementary Materials Website] <div>
 
*[http://genome.ucsf.edu/YeastReg/ Supplementary Materials Website] <div>
  
Line 188: Line 332:
 
'''Multiple point adsorption in a Heteropolymer Gel and the Tanaka Approach To Imprinting: Experiment and Theory.''' <div>
 
'''Multiple point adsorption in a Heteropolymer Gel and the Tanaka Approach To Imprinting: Experiment and Theory.''' <div>
 
K. Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Progress in Polymer Science, 28, 1489 (2003). <div>
 
K. Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Progress in Polymer Science, 28, 1489 (2003). <div>
−
* [http://chuanglabapps.jax.org/chuanglab/Papers/oaxaca03_sub.pdf PDF]
+
* [http://chuanglabwiki.jax.org/images/5/5a/Progress_in_Polymer_Science_2003_Ito-1.pdf PDF]
  
 
'''Anomalous Dynamics of Translocation.''' <div>
 
'''Anomalous Dynamics of Translocation.''' <div>
 
Jeffrey Chuang, Y. Kantor, and M. Kardar, Physical Review E, 65, 011802 (2001). <div>
 
Jeffrey Chuang, Y. Kantor, and M. Kardar, Physical Review E, 65, 011802 (2001). <div>
−
* [http://chuanglabapps.jax.org/chuanglab/Papers/translocate.pdf PDF]
+
* [http://chuanglabwiki.jax.org/images/f/f1/Phys_Rev_E_Stat_Nonlin_Soft_Matter_Phys_2002_Chuang.pdf PDF]
  
 
'''Effect of Reversible Cross-linker, N,N'-Bis(acryloyl)-cystamine, on Calcium Ion Adsorption by Imprinted Gels.''' <div>
 
'''Effect of Reversible Cross-linker, N,N'-Bis(acryloyl)-cystamine, on Calcium Ion Adsorption by Imprinted Gels.''' <div>
Line 208: Line 352:
 
'''Topological Repulsion between Polymer Globules.'''<div>
 
'''Topological Repulsion between Polymer Globules.'''<div>
 
Jeffrey Chuang, A. Yu. Grosberg, and T. Tanaka, Journal of Chemical Physics 112, 6434 (2000). <div>
 
Jeffrey Chuang, A. Yu. Grosberg, and T. Tanaka, Journal of Chemical Physics 112, 6434 (2000). <div>
−
* [http://chuanglabapps.jax.org/chuanglab/Papers/toporepulsion.pdf PDF]
+
* [http://chuanglabwiki.jax.org/images/a/ac/The_Journal_of_Chemical_Physics_2000_Chuang.pdf PDF]

Latest revision as of 13:30, 12 November 2024

In reverse chronological order.

STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication
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. In review.
Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma
Jill C. Rubinstein, Sergii Domanskyi, Todd B. Sheridan, Brian Sanderson, SungHee Park, Jessica Kaster, Haiyin Li, Olga Anczukow, Meenhard Herlyn, Jeffrey H. Chuang. Biorxiv preprint. In press, Cancer Research
Lessons Learned from 20 Years of Preclinical Testing in Pediatric Cancers
MA Smith et al, in review.
The CD123 Antibody-Drug Conjugate Pivekimab Sunirine Exerts Profound Activity in Preclinical Models of Pediatric Acute Lymphoblastic Leukemia
In review.

2024

Comprehensive single cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer
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. Nature Aging, in press.
Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments
Victor Wang, Zichao Liu, Jan Martinek, Jie Zhou, Hannah Boruchov, Kelly Ray, Karolina Palucka, Jeffrey Chuang. Communications Biology volume 7, Article number: 1201 (2024).
Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet Consortium
Paul Lott, Katherine Chiu, Juanita Elizabeth Quino, April Pangia Vang, Michael W Lloyd, Anuj Srivastava, PDXNet Consortium, Jeffrey H Chuang, Luis G Carvajal-Carmona. Cancer Research Communications (2024).
Assessment of Patient-Derived Xenograft Growth and Antitumor Activity: The NCI PDXNet Consensus Recommendations
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. Mol Cancer Ther (2024) 23 (7): 924–938.
A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis
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. Cancer Research. 2024;84:2060–72.
Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

Sergii Domanskyi, Anuj Srivastava, Jessica Kaster, Haiyin Li, Meenhard Herlyn, Jill C Rubinstein, Jeffrey H Chuang. Cell Reports Methods (2024). Volume 4, Issue 5, 20 May 2024, 100759

SAMPLER: unsupervised representations for rapid analysis of whole slide tissue images

Patience Mukashyaka, Todd B. Sheridan, Ali Foroughi pour, Jeffrey H. Chuang. eBioMedicine (2024). 99:104908

2023

High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos

Patience Mukashyaka, Pooja Kumar, David J. Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Olga Anczukow, Edison T. Liu, Jeffrey H. Chuang. Nature Communications 14, Article number: 8406 (2023)

Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma.

