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2021

Alba, V., Carthew, J.E., Carthew, R.W. and M. Mani (2021) Global constraints within the developmental program of the Drosophila wing. eLife 2021;10:e66750. doi:10.7554/eLife.66750

Auffinger A and CX Chen. (2021) Thouless-Anderson-Palmer equations for the Ghatak-Sherrington mean field spin glass model. arXiv:2103.13661

Kathryn S. Evans, Janneke Wit, Lewis Stevens, Steffen R. Hahnel, Briana Rodriguez, Grace Park, Mostafa Zamanian, Shannon C. Brady, Ellen Chao, Katherine Introcaso, Robyn E. Tanny, Erik C. Andersen. (2021). Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses. PLOS Pathogens. 17 (3) e1009297. doi.org/10.1371/journal.ppat.1009297

Freedman, S.L., Xu, B., Goyal, S., and M. Mani (2021) Revealing cell-fate bifurcations from transcriptomic trajectories of hematopoiesis. Proc Nat Acad Sci USA (in review). BioRxiv doi.org/10.1101/2021.05.03.442465

Johnson, E., Kath, W., and M. Mani (2021) EMBEDR: Distinguishing Signal from Noise in Single-Cell Omics Data. Cell Patterns (in revision). Posted April 26 2021 BioRxiv doi.org/10.1101/2020.11.18.389031

Ness-Cohn, E and Braun, R. (2021). TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data. bioRxiv. doi.org/10.1101/2020.11.19.389981

Ness-Cohn, Elan and Allada, Ravi and Braun, Rosemary. (2021). Comment on “Circadian rhythms in the absence of the clock gene Bmal1 ”. Science. 372 (6539) eabe9230. doi.org/10.1126/science.abe9230

Hayden Nunley, Xufeng Xue, Jianping Fu, David K. Lubensky. (2021) Generation of fate patterns via intercellular forces. bioRxiv2021.04.30.442205; doi: https://doi.org/10.1101/2021.04.30.442205

Joy Nyaanga, Christina Goss, Gaotian Zhang, Hannah N. Ahmed, Elliot J. Andersen, Isabella R. Miller, Justine K. Rozenich, Iris L. Swarthout, Jordan A. Vaughn, Erik C. Andersen, Niall M. Mangan, Sasha Shirman. (2021). Physical constraints on growth dynamics guide C. elegans developmental trajectories and animal shape. bioRxiv. doi.org/10.1101/2021.04.01.438121

Kristina Mallory, Joshua Rubin Abrams, Anne Schwartz, Maria-Veronica Ciocanel, Alexandria Volkening and Björn Sandstede. (2021). Influenza spread on context-specific networks lifted from interaction-based diary data. Royal Society Open Science. 8 (1) 191876. doi.org/10.1098/rsos.191876

Hailun Zhu, Sihai Dave Zhao, Alokananda Ray, Yu Zhang, Xin Li. (2021) A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing. bioRxiv 2021.06.12.448145; doi.org/10.1101/2021.06.12.448145 

Ritika Giri, Shannon Brady, Dimitrios K. Papadopoulous, Richard W. Carthew. Single-cell Senseless protein analysis reveals metastable states during transition to a sensory organ fate. https://doi.org/10.1101/2021.12.20.473498

Tomas Andreani, Clark Rosensweig, Shiju Sisobhan, Emmanuel Ogunlana, William Kath, Ravi Allada. Circadian programming of the ellipsoid body sleep homeostat in Drosophila. https://doi.org/10.1101/2021.10.22.465404

2020

Auffinger A and Y Zhou. (2020) On properties of the spherical mixed vector p-spin model. arXiv:2007.06019

Auffinger A and Q Zeng. (2020) Complexity of high dimensional Gaussian random fields with isotropic increments. arXiv:2007.07668

Auffinger A and J Gold. (2020) The number of saddles of the spherical p-spin model. arXiv:2007.09269

Rachael Bakker, Madhav Mani, and Richard W Carthew. (2020). The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts. eLife. 9. doi:10.7554/eLife.56076

Sebastian M. Bernasek, Nicolás Peláez, Richard W. Carthew, Neda Bagheri, Luís A. N. Amaral. (2020). Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila. PLOS Computational Biology. 16 (3)e1007406. doi:10.1371/journal.pcbi.1007406

Richard W Carthew, Amy Shyer. Editorial overview: Taking measure of developing plants and animals. Current Opinion in Genetics & Development. Volume 63, 2020, Pages iii-v. doi.org/10.1016/j.gde.2020.06.011

Mario U Gaimann, Maximilian Nguyen, Jonathan Desponds, Andreas Mayer. (2020). Early life imprints the hierarchy of T cell clone sizes. eLife. 9. doi.org/10.7554/eLife.61639

Evans, KS and Andersen, EC. (2020). The cadmium-responsive gene, cdr-6, does not influence Caenorhabditis elegans responses to exogenous zinc. microPublication biology. doi.org/10.17912/micropub.biology.000305

Kathryn S. Evans, Stefan Zdraljevic, Lewis Stevens, Kimberly Collins, Robyn E. Tanny, Erik C. Andersen. (2020). Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans. PLOS Genetics. 16 (11) e1008986. doi.org/10.1371/journal.pgen.1008986

Evans, Kathryn S. and Andersen, Erik C. (2020). The Gene scb-1 Underlies Variation in Caenorhabditis elegans Chemotherapeutic Responses. G3: Genes|Genomes|Genetics. 10 (6) g3.401310.2020. doi:10.1534/g3.120

Ritika Giri, Dimitrios K Papadopoulos, Diana M Posadas, Hemanth K Potluri, Pavel Tomancak, Madhav Mani, Richard W Carthew (2020). Ordered patterning of the sensory system is susceptible to stochastic features of gene expression. eLife. 9. doi:10.7554/eLife.53638

