Saket Navlakha

Associate Professor

Integrative Biology Laboratory

Pioneer Fund Developmental Chair

Saket Navlakha
Salk Institute for Biological Studies - Publications

all Publications


Ziamtsov, I., Navlakha, S. Machine learning approaches to improve three basic plant phenotyping tasks using 3D point clouds (2019) Plant Physiology. 181(2). DOI: https://doi.org/10.1104/pp.19.00524

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Conn, A., Chandrasekhar, A., Rongen, M.V., Leyser, O., Chory, J., Navlakha, S. Network trade-offs and homeostasis in Arabidopsis shoot architectures. (2019) PLOS Computational Biology. 15(9):e1007325. DOI: 10.1371/journal.pcbi.1007325

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Chandrasekhar, A., Navlakha, S. Neural arbors are Pareto optimal. (2019) Proc. Biol. Sci. 286(1902):20182727. DOI: 10.1098/rspb.2018.2727

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Suen, J.Y., Navlakha, S. Travel in city road networks follows similar transport trade-off principles to neural and plant arbors. (2019) J R Soc Interface. 16(154):20190041. DOI: 10.1098/rsif.2019.0041

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Rashid, S., Long, Z., Singh, S., Kohram, M., Vashistha, H., Navlakha, S., Salman, H., Oltvai, Z.N., Bar-Joseph, Z. Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains. (2019) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1816315116

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Dasgupta, S., Sheehan, T.C., Stevens, C.F., Navlakha, S. A neural data structure for novelty detection (2018) Proceedings of the National Academy of Sciences. DOI: https://doi.org/10.1073/pnas.1814448115

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Fleischer, J.G., Schulte, R., Tsai, H.H., Tyagi, S., Ibarra, A., Shokhirev, M.N., Huang, L., Hetzer, M.W., Navlakha, S. Predicting age from the transcriptome of human dermal fibroblasts. (2018) Genome Biology. 19(1):221. DOI: 10.1186/s13059-018-1599-6

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How, J.J., Navlakha, S. Evidence of Rentian Scaling of Functional Modules in Diverse Biological Networks. (2018) Neural Computation. 30(8):1-35. DOI: 10.1162/neco_a_01095

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Chandrasekhar, A., Gordon, D.M., Navlakha, S. A distributed algorithm to maintain and repair the trail networks of arboreal ants. (2018) Scientific Reports. 8(1):9297. DOI: 10.1038/s41598-018-27160-3

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Beukema, P., Cecil, K.L., Peterson, E., Mann, V.R., Matsushita, M., Takashima, Y., Navlakha, S., Barth, A.L. TrpM8-mediated somatosensation in mouse neocortex. (2018) Journal of Comparative Neurology. DOI: 10.1002/cne.24418

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Dasgupta, S., Stevens, C.F., Navlakha, S. A neural algorithm for a fundamental computing problem. (2017) Science. 358(6364):793-796. DOI: 10.1126/science.aam9868

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Navlakha, S., Bar-Joseph, Z., Barth, A.L. Network Design and the Brain. (2017) Trends in Cognitive Sciences. DOI: 10.1016/j.tics.2017.09.012

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Conn, A., Pedmale, U.V., Chory, J., Navlakha, S. High-Resolution Laser Scanning Reveals Plant Architectures that Reflect Universal Network Design Principles. (2017) Cell Systems. 5(1):53-62.e3. DOI: 10.1016/j.cels.2017.06.017

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Conn, A., Pedmale, U.V., Chory, J., Stevens, C.F., Navlakha, S. A Statistical Description of Plant Shoot Architecture. (2017) Current Biology. 27(14):2078-2088.e3. DOI: 10.1016/j.cub.2017.06.009

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Suen, J.Y., Navlakha, S. Using Inspiration from Synaptic Plasticity Rules to Optimize Traffic Flow in Distributed Engineered Networks. (2017) Neural Computation. 29(5):1204-1228. DOI: 10.1162/NECO_a_00945

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Navlakha, S. Learning the Structural Vocabulary of a Network. (2017) Neural Computation. 29(2):287-312. DOI: 10.1162/NECO_a_00924

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Singh, S., Rashid, S., Navlakha, S., Bar-Joseph, Z. Distributed Gradient Descent in Bacterial Food Search (2016) Proceedings of the 20th International Conference on Research in Computational Molecular Biology (RECOMB). DOI: 10.1007/978-3-319-31957-5