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. Cancer Res. 2023 Dec 15;83(24):4161-4178. doi: 10.1158/0008-5472.CAN-23-0604. PMID: 38098449; PMCID: PMC10722140.

Papillary Thyroid Cancer Immune Phenotypes via Tumor–Infiltrating Lymphocyte Spatial Analysis
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. Endocrine-Related Cancer, 2023. 30:9 e230110
In Vivo Activity of the Dual SYK/FLT3 Inhibitor TAK-659 Against Pediatric Acute Lymphoblastic Leukemia Xenografts
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. 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).
Integrative deep learning analysis improves colon adenocarcinoma patient stratification at risk for mortality
Jie Zhou, Ali Foroughi pour, Hany Deirawan, Fayez Daaboul, Thazin Aung, Rafic Beydoun, Fahad Shabbir Ahmed, Jeffrey H. Chuang. eBioMedicine. 2023. Vol. 94, 104726.
Challenges and opportunities for modeling aging and cancer

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. 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)
A path to translation: How 3D patient tumor avatars enable next generation precision oncology
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. Cancer Cell. Volume 40, Issue 12, 12 December 2022, Pages 1448-1453. https://doi.org/10.1016/j.ccell.2022.09.017
Deep Learning Image Analysis Quantifies Tumor Heterogeneity and Identifies Microsatellite Instability in Colon Cancer
Jill C. Rubinstein, Ali Foroughi pour, Jie Zhou, Todd Sheridan, Brian S White, and Jeffrey H. Chuang. 17 October 2022 Journal of Surgical Oncology. https://doi.org/10.1002/jso.27118
Genetically Diverse Mouse Platform to Xenograft Cancer Cells
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. Dis Model Mech (2022) 15 (9): dmm049457.
Regulated dicing of pre-mir-144 via reshaping of its terminal loop
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. Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7637–7654
Deep Learning Features Encode Interpretable Morphologies within Histological Images
Ali Foroughi Pour, Brian S. White, Jonghanne Park, Todd B. Sheridan, Jeffrey H. Chuang. Scientific Reports volume 12, Article number: 9428 (2022)
Cancer stem cells, not bulk tumor cells, determine mechanisms of resistance to SMO inhibitors
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 Research Communications (2022) 2 (6): 402–416.
PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery
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. NAR Cancer, Volume 4, Issue 2, June 2022, zcac014

Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function

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. Cell Reports Medicine. Volume 3, Issue 5, 17 May 2022, 100621
A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology
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. Nature Cancer vol. 3, pages 232–250 (2022)
Deep learning trained on H&E tumor ROIs predicts HER2 status and Trastuzumab treatment response in HER2+ breast cancer
Saman Farahmand, Aileen Fernandez, Fahad Shabbir Ahmed, David Rimm, Jeffrey H Chuang, Emily Reisenbichler, Kourosh Zarringhalam. Modern Pathology 35, pages 44–51 (2022).

Image Data at The Cancer Imaging Archive

2021

The Clp1 R140H mutation alters tRNA metabolism and mRNA 3’ processing in mouse models of pontocerebellar hypoplasia
Caitlin E. Monaghan, Scott I. Adamson, Mridu Kapur, Jeffrey H. Chuang, and Susan L. Ackerman. PNAS (2021) 118 (39) e2110730118.
Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment
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. Nature Communications. (2021) 12:5086
Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology
Markus Terrey, Scott Adamson, Jeffrey Chuang, and Susan Ackerman. eLife (2021) 10:e66904
Human KIT+ myeloid cells facilitate visceral metastasis by melanoma
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. J Exp Med (2021) 218 (6): e20182163.
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts
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. Nature Genetics volume 53, pages 86–99 (2021).

2020

Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images

Javad Noorbakhsh , Saman Farahmand, Ali Foroughi pour, Sandeep Namburi, Dennis Caruana, David Rimm, Mohammad Soltanieh-ha, Kourosh Zarringhalam, and Jeffrey H Chuang. Nature Communications 11: 6367 (2020).
JAX press release

The effect of blurring on lung cancer subtype classification accuracy of convolutional neural networks.

