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Publications

Selected Center Investigators’ Publications in Quantitative Biology

Stoeger, T., Gerlach, M., Morimoto, R.I., Amaral, L.A.N. (2018). Large-scale investigation of the reasons why potentially important genes are ignored. PLoS Biol 16(9): e2006643. https://doi.org/10.1371/journal.pbio.2006643

Braun, R.Kath, W. L., Iwanaszko, M., Kula-Eversole, E., Abbott, S. M., Reid, K.J., Zee, P. C., Allada, R.(2018). Universal method for robust detection of circadian state from gene expression. PNAS USA, pii: 201800314. doi: 10.1073/pnas.1800314115. [Epub ahead of print]

Nguyen, P, Braun, R. (2017) Semi-supervised network inference using simulated gene expression dynamics. Bioinformatics, 1;34(7), 1148-1156. doi: 10.1093/bioinformatics/btx748.

Lee D, Yang H, Kim J, Brady SC, Zamanian M, Kim H, Paik Y, Kruglyak L, Andersen EC, and Lee J. (2017). The genetic basis of natural variation in a phoretic behavior. Nature Communications8, 273. http://doi.org/10.1038/s41467-017-00386-x

Mangan, N. M., Kutz, J. N., Brunton, S. L., & Proctor, J. L. (2017). Model selection for dynamical systems via sparse regression and information criteriaProceedings. Mathematical, Physical, and Engineering Sciences473(2204), 20170009. http://doi.org/10.1098/rspa.2017.0009

Zdraljevic S, Strand C, Seidel HS, Cook DE, Doench JG, and Andersen EC. (2017) Natural variation in a single amino acid underlies physiological responses to topoisomerase II poisons. PLoS Genetics13(7), e1006891. http://doi.org/10.1371/journal.pgen.1006891

Jakobson, C. M., Tullman-Ercek, D., Slininger, M. F., & Mangan, N. M. (2017). A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestrationPLoS Computational Biology13(5), e1005525. http://doi.org/10.1371/journal.pcbi.1005525

Laricchia KM, Zdraljevic S, Cook De, and Andersen EC. (2017) Natural variation in the distribution and abundance of transposable elements across the Caenorhabditis elegans species. Molecular Biology and Evolution34(9), 2187–2202. http://doi.org/10.1093/molbev/msx155

Kim, S., Cassidy, J. J., Yang, B., Carthew, R. W., & Hilgenfeldt, S. (2016). Hexagonal Patterning of the Insect Compound Eye: Facet Area Variation, Defects, and Disorder. Biophysical Journal111(12), 2735–2746. http://doi.org/10.1016/j.bpj.2016.11.004

Li, J., Kath, W. L. (2016). A Path-Based Method for Simulating Large Deviations and Rare Events in Nonlinear Lightwave Systems, Stud. Appl. Math. 137,159-173.

Voong, L. N., Xi, L., Sebeson, A. C., Xiong, B., Wang, J.-P., & Wang, X. (2016). Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical MappingCell167(6), 1555–1570.e15. http://doi.org/10.1016/j.cell.2016.10.049

Mangan, N. M., Flamholz, A., Hood, R. D., Milo, R., & Savage, D. F. (2016). pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proceedings of the National Academy of Sciences of the United States of America113(36), E5354–E5362. http://doi.org/10.1073/pnas.1525145113

N M Mangan S L Brunton, J L Proctor, and J N Kutz. (2016) Inferring biological networks by sparse identification of nonlinear dynamics. IEEE Transactions on Molecular, Biological and Multi-Scale Communications, 2(1), 52-63.

Antonio Auffinger, Wei-Kuo Chen. (2016). The Legendre structure of the Parisi formula. Comm. in Math. Physics, 348(3), 751-770.

