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Publications of Center Research

Bakker, R., Mani, M., Carthew, R.W. (2020) The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts. eLife 2020;9:e56076

Ness-Cohn, E., Iwanaszko, M., Kath, W.L. Allada, R. Braun, R. (2020) TimeTrial: An interactive application for optimizing the design and analysis of transcriptomic times-series data in circadian biology research. J. Biological Rhythms (accepted with minor revisions); BioRxiv 2020.04.15.043695. 2020.

Li, K., Hope, M., Wang, X., Wang, J-P. (2020) RiboDiPA: A novel tool for differential pattern analysis in Ribo-seq data. BioRxiv  2020.04.20.050559. doi:

Evans, K.S., Andersen, E.C. (2020) The gene scb-1 underlies variation in Caenorhabditis elegans chemotherapeutic Rresponses. G3 (Bethesda) g3.401310.2020.

Bernasek, S., Peláez, N., Carthew, R.W., Bagheri, N., Amaral, L.A.N. (2020) Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila. PLoS Computational Biology

Giri, R., Papadopoulos, D.K., Posadas, D.M., Potluri, H., Tomancak, P., Mani, M., Carthew, R.W. (2020) Ordered patterning of the sensory system is susceptible to stochastic features of gene expression. eLife 2020;9:e53638.

Carthew, R.W., Shyer, A. (2020) Editorial Overview: Taking measure of developing plants and animals. Curr. Opin. Genet. Dev. 63, (in press)

Volkening, A.  (2020) Linking genotype, cell behavior, and phenotype: multidisciplinary perspectives with a basis in zebrafish patterns, Curr Opin Genet Dev. 63, (in press).

Volkening, A., Abbott, M.R., Chandra, N., Dubois, B., Lim, F., Sexton, D., Sandstede, B. (2020) Modeling stripe formation on growing zebrafish tailfins. Bulletin Mathematical Biology, 82(56), 2020.

McGuirl, M.R., Volkening, A., Sandstede, B. (2020) Topological data analysis of zebrafish patterns. Proceedings National Academy of Sciences USA, 117, 5113-5124.

Volkening, A., Sandstede, B. (2020) How zebrafish get their stripes…or spots. SIAM News, 53(2), 2020.

Cassidy, J.J., Bernasek, S., Bakker, R., Giri, R., Pelaez, N., Eder, B., Bobrowska, A., Bagheri, N., Amaral, L.A.N., Carthew, R.W.  (2019) Repressive gene regulation synchronizes development with cellular metabolism. Cell 178, 980-992.

This paper was highlighted in Cell with a Preview: Jaganathan et al (2019) Cell 178, 774-776. Highlighted in Science as Editors’ Choice: Science 365 (6455): p.70.

Shadkhoo S, Mani M. (2019) The role of intracellular interactions in the collective polarization of tissues and its interplay with cellular geometry. PLOS Computational Biology 15(11): e1007454.

Justin J. Cassidy, Sebastian M. Bernasek, Rachael Bakker, Ritika Giri, Nicolás Peláez, Bryan Eder, Anna Bobrowska, Neda Bagheri, Luis A. Nunes Amaral, Richard W. Carthew. Repressive Gene Regulation Synchronizes Development with Cellular Metabolism. Cell. Volume 178, Issue 4, 8 August 2019, Pages 980-992.e17.

Rosemary Braun*, William L. Kath, Marta Iwanaszko, Elzbieta Kula-Eversole, Sabra M. Abbott, Kathryn J. Reid, Phyllis C. Zee, and Ravi Allada. (2018) Universal method for robust detection of circadian state from gene expression Proc. Nat. Acad. Sci. USA.115 (39): E9247-E9256

Rosemary Braun*, William L. Kath, Marta Iwanaszko, Elzbieta Kula-Eversole, Sabra M. Abbott, Kathryn J. Reid, Phyllis C. Zee, and Ravi Allada. (2019) Reply to Laing et al.: Accurate prediction of circadian time across platforms. Proc. Nat. Acad. Sci. USA. 116 (12): 5206-5208

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Braun, R. and Shah, S. (2016) Network methods for pathway analysis of gene expression data. Computational and Structural Biotechnology Journal.

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.

Wells, D. K., Kath, W. L., & Motter, A. E. (2015). Control of Stochastic and Induced Switching in Biophysical Networks. Physical Review. X5, 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.

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.

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.

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.

Lu, Y., Liang, F.-X., & Wang, X. (2014). A synthetic biology approach identifies the mammalian UPR RNA ligase RtcBMolecular Cell55(5), 758–770.

Zhang, Q., Burdette, J. E., & Wang, J.-P. (2014). Integrative network analysis of TCGA data for ovarian cancerBMC Systems Biology8, 1338.

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.

Mangan, N. M., & Brenner, M. P. (2014). Systems analysis of the CO2concentrating mechanism in cyanobacteria. eLife3, e02043.

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.

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.

Braun, R. (2014). Systems Analysis of High–Throughput DataAdvances in Experimental Medicine and Biology844, 153–187.

Cornelius, S. P., Kath, W. L., & Motter, A. E. (2013). Realistic Control of Network Dynamics. Nature Communications4, 1942.

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.

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.

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.

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.

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.

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. 

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

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.

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.

Braun, R., Leibon, G., Pauls, S., & Rockmore, D. (2011). Partition decoupling for multi-gene analysis of gene expression profiling dataBMC Bioinformatics12, 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.

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.

Han, M.-H., Lin, C., Meng, S., & Wang, X. (2010). Proteomics Analysis Reveals Overlapping Functions of Clustered ProtocadherinsMolecular & Cellular Proteomics : MCP9(1), 71–83.

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.

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.

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

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.

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.

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.

Guimerà, R., & Amaral, L. A. N. (2005). Functional cartography of complex metabolic networks. Nature433(7028), 895–900.

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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