Alexander Karge, Nicolle A Bonar, Scott Wood, Christian P Petersen. (2020). tec-1 kinase negatively regulates regenerative neurogenesis in planarians. eLife. 9. doi.org/10.7554/eLife.47293

Nilay Kumar, Francisco Huizar, Trent Robinett, Keity J. Farf n-Pira, Dharsan Soundarrajan, Maria Unger, Pavel Brodskiy, Marcos Nahmad, Jeremiah J. Zartman. (2020) MAPPER: A new image analysis pipeline unmasks differential regulation of Drosophila wing features. bioRxiv 2020.12.16.422888 doi.org/10.1101/2020.12.16.422888

Keren Li, C Matthew Hope, Xiaozhong A Wang, g and Ji-Ping Wang. (2020). RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data. Nucleic Acids Research. 48 (21) 12016 to 12029. doi.org/10.1093/nar/gkaa1049

Elan Ness-Cohn, Marta Iwanaszko, William L. Kath, Ravi Allada, Rosemary Braun. (2020). TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research. Journal of Biological Rhythms. 35 (5) 439 to 451. doi.org/10.1177/0748730420934672

Schad, Erik G. and Petersen, Christian P. (2020). STRIPAK Limits Stem Cell Differentiation of a WNT Signaling Center to Control Planarian Axis Scaling. Current Biology. 30 (2) 254 to 263.e2. doi.org/10.1016/j.cub.2019.11.068

Volkening, Alexandria. (2020). Linking genotype, cell behavior, and phenotype: multidisciplinary perspectives with a basis in zebrafish patterns. Current Opinion in Genetics & Development. 63 (C) 78 to 85. doi.org/10.1016/j.gde.2020.05.010

Alexandria Volkening, Daniel F. Linder, Mason A. Porter , and Grzegorz A. Rempala. (2020). Forecasting Elections Using Compartmental Models of Infection. SIAM Review. 62 (4) 837 to 865. doi.org/10.1137/19M1306658

Melissa R. McGuirl, Alexandria Volkening, and Björn Sandstede. (2020). Topological data analysis of zebrafish patterns. Proceedings of the National Academy of Sciences. 117 (10) 5113 to 5124. doi:10.1073/pnas.1917763117

A Volkening, M R Abbott, N Chandra, B Dubois, F Lim, D Sexton, B Sandstede. (2020). Modeling Stripe Formation on Growing Zebrafish Tailfins. Bulletin of Mathematical Biology. 82 (5) . doi:10.1007/s11538-020-00731-0

Blake Shirman and Alexandria Volkening. What’s math got to do with patterns on fish? (2020) Manuscript. 

2019

Rosemary Braun, William L. Kath, 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. Proceedings of the National Academy of Sciences. 116 (12) p. 5206-5208. doi:10.1073/pnas.1819173116

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 (2019). Repressive Gene Regulation Synchronizes Development with Cellular Metabolism. Cell. 178 (4) 980 to 992.e17. doi:10.1016/j.cell.2019.06.023

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.

2018

Sebastian M. Bernasek, Jean-François Boisclair Lachance, Nicolás Peláez, Rachael Bakker, Heliodoro Tejedor Navarro, Luis A. N. Amaral, Neda Bagheri, Ilaria Rebay, Richard W. Carthew. (2018) Ratio-based sensing of two transcription factors regulates the transit to differentiation. Posted BioRxiv doi.org/10.1101/430744

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. Proceedings of the National Academy of Sciences. 115 (39) E9247 to E9256. doi:10.1073/pnas.1800314115

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 Communications, 8, 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 criteria. Proceedings. Mathematical, Physical, and Engineering Sciences, 473(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 Genetics, 13(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 sequestration. PLoS Computational Biology, 13(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 Evolution, 34(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 Journal, 111(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 Mapping. Cell, 167(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 America, 113(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. Genetics, 204(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. eLife, 4, 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. X, 5, 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 Networks. PLoS Computational Biology, 11(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 Macro, 7(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 Genetics, 10(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 RtcB. Molecular Cell, 55(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 cancer. BMC Systems Biology, 8, 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 Bioengineering, 111(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. eLife, 3, 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 ectoderm. Developmental Cell, 31(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 Architecture. Integrative and Comparative Biology, 54(2), 296–306. http://doi.org/10.1093/icb/icu037

Braun, R. (2014). Systems Analysis of High–Throughput Data. Advances in Experimental Medicine and Biology, 844, 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 Communications, 4, 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 America, 110(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 signaling. Proceedings of the National Academy of Sciences of the United States of America, 110(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 Biology, 8(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 Biology, 8(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 interactions. Developmental Biology, 366(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 Genetics, 44(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 yeast. Nature, 486(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 Polarity. Current Biology : CB, 22(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 Biology, 7(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 data. BMC Bioinformatics, 12, 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 Cell, 43(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-Inhibition. PLoS Computational Biology, 7(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 Protocadherins. Molecular & Cellular Proteomics : MCP, 9(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 Model. BMC Bioinformatics, 11, 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 silencing. Genes & Development, 23(3), 304–317. http://doi.org/10.1101/gad.1749809

Kulić, I. M., Mani, M., Mohrbach, H., Thaokar, R., & Mahadevan, L. (2009). Botanical ratchets. Proceedings of the Royal Society B: Biological Sciences, 276(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 America, 104(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 Genes. PLoS Computational Biology, 3(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 America, 104(39), 15224–15229. http://doi.org/10.1073/pnas.0703740104

Guimerà, R., & Amaral, L. A. N. (2005). Functional cartography of complex metabolic networks. Nature, 433(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