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Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., Schatz, M. C. (December 2019) Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics, 20 (Suppl). p. 641. ISSN 1471-2105 (Public Dataset)
Carter, J. A., Gilbo, P., Atwal, G. S. (December 2019) IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma. Nat Med, 25 (12). pp. 1833-1835. ISSN 1078-8956 (Public Dataset)
Chandrasekhar, A., Gordon, D. M., Navlakha, S. (June 2018) A distributed algorithm to maintain and repair the trail networks of arboreal ants. Sci Rep, 8 (1). p. 9297. ISSN 2045-2322 (Public Dataset)
Chang, W. I., Lampe, J. (1992) Theoretical and Empirical Comparisons of Approximate String Matching Algorithms. Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching, 644. pp. 175-184. ISSN 0302-9743
Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., Eberle, M. A. (December 2019) Paragraph: A graph-based structural variant genotyper for short-read sequence data. Genome Biology, 20 (1). Article 291. ISSN 14747596 (ISSN)
Cohen, Yarden, Engel, Tatiana A, Langdon, Christopher, Lindsay, Grace W, Ott, Torben, Peters, Megan AK, Shine, James M, Breton-Provencher, Vincent, Ramaswamy, Srikanth (November 2022) Recent Advances at the Interface of Neuroscience and Artificial Neural Networks. The Journal of Neuroscience, 42 (45). pp. 8514-8523. ISSN 1529-2401
Czégel, Dániel, Giaffar, Hamza, Tenenbaum, Joshua B, Szathmáry, Eörs (February 2022) Bayes and Darwin: How replicator populations implement Bayesian computations. BioEssays : news and reviews in molecular, cellular and developmental biology. e2100255. ISSN 1521-1878
Dasgupta, S., Stevens, C. F., Navlakha, S. (November 2017) A neural algorithm for a fundamental computing problem. Science, 358 (6364). pp. 793-796. ISSN 0036-8075 (Public Dataset)
Duggal, Geet, Navlakha, Saket, Girvan, Michelle, Kingsford, Carl (July 2010) Uncovering Many Views of Biological Networks Using Ensembles of Near-Optimal Partitions. MultiClust: 1st International Workshop on Discovering, Summarizing and Using Multiple ClusteringsHeld in Conjunction with KDD-2019.
Emek, Yuval, Navlakha, Saket (April 2022) Special Issue: Biological Distributed Algorithms 2021. Journal of Computational Biology, 29 (4). p. 305. ISSN 1557-8666
Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., Regev, A. (October 2019) Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol, 20 (1). p. 213. ISSN 1474-7596
Hubisz, M., Siepel, A. (January 2020) Inference of Ancestral Recombination Graphs Using ARGweaver. Methods Mol Biol, 2090. pp. 231-266. ISSN 1064-3745
Kiyani, E, Silber, S, Kooshkbaghi, M, Karttunen, M (December 2022) Machine-learning-based data-driven discovery of nonlinear phase-field dynamics. Physical Review E, 106 (6). ISSN 2470-0045
Krauthammer, M., Kra, P., Iossifov, I., Gomez, S. M., Hripcsak, G., Hatzivassiloglou, V., Friedman, C., Rzhetsky, A. (2002) Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics, 18 Sup. S249-57. ISSN 1367-4803 (Print)1367-4803 (Linking)
Marr, T. G., Yan, X., Yu, Q. (1992) Genomic mapping by single copy landmark detection: a predictive model with a discrete mathematical approach. Mamm Genome, 3 (11). pp. 644-9. ISSN 0938-8990 (Print)0938-8990 (Linking)
Navlakha, S., Ahammad, P., Myers, E. W. (October 2013) Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging. BMC Bioinformatics, 14. p. 294. ISSN 1471-2105
Navlakha, S., Bar-Joseph, Z. (November 2011) Algorithms in nature: the convergence of systems biology and computational thinking. Mol Syst Biol, 7. p. 546. ISSN 1744-4292
Navlakha, S., Bar-Joseph, Z. (January 2015) Distributed information processing in biological and computational systems. Communications of the ACM, 58 (1). pp. 94-102. ISSN 00010782 (ISSN)
Navlakha, S., Bar-Joseph, Z., Barth, A. L. (January 2018) Network Design and the Brain. Trends Cogn Sci, 22 (1). pp. 64-78. ISSN 1364-6613
Navlakha, S., Barth, A. L., Bar-Joseph, Z. (July 2015) Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks. PLoS Comput Biol, 11 (7). e1004347. ISSN 1553-734x
Navlakha, S., Faloutsos, C., Bar-Joseph, Z. (September 2015) MassExodus: modeling evolving networks in harsh environments. Data Mining and Knowledge Discovery, 29 (5). pp. 1211-1232. ISSN 13845810 (ISSN)
Navlakha, S., Gitter, A., Bar-Joseph, Z. (August 2012) A network-based approach for predicting missing pathway interactions. PLoS Comput Biol, 8 (8). e1002640. ISSN 1553-734x
Navlakha, S., He, X., Faloutsos, C., Bar-Joseph, Z. (July 2014) Topological properties of robust biological and computational networks. J R Soc Interface, 11 (96). p. 20140283. ISSN 1742-5662
Navlakha, S., Kingsford, C. (November 2010) Exploring biological network dynamics with ensembles of graph partitions. Pac Symp Biocomput. pp. 166-177. ISSN 2335-6928
Navlakha, S., Kingsford, C. (April 2011) Network archaeology: uncovering ancient networks from present-day interactions. PLoS Comput Biol, 7 (4). e1001119. ISSN 1553-734x (Public Dataset)