Yu JS, Bagheri N. (2016) Multi-class and multi-scale models of complex biological phenomena. Curr Opin Biotech, 39, 167-173. PMID:27115496. https://doi.org/10.1016/j.copbio.2016.04.002

Cook DE, Zdraljevic S, Tanny RE, Seo B, Riccardi DD, Noble LM, Rockman MV, Alkema MJ, Braendle C, Kammenga JE, Wang J, Krulgyak L, Felix MA, Lee J, and Andersen EC. (2016) The genetic basis of natural variation in C. elegans telomere length. Genetics204(1), 371–383. http://doi.org/10.1534/genetics.116.191148

Braun, R. and Shah, S. (2016) Network methods for pathway analysis of gene expression data. Computational and Structural Biotechnology Journal. http://arxiv.org/abs/1411.1993

Peláez N, Gavalda-Miralles A, Wang B, Tejedor Navarro H, Gudjonson H, Rebay, I, Dinner, AR, Katsaggelos AK, Amaral LAN and Carthew RW (2015). Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation. eLife4, e08924. http://doi.org/10.7554/eLife.08924

Wells, D. K., Kath, W. L., & Motter, A. E. (2015). Control of Stochastic and Induced Switching in Biophysical Networks. Physical Review. X5, 031036. http://doi.org/10.1103/PhysRevX.5.031036

Wells, D. K., Chuang, Y., Knapp, L. M., Brockmann, D., Kath, W. L., & Leonard, J. N. (2015). Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune NetworksPLoS Computational Biology11(4), e1004181. http://doi.org/10.1371/journal.pcbi.1004181

Antonio Auffinger, Wei-Kuo Chen. (2015) The Parisi formula has a unique minimizer. Comm. in Math. Phys., 335(3), 1429-1444.

Buitrago-Delgado, E., Nordin, K., Rao, A., Geary, L., and LaBonne, C. (2015). Shared Pluripotency Programs Suggest Derivation of Vertebrate Neural Crest from Blastula Cells. Science (New York, N.Y.)348(6241), 1332–1335. http://doi.org/10.1126/science.aaa3655

Ciaccio, M. F., Chen, V. C., Jones, R. B., & Bagheri, N. (2015). The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. Integrative Biology : Quantitative Biosciences from Nano to Macro7(7), 776–791. http://doi.org/10.1039/c5ib00065c

Antonio Auffinger, Wei-Kuo Chen. (2015). On properties of Parisi measures. Probab. Theory and Rel. Fields. 161(3), 817-850.

Popovic, R., Martinez-Garcia, E., Giannopoulou, E. G., Zhang, Q., Zhang, Q., Ezponda, T., Shah, M. Y., Zheng, Y. P., Will, C. M., Small, E. C., Hua, J. Y., Bulic, M., Jiang, Y. W., Carrara, M., Calogero, R. A., Kath, W. L., Kelleher, N. L., Wang, J. P., Elemento O. and Licht, J. D. (2014). Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation. PLoS Genetics10(9), e1004566. http://doi.org/10.1371/journal.pgen.1004566

Lu, Y., Liang, F.-X., & Wang, X. (2014). A synthetic biology approach identifies the mammalian UPR RNA ligase RtcBMolecular Cell55(5), 758–770. http://doi.org/10.1016/j.molcel.2014.06.032

Zhang, Q., Burdette, J. E., & Wang, J.-P. (2014). Integrative network analysis of TCGA data for ovarian cancerBMC Systems Biology8, 1338. http://doi.org/10.1186/s12918-014-0136-9

Duncan, M. T., Shin, S., Wu, J. J., Mays, Z., Weng, S., Bagheri, N., Miller, W.M., Shea, L.D. (2014). Dynamic Transcription Factor Activity Profiles Reveal Key Regulatory Interactions During Megakaryocytic and Erythroid Differentiation. Biotechnology and Bioengineering111(10), 2082–2094. http://doi.org/10.1002/bit.25262

Mangan, N. M., & Brenner, M. P. (2014). Systems analysis of the CO2concentrating mechanism in cyanobacteria. eLife3, e02043. http://doi.org/10.7554/eLife.02043

Nordin, K., and LaBonne, C. (2014). Sox5 is a DNA binding co-factor for BMP R-Smads that directs target specificity during patterning of the early ectodermDevelopmental Cell31(3), 374–382. http://doi.org/10.1016/j.devcel.2014.10.003

Ciaccio, M. F., Finkle, J. D., Xue, A. Y., & Bagheri, N. (2014). A Systems Approach to Integrative Biology: An Overview of Statistical Methods to Elucidate Association and ArchitectureIntegrative and Comparative Biology54(2), 296–306. http://doi.org/10.1093/icb/icu037