Tejal Nair, Ali Foroughi pour, Jeffrey H. Chuang. 2020 IEEE International Conference on Bioinformatics and Biomedicine, conference abstract. PDF

GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis

Markus Terrey, Scott I Adamson, Alana L Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H Chuang, Susan L Ackerman eLife 2020;9:e62731 doi: 10.7554/eLife.62731

Integrative Deep Learning for PanCancer Molecular Subtype Classification Using Histopathological Images and RNAseq Data
Fatima Zare, Javad Noorbakhsh,Tianyu Wang, Jeffrey H. Chuang, Sheida Nabavi. BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. September 2020 Article No.: 8 Pages 1–8

PDF

Expression of the Neuronal tRNA n-Tr20 Regulates Synaptic Transmission and Seizure Susceptibility

Mridu Kapur, Archan Ganguly, Gabor Nagy, Scott I. Adamson, Jeffrey H. Chuang, Wayne N. Frankel, Susan L. Ackerman. Neuron 108(1):193-208.e9 (2020)

Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis

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. Cancer Res 2020;80:2286–97 PubMedCentral open access

pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks
Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. Bioinformatics (2020), 36:10, 15 May 2020, Pages 3234–3235

Biorxiv preprint

Molecular biology and evolution of cancer: from discovery to action

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. Mol Biol Evol. 2020 Feb 1;37(2):320-326.

Treating cancer as an invasive species

Javad Noorbakhsh, Zi-ming Zhao, James C. Russell, Jeffrey H. Chuang. Mol. Cancer Res. (2020). 18:20–6 doi:10.1158/1541-7786.MCR-19-0262

Earlier works

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms

Minji Kim; Meizhen Zheng; Simon Zhongyuan Tian; Byoungkoo Lee; Jeffrey H. Chuang; Yijun Ruan. Genome Biology 20:251 (2019).

Longitudinal molecular trajectories of diffuse glioma patients.

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. Nature, Nature 576:112–120 (2019) doi: 10.1038/s41586-019-1775-1.

BMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastoma

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. Sci Rep. 2019 Oct 10;9(1):14569. doi: 10.1038/s41598-019-51270-1

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines

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. BMC Medical Genomics (2019) 12:92

The implications of frameshift mutation burden on immune cell landscape and survival outcome in patients with non-small cell lung cancer (NSCLC)

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. J Thorac Oncol. 2019 Jun 22. pii: S1556-0864(19)30496-4. doi: 10.1016/j.jtho.2019.06.016

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors

Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard Laubenbacher, Jeffrey H. Chuang. PLoS Computational Biology 15(6): e1007026 (2019).

Unstable Genome and Transcriptome Dynamics during Tumor Metastasis Contribute to Therapeutic Heterogeneity in Colorectal Cancers.

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. Clin Cancer Res. 2019 May 1;25(9):2821-2834. doi: 10.1158/1078-0432.CCR-18-3460

Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinoma

Young Kwang Chae, Jonathan Anker , Michael Oh , Preeti Bais , Sandeep Namburi , Sarita Agte , Francis Giles , Jeffrey Chuang. Scientific Reports 9:3235 (2019).

CCNE1 Amplification Is Associated with Poor Prognosis in Patients with Triple Negative Breast Cancer

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. BMC Cancer (2019) 19:96.

Whole-exome sequencing capture kit biases yield false negative mutation calls in TCGA cohorts

Victor G. Wang, Hyunsoo Kim, Jeffrey H. Chuang. PLoS ONE 13(10): e0204912. (2018).

High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts
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. Scientific Reports 8: 17937 (2018).

Biorxiv version.

Distribution-based measures of tumor heterogeneity are sensitive to mutation calling and lack strong clinical predictive power
Javad Noorbakhsh, Hyunsoo Kim, Sandeep Namburi, Jeffrey Chuang. Scientific Reports 8:11445 DOI:10.1038/s41598-018-29154-7 (2018).

Biorxiv version.

SARNAclust: Semi-Automatic Detection Of RNA Protein Binding Motifs From Immunoprecipitation Data

Ivan Dotu, Scott Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras, and Jeffrey H Chuang. PLoS Comput Biol 14 (3): e1006078. (2018)

Alterations in the Rho pathway contribute to Epstein-Barr virus-induced lymphomagenesis in immunosuppressed environments

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. Blood 131:1931-1941 (2018).

Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma

Young Kwang Chae, Jonathan F. Anker, Preeti Bais, Sandeep Namburi, Francis J. Giles and Jeffrey H. Chuang. Oncotarget. 9:7949-7960 (2018)

Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures

Javad Noorbakhsh and Jeffrey H Chuang, Nature Genetics 49, 1288–1289 doi:10.1038/ng.3876 (2017).

CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens

Preeti Bais, Sandeep Namburi, Daniel M. Gatti, Xinyu Zhang, Jeffrey H. Chuang. Bioinformatics, 33:3110-3112 (2017)

Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation

Ryuta Ishimura, Gabor Nagy, Ivan Dotu, Jeffrey H Chuang, and Susan Ackerman. eLife 10.7554/eLife.14295. (2016)

The Tandem Duplicator Phenotype as a Distinct Genomic Configuration in Cancer

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. PNAS 113:17 E2373-E2382 (2016).

Genetic Architectures of Quantitative Variation in RNA Editing Pathways

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. Genetics 202:798 (2016).

Loss of Tumor Suppressive MicroRNA-31 Enhances TRADD/NF-κB Signaling in Glioblastoma

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. Oncotarget 6:17805 (2015).

Identification of Tumor Subtypes of Endometrial Carcinoma by Integration of Heterogeneous Datasets

Hyunsoo Kim, Markus Bredel, Haesun Park, Jeffrey H Chuang. J Med Diagn Meth 4:189 (2015).

Functional chromatin features are associated with structural mutations in cancer

Krzysztof R Grzeda, Beryl Royer-Bertrand, Koichiro Inaki, Hyunsoo Kim, Axel M Hillmer, Edison T Liu, Jeffrey H Chuang. BMC Genomics 15:1013 (2014).

Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration
Ryuta Ishimura, Gabor Nagy, Ivan Dotu, Huihao Zhou, Xiang-Lei Yang, Paul Schimmel, Satoru Senju, Yasuharu Nishimura, Jeffrey H. Chuang, and Susan L. Ackerman. Science 345, 455–459 (2014).
Dynamics of the ethanolamine glycerophospholipid remodeling network

Lu Zhang, Norberto Díaz–Díaz, Kourosh Zarringhalam, Martin Hermansson, Pentti Somerharju, and Jeffrey Chuang. PLoS ONE 7(12): e50858 (2012). doi:10.1371/journal.pone.0050858

Integrating chemical footprinting data into RNA secondary structure prediction

Kourosh Zarringhalam, Michelle Meyer, Ivan Dotu, Jeffrey H Chuang, and Peter Clote. PLoS ONE 7(10): e45160. (2012) doi:10.1371/journal.pone.0045160

Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition

Kourosh Zarringhalam, Lu Zhang, Michael A Kiebish, Kui Yang, Xianlin Han, Richard W Gross, and Jeffrey H Chuang. PLoS ONE 7(5): e37293. (2012) doi:10.1371/journal.pone.0037293.

Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes
Deborah I Ritter, Zhiqiang dong, Su Guo, Jeffrey H Chuang, PLoS ONE 7(5): e35202 (2012). doi:10.1371/journal.pone.0035202.
CodingMotif: Exact Determination of Overrepresented Nucleotide Motifs in Coding Sequences
Yang Ding, William A Lorenz and Jeffrey H Chuang. BMC Bioinformatics. 13:32 (2012).
Expression divergence measured by transcriptome sequencing of four yeast species

Busby MA, Gray JM, Costa AM, Stewart C, Stromberg MP, Barnett D, Chuang JH, Springer M, Marth GT. BMC Genomics. 12:635 (2011).

A Mathematical Model for the Determination of Steady-State Cardiolipin Remodeling Mechanisms Using Lipidomic Data

Lu Zhang, Robert J. A. Bell, Michael A. Kiebish, Thomas N. Seyfried, Xianlin Han, Richard W. Gross, Jeffrey H. Chuang PLoS ONE 6:e21170 (2011)

A molecular-imprint nanosensor for ultrasensitive detection of proteins
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. Nature Nanotechnology 5:597 (2010).
The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity

Deborah I. Ritter, Qiang Li, Dennis Kostka, Katherine S Pollard, Su Guo, Jeffrey H Chuang. Mol Biol Evol. 27(10): 2322–2332. (2010).

