Difference between revisions of "Publications"
Line 11: | Line 11: | ||
'''MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms''' <div> | '''MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms''' <div> | ||
Minji Kim; Meizhen Zheng; Simon Zhongyuan Tian; Byoungkoo Lee; Jeffrey H. Chuang; Yijun Ruan. In press, Genome Biology. | Minji Kim; Meizhen Zheng; Simon Zhongyuan Tian; Byoungkoo Lee; Jeffrey H. Chuang; Yijun Ruan. In press, Genome Biology. | ||
+ | |||
+ | '''Longitudinal molecular trajectories of diffuse glioma patients.''' <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. | ||
'''Molecular biology and evolution of cancer: from discovery to action''' <div> | '''Molecular biology and evolution of cancer: from discovery to action''' <div> |
Revision as of 08:45, 12 November 2019
In reverse chronological order.
Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and AnalysisHenry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. Biorxiv preprint
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithmsMinji Kim; Meizhen Zheng; Simon Zhongyuan Tian; Byoungkoo Lee; Jeffrey H. Chuang; Yijun Ruan. In press, Genome Biology.
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, Nov 20 2019. doi: 10.1038/s41586-019-1775-1.
Molecular biology and evolution of cancer: from discovery to actionVictor 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 xenograftsJavad 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 neoantigensHyunsoo 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- 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).- PDF
- 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).- PDF
- 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.
- Supplementary Materials Website
- PDF