Braun, R. (2014). Systems Analysis of High–Throughput DataAdvances in Experimental Medicine and Biology844, 153–187. http://doi.org/10.1007/978-1-4939-2095-2_8

Cornelius, S. P., Kath, W. L., & Motter, A. E. (2013). Realistic Control of Network Dynamics. Nature Communications4, 1942. http://doi.org/10.1038/ncomms2939

Lim, C., Allada, R. (2013) ATAXIN-2 activates PERIOD translation to sustain circadian rhythms in Drosophila, Science, 340(6134), 875-879. DOI: 10.1126/science.1234785

Lear, B.C., Merrill, C.E., Lin, J.M., Schroeder, A., Zhang, L., and Allada, R. (2005) A novel G-protein coupled receptor, groom-of-PDF, is required for PDF neuron action in circadian behavior, Neuron, 48(2), 221-227. DOI: 10.1016/j.neuron.2005.09.008

Moyle-Heyrman, G., Zaichuk, T., Xi, L., Zhang, Q., Uhlenbeck, O. C., Holmgren, R., Widom, J., Wang, J.-P. (2013). Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. Proceedings of the National Academy of Sciences of the United States of America110(50), 20158–20163. http://doi.org/10.1073/pnas.1315809110

Antonio Auffinger, Gerard Ben Arous and Jiri Cerny. (2013). Random matrices and complexity of spherical spin glasses, Comm. on Pure and Applied Mathematics, 66(2), 165-201.

Truong Quang B.A., Mani, M., Markova, O., Lecuit, T., Lenne, P.F. (2013) Principles of E-cadherin supramolecular organization in vivo: B.A.T.. Current Biology, 23(22), 2197-2207. DOI: 10.1016/j.cub.2013.09.015

Mani, M., Goyal, S., Irvine, K. D., & Shraiman, B. I. (2013). Collective polarization model for gradient sensing via Dachsous-Fat intercellular signalingProceedings of the National Academy of Sciences of the United States of America110(51), 20420–20425. http://doi.org/10.1073/pnas.1307459110

Antonio Auffinger, Gerard Ben Arous. (2013) Complexity of random smooth functions of many variables, Annals of Probability, 41(6), 4214-4247.

Seaver, S. M. D., Sales-Pardo, M., Guimerà, R., & Amaral, L. A. N. (2012). Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient. PLoS Computational Biology8(11), e1002762. http://doi.org/10.1371/journal.pcbi.1002762

McMullen, P. D., Aprison, E. Z., Winter, P. B., Amaral, L. A. N., Morimoto, R. I., & Ruvinsky, I. (2012). Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress. PLoS Computational Biology8(1), e1002338. http://doi.org/10.1371/journal.pcbi.1002338

Prasad, M. S., Sauka-Spengler, T., & LaBonne, C. (2012). Induction of the neural crest state: Control of stem cell attributes by gene regulatory, post-transcriptional and epigenetic interactionsDevelopmental Biology366(1), 10–21. http://doi.org/10.1016/j.ydbio.2012.03.014

Andersen EC, Gerke JP, Shapiro JA, Crissman JR, Ghosh R, Bloom JS, Felix MA, Kruglyak. (2012).  Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nature Genetics44(3), 285–290. http://doi.org/10.1038/ng.1050 

Brogaard, K., Xi, L., Wang, J.-P., & Widom, J. (2012). A base pair resolution map of nucleosome positions in yeastNature486(7404), 496–501. http://doi.org/10.1038/nature11142

Kaz, D.M., McGorty, R., Mani, M., Brenner, M., Manoharan, V.N. (2012). Physical ageing of the contact line on colloidal particles at liquid interfaces. Nature Materials, 11(2), 138-142. DOI: 10.1038/nmat3190

Ambegaonkar, A. A., Pan, G., Mani, M., Feng, Y., & Irvine, K. D. (2012). Propagation of Dachsous-Fat Planar Cell PolarityCurrent Biology : CB22(14), 1302–1308. http://doi.org/10.1016/j.cub.2012.05.049

Gemp, I. M., Carthew, R. W., & Hilgenfeldt, S. (2011). Cadherin-Dependent Cell Morphology in an Epithelium: Constructing a Quantitative Dynamical Model. PLoS Computational Biology7(7), e1002115. http://doi.org/10.1371/journal.pcbi.1002115

