Christopher H. Wiggins - Publications

Affiliations: 
Applied Mathematics Columbia University, New York, NY 
Area:
machine learning, statistics, computational biology, applied mathematics, theoretical physics
Website:
http://www.columbia.edu/~chw2/

69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Lammers NC, Galstyan V, Reimer A, Medin SA, Wiggins CH, Garcia HG. Multimodal transcriptional control of pattern formation in embryonic development. Proceedings of the National Academy of Sciences of the United States of America. PMID 31882445 DOI: 10.1073/Pnas.1912500117  0.01
2018 Park S, Megjhani M, Frey HP, Grave E, Wiggins C, Terilli KL, Roh DJ, Velazquez A, Agarwal S, Connolly ES, Schmidt JM, Claassen J, Elhadad N. Predicting delayed cerebral ischemia after subarachnoid hemorrhage using physiological time series data. Journal of Clinical Monitoring and Computing. PMID 29556884 DOI: 10.1007/S10877-018-0132-5  1
2018 Mayya V, Judokusumo E, Abu Shah E, Peel CG, Neiswanger W, Depoil D, Blair DA, Wiggins CH, Kam LC, Dustin ML. Durable Interactions of T Cells with T Cell Receptor Stimuli in the Absence of a Stable Immunological Synapse. Cell Reports. 22: 340-349. PMID 29320731 DOI: 10.1016/J.Celrep.2017.12.052  1
2016 Voelker MN, Kraff O, Brenner D, Wollrab A, Weinberger O, Berger MC, Robinson S, Bogner W, Wiggins C, Trampel R, Stöcker T, Niendorf T, Quick HH, Norris DG, Ladd ME, et al. The traveling heads: multicenter brain imaging at 7 Tesla. Magma (New York, N.Y.). PMID 27097904 DOI: 10.1007/S10334-016-0541-8  1
2016 Mugler A, Kittisopikul M, Hayden L, Liu J, Wiggins CH, Süel GM, Walczak AM. Noise Expands the Response Range of the Bacillus subtilis Competence Circuit. Plos Computational Biology. 12: e1004793. PMID 27003682 DOI: 10.1371/Journal.Pcbi.1004793  1
2015 Pivovarov R, Perotte AJ, Grave E, Angiolillo J, Wiggins CH, Elhadad N. Learning Probabilistic Phenotypes from Heterogeneous EHR Data. Journal of Biomedical Informatics. PMID 26464024 DOI: 10.1016/J.Jbi.2015.10.001  1
2015 Emmett KJ, Rosenstein JK, van de Meent JW, Shepard KL, Wiggins CH. Statistical inference for nanopore sequencing with a biased random walk model. Biophysical Journal. 108: 1852-5. PMID 25902425 DOI: 10.1016/J.Bpj.2015.03.013  1
2015 Greenfeld M, van de Meent JW, Pavlichin DS, Mabuchi H, Wiggins CH, Gonzalez RL, Herschlag D. Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. Bmc Bioinformatics. 16: 3. PMID 25591752 DOI: 10.1186/S12859-014-0429-4  1
2015 Mayya V, Neiswanger W, Medina R, Wiggins CH, Dustin ML. Integrative analysis of T cell motility from multi-channel microscopy data using TIAM. Journal of Immunological Methods. 416: 84-93. PMID 25445324 DOI: 10.1016/J.Jim.2014.11.004  1
2014 Abate F, Zairis S, Ficarra E, Acquaviva A, Wiggins CH, Frattini V, Lasorella A, Iavarone A, Inghirami G, Rabadan R. Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. Bmc Systems Biology. 8: 97. PMID 25183062 DOI: 10.1186/S12918-014-0097-Z  1
2014 Johnson S, van de Meent JW, Phillips R, Wiggins CH, Lindén M. Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion. Nucleic Acids Research. 42: 10265-77. PMID 25120267 DOI: 10.1093/Nar/Gku563  1
2014 van de Meent JW, Bronson JE, Wiggins CH, Gonzalez RL. Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments. Biophysical Journal. 106: 1327-37. PMID 24655508 DOI: 10.1016/J.Bpj.2013.12.055  1
2014 Gansell AR, Meent JWvd, Zairis S, Wiggins CH. Stylistic clusters and the Syrian/South Syrian tradition of first-millennium BCE Levantine ivory carving: A machine learning approach Journal of Archaeological Science. 44: 194-205. DOI: 10.1016/J.Jas.2013.11.005  1
2013 van de Meent JW, Bronson JE, Wood F, Gonzalez RL, Wiggins CH. Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data. Jmlr Workshop and Conference Proceedings. 28: 361-369. PMID 26985282  1
2013 Mancini F, Wiggins CH, Marsili M, Walczak AM. Time-dependent information transmission in a model regulatory circuit. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 022708. PMID 24032865 DOI: 10.1103/Physreve.88.022708  1
