Difference between revisions of "Publications"
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+ | '''Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments''' | ||
+ | [https://www.researchsquare.com/article/rs-2968528/v1 Victor Wang, Zichao Liu, Jan Martinek, Jie Zhou, Hannah Boruchov, Kelly Ray, Karolina Palucka, Jeffrey Chuang. Research square preprint. In review.] | ||
'''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 | + | [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 review.] |
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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> | '''Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet Consortium'''<div> | ||
− | [https:// | + | [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> |
'''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. (in press, Molecular Cancer Therapeutics). <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. (in press, Molecular Cancer Therapeutics). <div> | ||
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+ | '''A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis'''<div> | ||
+ | [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> | ||
'''Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples''' <div> | '''Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples''' <div> | ||
− | [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). | + | [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] |
'''SAMPLER: unsupervised representations for rapid analysis of whole slide tissue images'''<div> | '''SAMPLER: unsupervised representations for rapid analysis of whole slide tissue images'''<div> |
Latest revision as of 12:42, 26 July 2024
In reverse chronological order.
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. Research square preprint. In review.
Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma2023
High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos2022
NIH SenNet Consortium: Mapping the landscape of senescent cells throughout the human lifespan to understand physiological healthTranscriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function
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- 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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- PDF
- JAX Press Release