Braun, R., Leibon, G., Pauls, S., & Rockmore, D. (2011). Partition decoupling for multi-gene analysis of gene expression profiling dataBMC Bioinformatics12, 497. http://doi.org/10.1186/1471-2105-12-497

Su, H., Meng, S., Lu, Y., Trombly, M. I., Chen, J., Lin, C., Turk, A., Wang, X. (2011). Mammalian hyperplastic discs homolog EDD regulates microRNA-mediated gene silencing. Molecular Cell43(1), 97–109. http://doi.org/10.1016/j.molcel.2011.06.013

Su H, Meng S, Lu Y, Trombly MI, Chen J, Lin C, Turk A and Wang X. (2011). Mammalian hyperplastic discs homolog EDD regulates microRNA-mediated gene silencing. Mol Cell 43, 97-109.

Bagheri, N., Shiina, M., Lauffenburger, D. A., & Korn, W. M. (2011). A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-InhibitionPLoS Computational Biology7(2), e1001085. http://doi.org/10.1371/journal.pcbi.1001085

Han, M.-H., Lin, C., Meng, S., & Wang, X. (2010). Proteomics Analysis Reveals Overlapping Functions of Clustered ProtocadherinsMolecular & Cellular Proteomics : MCP9(1), 71–83. http://doi.org/10.1074/mcp.M900343-MCP200

Xi, L., Fondufe-Mittendorf, Y., Xia, L., Flatow, J., Widom, J., & Wang, J.-P. (2010). Predicting nucleosome positioning using a duration Hidden Markov ModelBMC Bioinformatics11, 346. http://doi.org/10.1186/1471-2105-11-346

Malmgren, RD. Stouffer, DB. Campanharo, ASLO. Amaral, LAN. (2009) On Universality in Human Correspondence Activity. Science, 325(5948), 1696-1700. doi: 10.1126/science.1174562

Su, H., Trombly, M. I., Chen, J., & Wang, X. (2009). Essential and overlapping functions for mammalian Argonautes in microRNA silencingGenes & Development23(3), 304–317. http://doi.org/10.1101/gad.1749809

Kulić, I. M., Mani, M., Mohrbach, H., Thaokar, R., & Mahadevan, L. (2009). Botanical ratchetsProceedings of the Royal Society B: Biological Sciences276(1665), 2243–2247. http://doi.org/10.1098/rspb.2008.1685

Käfer, J., Hayashi, T., Marée, A. F. M., Carthew, R. W., & Graner, F. (2007). Cell adhesion and cortex contractility determine cell patterning in the Drosophilaretina. Proceedings of the National Academy of Sciences of the United States of America104(47), 18549–18554. http://doi.org/10.1073/pnas.0704235104

Keegan, K. P., Pradhan, S., Wang, J.-P., & Allada, R. (2007). Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed GenesPLoS Computational Biology3(11), e208. http://doi.org/10.1371/journal.pcbi.0030208

Sales-Pardo, M., Guimerà, R., Moreira, A. A., & Amaral, L. A. N. (2007). Extracting the hierarchical organization of complex systems. Proceedings of the National Academy of Sciences of the United States of America104(39), 15224–15229. http://doi.org/10.1073/pnas.0703740104

Guimerà, R., & Amaral, L. A. N. (2005). Functional cartography of complex metabolic networks. Nature433(7028), 895–900. http://doi.org/10.1038/nature03288

Light, W., Vernon, A. E., Lasorella, A., Iavarone, A., LaBonne, C. (2005) Xenopus Id3 is required downstream of Myc for the formation of multipotent neural crest progenitor cells. Development, 132(8):1831-41. DOI: 10.1242/dev.01734

Bellmeyer A1, Krase J, Lindgren J, LaBonne C. (2003) The protooncogene c-myc is an essential regulator of neural crest formation in Xenopus. Dev Cell, 4(6), 827-39. PMID: 12791268

Lin JM, Kilman VL, Keegan K, Paddock B, Emery-Le M, Rosbash M, and Allada R. (2002) A Role for Casein Kinase 2alpha in the Drosophila Circadian Clock, Nature, 420(6917), 816-820. DOI: 10.1038/nature01235

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