2013 Bertrand A, Pasquier A, Petiet A, Wiggins C, Kraska A, Joseph-Mathurin N, Aujard F, Mestre-Francés N, Dhenain M. Micro-MRI study of cerebral aging: ex vivo detection of hippocampal subfield reorganization, microhemorrhages and amyloid plaques in mouse lemur primates. Plos One. 8: e56593. PMID 23460806 DOI: 10.1371/journal.pone.0056593  0.01
2013 Meent Jvd, Gonzalez RL, Wiggins CH. Learning Kinetic Models from Single-Molecule FRET Data using Bayesian Inference Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2845  1
2013 Lindén M, Johnson S, Meent Jvd, Phillips R, Wiggins CH. Analysis of DNA Looping Kinetics in Tethered Particle Motion Experiments using Hidden Markov Models Biophysical Journal. 104: 4-8. DOI: 10.1016/J.Bpj.2012.11.2329  1
2013 Van De Meent JW, Bronson JE, Wood F, Gonzalez RL, Wiggins CH. Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data 30th International Conference On Machine Learning, Icml 2013. 1020-1028.  1
2012 Walczak AM, Mugler A, Wiggins CH. Analytic methods for modeling stochastic regulatory networks. Methods in Molecular Biology (Clifton, N.J.). 880: 273-322. PMID 23361990 DOI: 10.1007/978-1-61779-833-7_13  1
2012 Dewar M, Wiggins C, Wood F. Inference in hidden Markov models with explicit state duration distributions Ieee Signal Processing Letters. 19: 235-238. DOI: 10.1109/Lsp.2012.2184795  1
2011 Raj A, Dewar M, Palacios G, Rabadan R, Wiggins CH. Identifying hosts of families of viruses: a machine learning approach. Plos One. 6: e27631. PMID 22174744 DOI: 10.1371/Journal.Pone.0027631  1
2011 Mugler A, Grinshpun B, Franks R, Wiggins CH. Statistical method for revealing form-function relations in biological networks. Proceedings of the National Academy of Sciences of the United States of America. 108: 446-51. PMID 21183719 DOI: 10.1073/Pnas.1008898108  1
2010 Bronson JE, Hofman JM, Fei J, Gonzalez RL, Wiggins CH. Graphical models for inferring single molecule dynamics. Bmc Bioinformatics. 11: S2. PMID 21034427 DOI: 10.1186/1471-2105-11-S8-S2  1
2010 Mugler A, Walczak AM, Wiggins CH. Information-optimal transcriptional response to oscillatory driving. Physical Review Letters. 105: 058101. PMID 20867954 DOI: 10.1103/Physrevlett.105.058101  1
2010 Li X, Panea C, Wiggins CH, Reinke V, Leslie C. Learning "graph-mer" motifs that predict gene expression trajectories in development. Plos Computational Biology. 6: e1000761. PMID 20454681 DOI: 10.1371/Journal.Pcbi.1000761  1
2010 Raj A, Wiggins CH. An information-theoretic derivation of min-cut-based clustering. Ieee Transactions On Pattern Analysis and Machine Intelligence. 32: 988-95. PMID 20431126 DOI: 10.1109/Tpami.2009.124  1
2009 Mugler A, Ziv E, Nemenman I, Wiggins CH. Quantifying evolvability in small biological networks. Iet Systems Biology. 3: 379-87. PMID 21028928 DOI: 10.1049/Iet-Syb.2008.0165  1
2009 Bronson JE, Fei J, Hofman JM, Gonzalez RL, Wiggins CH. Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophysical Journal. 97: 3196-205. PMID 20006957 DOI: 10.1016/J.Bpj.2009.09.031  1
2009 Mugler A, Walczak AM, Wiggins CH. Spectral solutions to stochastic models of gene expression with bursts and regulation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 041921. PMID 19905356 DOI: 10.1103/Physreve.80.041921  1
2009 Fei J, Bronson JE, Hofman JM, Srinivas RL, Wiggins CH, Gonzalez RL. Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proceedings of the National Academy of Sciences of the United States of America. 106: 15702-7. PMID 19717422 DOI: 10.1073/Pnas.0908077106  1
2009 Walczak AM, Mugler A, Wiggins CH. A stochastic spectral analysis of transcriptional regulatory cascades. Proceedings of the National Academy of Sciences of the United States of America. 106: 6529-34. PMID 19351901 DOI: 10.1073/Pnas.0811999106  1
