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Publication List (reverse chronological order)

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. Submitted for publication. Biorxiv version: SARNAclust: Semi-Automatic Detection Of RNA Protein Binding Motifs From Immunoprecipitation Data (2017).

Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures

Nature Genetics, Javad Noorbakhsh and Jeffrey H Chuang, in press (2017).

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

Preeti Bais, Sandeep Namburi, Daniel M. Gatti, Xinyu Zhang, Jeffrey H. Chuang. Bioinformatics 2017 btx375. doi: 10.1093/bioinformatics/btx375

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)

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 and Jeffrey H. Chuang. Mol Bio Evol 27:2322 (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

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

cneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene Regulation

Brain Mitochondrial Lipid Abnormalities in Mice Susceptible to Spontaneous Gliomas.

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

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).
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Sequences Conserved by Selection across Mouse and Human Malaria Species.

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).
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Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence.

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).
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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).
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Anomalous Dynamics of Translocation.

  • Jeffrey Chuang, Y. Kantor, and M. Kardar, Physical Review E, 65, 011802 (2001).
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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).
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Free Energy Self-Averaging in Protein-Sized Heteropolymers.

  • Jeffrey Chuang, A. Yu. Grosberg, and M. Kardar, Physical Review Letters, 87, 078104 (2001).
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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).
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Topological Repulsion between Polymer Globules.

  • Jeffrey Chuang, A. Yu. Grosberg, and T. Tanaka, Journal of Chemical Physics 112, 6434 (2000).
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