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Chandrasekaran, S., Navlakha, S., Audette, N.J., McCreary, D.D., Suhan, J., Bar-Joseph, Z., Barth, A.L. Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex. (2015) Journal of Neuroscience. 35(50):16450-62. DOI: 10.1523/JNEUROSCI.1573-15.2015

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Navlakha, S., Barth, A.L., Bar-Joseph, Z. Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks. (2015) PLOS Computational Biology. 11(7):e1004347. DOI: 10.1371/journal.pcbi.1004347

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Navlakha, S., Bar-Joseph, Z. Distributed Information Processing in Biological and Computational Systems (2015) Communications of the ACM. 58(1). DOI: 10.1145/2678280

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Navlakha, S., Faloutsos, C., Bar-Joseph, Z. MASSEXODUS: modeling evolving networks in harsh environments (2015) Data Min Knowl Disc. 29(5). DOI: 10.1007/s10618-014-0399-1

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Navlakha, S., He, X., Faloutsos, C., Bar-Joseph, Z. Topological properties of robust biological and computational networks. (2014) J R Soc Interface. 11(96):20140283. DOI: 10.1098/rsif.2014.0283

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Navlakha, S., Ahammad, P., Myers, E.W. Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging. (2013) BMC Bioinformatics. 14:294. DOI: 10.1186/1471-2105-14-294

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Navlakha, S., Suhan, J., Barth, A.L., Bar-Joseph, Z. A high-throughput framework to detect synapses in electron microscopy images. (2013) Bioinformatics . 29(13):i9-17. DOI: 10.1093/bioinformatics/btt222

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Patro, R., Sefer, E., Malin, J., Marçais, G., Navlakha, S., Kingsford, C. Parsimonious reconstruction of network evolution. (2012) Algorithms Mol Biol. 7(1):25. DOI: 10.1186/1748-7188-7-25


Navlakha, S., Gitter, A., Bar-Joseph, Z. A network-based approach for predicting missing pathway interactions. (2012) PLOS Computational Biology. 8(8):e1002640. DOI: 10.1371/journal.pcbi.1002640

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Navlakha, S., Bar-Joseph, Z. Algorithms in nature: the convergence of systems biology and computational thinking. (2011) Mol. Syst. Biol. 7:546. DOI: 10.1038/msb.2011.78

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Navlakha, S., Kingsford, C. Network archaeology: uncovering ancient networks from present-day interactions. (2011) PLOS Computational Biology. 7(4):e1001119. DOI: 10.1371/journal.pcbi.1001119

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Thor, A., Anderson, P., Raschid, L., Navlakha, S., Saha, B., Khuler, S., Zhang, X.N. Link Prediction for Annotation Graphs Using Graph Summarization. The Semantic Web – ISWC 2011. (2011) Lecture Notes in Computer Science. 7031. DOI: https://doi.org/10.1007/978-3-642-25073-6_45

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Navlakha, S., Kingsford, C. The power of protein interaction networks for associating genes with diseases. (2010) Bioinformatics . 26(8):1057-63. DOI: 10.1093/bioinformatics/btq076

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Navlakha, S., White, J., Nagarajan, N., Pop, M., Kingsford, C. Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. (2010) Journal of Computational Biology. 17(3):503-16. DOI: 10.1089/cmb.2009.0173

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White, J.R., Navlakha, S., Nagarajan, N., Ghodsi, M.R., Kingsford, C., Pop, M. Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. (2010) BMC Bioinformatics. 11:152. DOI: 10.1186/1471-2105-11-152

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Navlakha, S., Kingsford, C. Exploring biological network dynamics with ensembles of graph partitions. (2010) Pac Symp Biocomput.:166-77 DOI: 10.1142/9789814295291_0019

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Navlakha, S., Schatz, M.C., Kingsford, C. Revealing biological modules via graph summarization. (2009) Journal of Computational Biology. 16(2):253-64. DOI: 10.1089/cmb.2008.11TT

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Education

MEng and BS, Computer Science, Cornell University
PhD, Computer Science, University of Maryland College Park


Awards & Honors

  • 2019 CAREER Award
  • 2018 Pew Scholar
  • 2013 NIH F32 postdoctoral fellowship award