2008 Mugler A, Ziv E, Nemenman I, Wiggins CH. Serially regulated biological networks fully realise a constrained set of functions. Iet Systems Biology. 2: 313-22. PMID 19045826 DOI: 10.1049/Iet-Syb:20080097  1
2008 Dubin-Thaler BJ, Hofman JM, Cai Y, Xenias H, Spielman I, Shneidman AV, David LA, Döbereiner HG, Wiggins CH, Sheetz MP. Quantification of cell edge velocities and traction forces reveals distinct motility modules during cell spreading. Plos One. 3: e3735. PMID 19011687 DOI: 10.1371/Journal.Pone.0003735  1
2008 Hofman JM, Wiggins CH. Bayesian approach to network modularity. Physical Review Letters. 100: 258701. PMID 18643711 DOI: 10.1103/Physrevlett.100.258701  1
2007 Ziv E, Nemenman I, Wiggins CH. Optimal signal processing in small stochastic biochemical networks. Plos One. 2: e1077. PMID 17957259 DOI: 10.1371/Journal.Pone.0001077  1
2007 Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C. Learning regulatory programs that accurately predict differential expression with MEDUSA. Annals of the New York Academy of Sciences. 1115: 178-202. PMID 17934055 DOI: 10.1196/Annals.1407.020  1
2007 Albritton KH, Wiggins CH, Nelson HE, Weeks JC. Site of oncologic specialty care for older adolescents in Utah. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 25: 4616-21. PMID 17925557 DOI: 10.1200/JCO.2006.08.4103  1
2007 David LA, Wiggins CH. Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. Annals of the New York Academy of Sciences. 1115: 90-101. PMID 17925346 DOI: 10.1196/Annals.1407.009  1
2007 Crut A, Koster DA, Seidel R, Wiggins CH, Dekker NH. Fast dynamics of supercoiled DNA revealed by single-molecule experiments. Proceedings of the National Academy of Sciences of the United States of America. 104: 11957-62. PMID 17623785 DOI: 10.1073/Pnas.0700333104  1
2007 Sims TN, Soos TJ, Xenias HS, Dubin-Thaler B, Hofman JM, Waite JC, Cameron TO, Thomas VK, Varma R, Wiggins CH, Sheetz MP, Littman DR, Dustin ML. Opposing effects of PKCtheta and WASp on symmetry breaking and relocation of the immunological synapse. Cell. 129: 773-85. PMID 17512410 DOI: 10.1016/J.Cell.2007.03.037  1
2007 Dubin-Thaler BJ, Hofman JM, Xenias HV, Spielman IA, Shneidman AH, David L, Dobereiner H, Wiggins C, Sheetz MP. Quantification of Cell Movement Reveals Distinct Edge Motility Types During Cell Spreading Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2007.391.1  1
2006 Munk T, Hallatschek O, Wiggins CH, Frey E. Dynamics of semiflexible polymers in a flow field. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 74: 041911. PMID 17155100 DOI: 10.1103/Physreve.74.041911  1
2006 Cai Y, Biais N, Giannone G, Tanase M, Jiang G, Hofman JM, Wiggins CH, Silberzan P, Buguin A, Ladoux B, Sheetz MP. Nonmuscle myosin IIA-dependent force inhibits cell spreading and drives F-actin flow. Biophysical Journal. 91: 3907-20. PMID 16920834 DOI: 10.1529/Biophysj.106.084806  1
2006 Döbereiner HG, Dubin-Thaler BJ, Hofman JM, Xenias HS, Sims TN, Giannone G, Dustin ML, Wiggins CH, Sheetz MP. Lateral membrane waves constitute a universal dynamic pattern of motile cells. Physical Review Letters. 97: 038102. PMID 16907546 DOI: 10.1103/Physrevlett.97.038102  1
2006 Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. Bmc Bioinformatics. 7: S7. PMID 16723010 DOI: 10.1186/1471-2105-7-S1-S7  1
2006 Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C. A classification-based framework for predicting and analyzing gene regulatory response. Bmc Bioinformatics. 7: S5. PMID 16723008 DOI: 10.1186/1471-2105-7-S1-S5  1
2006 Ada-Nguema AS, Xenias H, Hofman JM, Wiggins CH, Sheetz MP, Keely PJ. The small GTPase R-Ras regulates organization of actin and drives membrane protrusions through the activity of PLCepsilon. Journal of Cell Science. 119: 1307-19. PMID 16537651 DOI: 10.1242/Jcs.02835  0.01
2006 Koster DA, Wiggins CH, Dekker NH. Multiple events on single molecules: unbiased estimation in single-molecule biophysics. Proceedings of the National Academy of Sciences of the United States of America. 103: 1750-5. PMID 16439482 DOI: 10.1073/Pnas.0510509103  1
