Difference between revisions of "Publications"
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'''Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma'''<div> | '''Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma'''<div> | ||
| − | [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 | + | [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> |
| − | + | '''The CD123 Antibody-Drug Conjugate Pivekimab Sunirine Exerts Profound Activity in Preclinical Models of Pediatric Acute Lymphoblastic Leukemia''' <div> | |
| − | ''' | + | In review. <div> |
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''2024'' | ''2024'' | ||
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| + | '''Lessons Learned from 20 Years of Preclinical Testing in Pediatric Cancers'''<div> | ||
| + | [https://www.sciencedirect.com/science/article/pii/S0163725824001621 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. Pharmacology & Therapeutics. Volume 264, December 2024, 108742.]<div> | ||
'''Comprehensive single cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer''' <div> | '''Comprehensive single cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer''' <div> | ||
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> | 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> | ||
| − | '''Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments''' | + | '''Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments''' <div> |
[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> | [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> | ||
| + | *[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.] | ||
'''Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet Consortium'''<div> | '''Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet Consortium'''<div> | ||
| Line 24: | Line 27: | ||
'''Assessment of Patient-Derived Xenograft Growth and Antitumor Activity: The NCI PDXNet Consensus Recommendations'''<div> | '''Assessment of Patient-Derived Xenograft Growth and Antitumor Activity: The NCI PDXNet Consensus Recommendations'''<div> | ||
| − | 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. ( | + | [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> |
'''A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis'''<div> | '''A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis'''<div> | ||
Latest revision as of 11:29, 15 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
The CD123 Antibody-Drug Conjugate Pivekimab Sunirine Exerts Profound Activity in Preclinical Models of Pediatric Acute Lymphoblastic Leukemia
In review.
2024
Lessons Learned from 20 Years of Preclinical Testing in Pediatric Cancers
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. Pharmacology & Therapeutics. Volume 264, December 2024, 108742.
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
SAMPLER: unsupervised representations for rapid analysis of whole slide tissue images
2023
High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos
Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma.
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
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).
- PubMed Central Link
- JAX Press Release
- NCI news story
2020
Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological imagesJavad 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).
The effect of blurring on lung cancer subtype classification accuracy of convolutional neural networks.
JAX press releaseTejal 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 homeostasisIntegrative Deep Learning for PanCancer Molecular Subtype Classification Using Histopathological Images and RNAseq DataFatima 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 1–8Expression of the Neuronal tRNA n-Tr20 Regulates Synaptic Transmission and Seizure SusceptibilitySystematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and AnalysisYvonne 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 tracksHenry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. Bioinformatics (2020), 36:10, 15 May 2020, Pages 3234–3235Molecular biology and evolution of cancer: from discovery to actionTreating cancer as an invasive species
Earlier works
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithmsLongitudinal molecular trajectories of diffuse glioma patients.BMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastomaGenomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelinesThe implications of frameshift mutation burden on immune cell landscape and survival outcome in patients with non-small cell lung cancer (NSCLC)Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for ProfessorsUnstable Genome and Transcriptome Dynamics during Tumor Metastasis Contribute to Therapeutic Heterogeneity in Colorectal Cancers.Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinomaCCNE1 Amplification Is Associated with Poor Prognosis in Patients with Triple Negative Breast CancerWhole-exome sequencing capture kit biases yield false negative mutation calls in TCGA cohortsVictor 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 xenograftsHyunsoo 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).Distribution-based measures of tumor heterogeneity are sensitive to mutation calling and lack strong clinical predictive powerJavad Noorbakhsh, Hyunsoo Kim, Sandeep Namburi, Jeffrey Chuang. Scientific Reports 8:11445 DOI:10.1038/s41598-018-29154-7 (2018).SARNAclust: Semi-Automatic Detection Of RNA Protein Binding Motifs From Immunoprecipitation DataAlterations in the Rho pathway contribute to Epstein-Barr virus-induced lymphomagenesis in immunosuppressed environmentsMutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinomaUncertainties in tumor allele frequencies limit power to infer evolutionary pressuresJavad 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 neoantigensActivation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation InitiationThe Tandem Duplicator Phenotype as a Distinct Genomic Configuration in CancerGenetic Architectures of Quantitative Variation in RNA Editing PathwaysLoss of Tumor Suppressive MicroRNA-31 Enhances TRADD/NF-κB Signaling in GlioblastomaIdentification of Tumor Subtypes of Endometrial Carcinoma by Integration of Heterogeneous DatasetsHyunsoo Kim, Markus Bredel, Haesun Park, Jeffrey H Chuang. J Med Diagn Meth 4:189 (2015).
Functional chromatin features are associated with structural mutations in cancerRibosome stalling induced by mutation of a CNS-specific tRNA causes neurodegenerationRyuta 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 networkIntegrating chemical footprinting data into RNA secondary structure predictionStatistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species compositionTranscriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental GenesDeborah 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 SequencesYang Ding, William A Lorenz and Jeffrey H Chuang. BMC Bioinformatics. 13:32 (2012).Expression divergence measured by transcriptome sequencing of four yeast speciesA Mathematical Model for the Determination of Steady-State Cardiolipin Remodeling Mechanisms Using Lipidomic DataA molecular-imprint nanosensor for ultrasensitive detection of proteinsDong 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).- Highlight on Nature Chemistry
- Highlight on Nature Methods
The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer ActivityDynamic simulation of cardiolipin remodeling: Greasing the wheels for an interpretative approach to lipidomicsMichael 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 enhancersQiang 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 SequencesDeniz 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 genesWeak preservation of local neutral mutation rates across mammalian genomesHideo 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 cancercneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene RegulationJ. Persampieri, D. I. Ritter, D. Lees, J. Lehoczky, Q. Li, S. Guo, and Jeffrey H. Chuang. Bioinformatics, 24:2418-2419 (2008).- cneViewer website 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.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).- PDF
- Supplementary Materials Website
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).- Supplementary Materials Website 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).
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- Synopsis
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.
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- JAX Press Release