Dynamic simulation of cardiolipin remodeling: Greasing the wheels for an interpretative approach to lipidomics
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. J. Lipid Res. 51:2153 (2010).
A systematic approach to identify functional motifs within vertebrate developmental enhancers
Qiang Li, Deborah Ritter, Nan Yang, Zhiqiang Dong, Hao Li, Jeffrey H. Chuang, Su Guo. Developmental Biology 337:484 (2010).
COMIT: Identification of Noncoding Motifs under Selection in Coding Sequences
Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, and Jeffrey H. Chuang. Genome Biology 10:R133 (2009).
The effect of Plasmodium falciparum Sir2a histone deacetylase on clonal and longitudinal variation in expression of the var family of virulence genes

Merrick CJ, Dzikowski R, Imamura H, Chuang J, Deitsch K, Duraisingh MT. Int J Parasitol. 40:35 (2009).

Weak preservation of local neutral mutation rates across mammalian genomes

Hideo Imamura, John E Karro and Jeffrey H. Chuang. BMC Evolutionary Biology (2009), 9:89

Cardiolipin and electron transport chain abnormalities in mouse brain tumor mitochondria: Lipidomic evidence supporting the Warburg theory of cancer

Michael A. Kiebish, Xianlin Han, Hua Cheng, Jeffrey H. Chuang and Thomas N. Seyfried. Journal of Lipid Research, Vol. 49, 2545-2556 (2008)

cneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene Regulation
J. Persampieri, D. I. Ritter, D. Lees, J. Lehoczky, Q. Li, S. Guo, and Jeffrey H. Chuang. Bioinformatics, 24:2418-2419 (2008).
Brain Mitochondrial Lipid Abnormalities in Mice Susceptible to Spontaneous Gliomas.

M.A. Kiebish, X. Han, H. Cheng, Jeffrey H. Chuang, and T.N. Seyfried. Lipids 43, 951-9 (2008).

Measuring the Prevalence of Regional Mutation Rates: An Analysis of Silent Substitutions in Mammals, Fungi, and Insects.

A.K. Fox, B.B. Tuch, and Jeffrey H. Chuang. BMC: Evolutionary Biology, 8, 186 (2008).

Lipidomic Analysis and Electron Transport Chain Activities in C57BL/6J Mouse Brain Mitochondria.

M.A. Kiebish, X. Han, H. Cheng, A. Lunford, C.F. Clarke, H. Moon, Jeffrey H. Chuang, and T.N. Seyfried. Journal of Neurochemistry 106, 299–312(2008).

Similarity of Synonymous Substitutions Rates Across Mammalian Genomes.
Jeffrey H. Chuang and H. Li. Journal of Molecular Evolution, 65, 236 (2007).
Sequences Conserved by Selection across Mouse and Human Malaria Species.
H. Imamura, J. Persampieri, and Jeffrey H. Chuang. BMC: Genomics, 8, 372 (2007).
Smart Polymers: Applications in Biotechnology and Biomedicine, Second Edition. Chapter title: Imprinting Using Smart Polymers.
C. Alvarez-Lorenzo, A. Concheiro, Jeffrey Chuang and A. Yu. Grosberg. CRC Press: Boca Raton (2007).
Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence.
C.S. Chin, Jeffrey H. Chuang, and H. Li. Genome Research, 15, 205 (2005).
Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome.
Jeffrey Chuang and H. Li, PLOS Biology, 2, 0253, doi:10.1371/journal.pbio (2004).
Multiple Contact Adsorption of Target Molecules by Heteropolymer Gels.
K. Ito, J. Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Macromolecular Symposia 207, 1 (2004).
Multiple point adsorption in a Heteropolymer Gel and the Tanaka Approach To Imprinting: Experiment and Theory.
K. Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Progress in Polymer Science, 28, 1489 (2003).
Anomalous Dynamics of Translocation.
Jeffrey Chuang, Y. Kantor, and M. Kardar, Physical Review E, 65, 011802 (2001).
Effect of Reversible Cross-linker, N,N'-Bis(acryloyl)-cystamine, on Calcium Ion Adsorption by Imprinted Gels.
H. Hiratani, C. Alvarez-Lorenzo, Jeffrey Chuang, O. Guney, A. Yu.Grosberg, and T. Tanaka, Langmuir, 17, 4431 (2001).
Free Energy Self-Averaging in Protein-Sized Heteropolymers.
Jeffrey Chuang, A. Yu. Grosberg, and M. Kardar, Physical Review Letters, 87, 078104 (2001).
Frustrations in Polymer Gels and Their Minimization through Molecular Imprinting.
T. Enoki, Jeffrey Chuang, T. Tanaka, A. Yu. Grosberg, et al., Physical Review Letters, 85, 5000 (2000).
Topological Repulsion between Polymer Globules.
Jeffrey Chuang, A. Yu. Grosberg, and T. Tanaka, Journal of Chemical Physics 112, 6434 (2000).