2006 Ada-Nguema AS, Xenias H, Hofman JM, Wiggins CH, Sheetz M, Keely PJ. Erratum: The small GTPase R-Ras regulates organization of actin and drives membrane protrusions through the activity of PLCε (J. Cell Sci. vol. 119 (1307-1319)) Journal of Cell Science. 119. DOI: 10.1242/Jcs.03260  1
2005 Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C. Combining sequence and time series expression data to learn transcriptional modules. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 2: 194-202. PMID 17044183 DOI: 10.1109/Tcbb.2005.34  1
2005 Ziv E, Middendorf M, Wiggins CH. Information-theoretic approach to network modularity. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 71: 046117. PMID 15903736 DOI: 10.1103/Physreve.71.046117  1
2005 Middendorf M, Ziv E, Wiggins CH. Inferring network mechanisms: the Drosophila melanogaster protein interaction network. Proceedings of the National Academy of Sciences of the United States of America. 102: 3192-7. PMID 15728374 DOI: 10.1073/Pnas.0409515102  1
2005 Ziv E, Koytcheff R, Middendorf M, Wiggins C. Systematic identification of statistically significant network measures. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 71: 016110. PMID 15697661 DOI: 10.1103/Physreve.71.016110  1
2005 Middendorf M, Kundaje A, Shah M, Freund Y, Wiggins CH, Leslie C. Motif discovery through predictive modeling of gene regulation Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3500: 538-552.  1
2004 Middendorf M, Ziv E, Adams C, Hom J, Koytcheff R, Levovitz C, Woods G, Chen L, Wiggins C. Discriminative topological features reveal biological network mechanisms. Bmc Bioinformatics. 5: 181. PMID 15555081 DOI: 10.1186/1471-2105-5-181  1
2004 Bohbot-Raviv Y, Zhao WZ, Feingold M, Wiggins CH, Granek R. Relaxation dynamics of semiflexible polymers. Physical Review Letters. 92: 098101. PMID 15089516 DOI: 10.1103/Physrevlett.92.098101  1
2003 Wiggins C, Nemenman I. Process pathway inference via time series analysis Experimental Mechanics. 43: 361-370. DOI: 10.1007/Bf02410536  1
2003 Wiggins CH, Nemenman I. Process pathway inference via time series analysis Experimental Mechanics. 43: 361-370.  1
2001 Belmonte A, Shelley MJ, Eldakar ST, Wiggins CH. Dynamic patterns and self-knotting of a driven hanging chain. Physical Review Letters. 87: 114301. PMID 11531527 DOI: 10.1103/Physrevlett.87.114301  1
2001 Wiggins CH. Biopolymer mechanics: stability, dynamics, and statistics Mathematical Methods in the Applied Sciences. 24: 1325-1335. DOI: 10.1002/Mma.182  1
1998 Wiggins CH, Riveline D, Ott A, Goldstein RE. Trapping and wiggling: elastohydrodynamics of driven microfilaments. Biophysical Journal. 74: 1043-60. PMID 9533717 DOI: 10.1016/S0006-3495(98)74029-9  1
1998 Goldstein RE, Powers TR, Wiggins CH. Viscous Nonlinear Dynamics Of Twist And Writhe Physical Review Letters. 80: 5232-5235. DOI: 10.1103/Physrevlett.80.5232  1
1998 Wiggins CH, Goldstein RE. Flexive And Propulsive Dynamics Of Elastica At Low Reynolds Number Physical Review Letters. 80: 3879-3882. DOI: 10.1103/Physrevlett.80.3879  1
1998 Wiggins CH, Goldstein RE. Flexive and propulsive dynamics of elastica at low reynolds number Physical Review Letters. 80: 3879-3882.  1
1998 Goldstein RE, Powers TR, Wiggins CH. Viscous nonlinear dynamics of twist and writhe Physical Review Letters. 80: 5232-5235.  1
1997 Riveline D, Wiggins CH, Goldstein RE, Ott A. Elastohydrodynamic study of actin filaments using fluorescence microscopy Physical Review E. 56. DOI: 10.1103/Physreve.56.R1330  1
1997 Riveline D, Wiggins CH, Goldstein RE, Ott A. Elastohydrodynamic study of actin filaments using fluorescence microscopy Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 56: R1330-R1333.  1
1995 Wiggins CH, Spiegelman MW. Magma migration and magmatic solitary waves in 3-D Geophysical Research Letters. 22: 1289-1292. DOI: 10.1029/95Gl00269  0.01
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