Publications

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In reverse chronological order.

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. Biorxiv preprint.

Pan-cancer classifications of tumor histological images using deep learning

Javad Noorbakhsh, Saman Farahmand, Mohammad Soltanieh-ha, Sandeep Namburi, Kourosh Zarringhalam, Jeffrey Chuang. Biorxiv preprint

pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks

Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. 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. Molecular Biology and Evolution, https://doi.org/10.1093/molbev/msz242 23 October 2019

Treating cancer as an invasive species

Javad Noorbakhsh, Zi-ming Zhao, James C. Russell, Jeffrey H. Chuang. In press, Molecular Cancer Research. 10.1158/1541-7786.MCR-19-0262

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).