Navlakha, S., Kingsford, C. (April 2010) The power of protein interaction networks for associating genes with diseases. Bioinformatics, 26 (8). pp. 1057-63. ISSN 1367-4803 (Public Dataset)
Navlakha, S., Schatz, M. C., Kingsford, C. (February 2009) Revealing biological modules via graph summarization. J Comput Biol, 16 (2). pp. 253-64. ISSN 1066-5277
Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., Jiang, N., Hirsch, C. N., Hufford, M. B. (December 2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol, 20 (1). p. 275. ISSN 1474-7596 (Public Dataset)
Patro, R., Sefer, E., Malin, J., Marçais, G., Navlakha, S., Kingsford, C. (September 2012) Parsimonious reconstruction of network evolution. Algorithms for Molecular Biology, 7 (25). (Public Dataset)
Petti, Samantha, Bhattacharya, Nicholas, Rao, Roshan, Dauparas, Justas, Thomas, Neil, Zhou, Juannan, Rush, Alexander M, Koo, Peter, Ovchinnikov, Sergey End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. Bioinformatics. ISSN 1367-4803
Rashid, Sabrina, Singh, Shashank, Navlakha, Saket, Bar-Joseph, Ziv (May 2019) A bacterial based distributed gradient descent model for mass scale evacuations. Swarm and Evolutionary Computation, 46. pp. 97-103. ISSN 2210-6502
Rodriguez-Esteban, R., Iossifov, I., Rzhetsky, A. (September 2006) Imitating manual curation of text-mined facts in biomedicine. PLoS Comput Biol, 2 (9). e118. ISSN 1553-7358 (Electronic)1553-734X (Linking)
Rzhetsky, A., Iossifov, I., Loh, J. M., White, K. P. (March 2006) Microparadigms: chains of collective reasoning in publications about molecular interactions. Proceedings of the National Academy of Sciences of the United States of America, 103 (13). pp. 4940-5. ISSN 0027-8424
Shuvaev, Sergey, Lazutkin, Alexander, Kiryanov, Roman, Anokhin, Konstantin, Enikolopov, Grigori, Koulakov, Alexei A (March 2022) Spatiotemporal 3D image registration for mesoscale studies of brain development. Scientific Reports, 12 (1). p. 3648. ISSN 2045-2322
Sindhwani, S., Syed, A.M., Ngai, J., Kingston, B.R., Maiorino, L., Rothschild, J., MacMillan, P., Zhang, Y., Rajesh, N.U., Hoang, T., Wu, J.L.Y., Wilhelm, S., Zilman, A., Gadde, S., Sulaiman, A., Ouyang, B., Lin, Z., Wang, L., Egeblad, M., Chan, W.C.W. (January 2020) The entry of nanoparticles into solid tumours. Nat Mater. ISSN 1476-1122 (Public Dataset)
Singh, Shashank, Rashid, Sabrina, Long, Zhicheng, Navlakha, Saket, Salman, Hanna, Oltvai, Zoltan, Bar-Joseph, Ziv (April 2016) Distributed Gradient Descent in Bacterial Food Search. Research in Computational Molecular Biology, 9649. ISSN 978-3-319-31957-5
Suen, Jonathan Y, Navlakha, Saket (March 2022) A feedback control principle common to several biological and engineered systems. Journal of the Royal Society Interface, 19 (188). p. 20210711. ISSN 1742-5662
Tello-Ruiz, M. K., Marco, C. F., Hsu, F. M., Khangura, R. S., Qiao, P., Sapkota, S., Stitzer, M. C., Wasikowski, R., Wu, H., Zhan, J., Chougule, K., Barone, L. C., Ghiban, C., Muna, D., Olson, A. C., Wang, L., Ware, D., Micklos, D. A. (October 2019) Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS ONE, 14 (10). Article number e0224086. ISSN 19326203 (ISSN)
Wang, J. T. L., Marr, T. G., Shasha, D., Shapiro, B. A., Chirn, G. W. (July 1994) Discovering Active Motifs in Sets of Related Protein Sequences and Using Them for Classification. Nucleic Acids Research, 22 (14). pp. 2769-2775. ISSN 0305-1048
Zaki, A., Mitra, P. P., Rasmussen, L. K., Chatterjee, S. (March 2019) Estimate exchange over network is good for distributed hard thresholding pursuit. Signal Processing, 156. pp. 1-11. ISSN 01651684 (ISSN)
Belkin, M., Hsu, D., Mitra, P. P. (December 2018) Overfitting or perfect fitting? Risk bounds for classification and regression rules that interpolate. In: 32nd Conference on Neural Information Processing Systems, NeurIPS 2018, Montreal, Canada.
Mitra, P. P. (November 2018) Fast convergence for stochastic and distributed gradient descent in the interpolation limit. European Signal Processing Conference, EUSIPCO, pp. 1890-1894. ISBN 22195491 (ISSN); 9789082797015 (ISBN)
Navlakha, S., Rastogi, R., Shrivastava, N. (June 2008) Graph summarization with bounded error. ACM, 419-431; Art no. 1376661. ISBN 07308078 (ISSN); 9781605581026 (ISBN)
Navlakha, S., White, J., Nagarajan, N., Pop, M., Kingsford, C. (May 2009) Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5541 L . Springer, pp. 400-417. ISBN 03029743 (ISSN); 9783642020070 (ISBN)
Shahri, H. H., Namata, G., Navlakha, S., Deshpande, A., Roussopoulos, N. (September 2007) A graph-based approach to vehicle tracking in traffic camera video streams. Proceedings of the 4th workshop on Data management for sensor networks: in conjunction with 33rd International Conference on Very Large Data Bases , 273 . ACM International Conference Proceeding Series, pp. 19-24. ISBN 9781595939111 (ISBN)
Thor, A., Anderson, P., Raschid, L., Navlakha, S., Saha, B., Khuller, S., Zhang, X. N. (October 2011) Link prediction for annotation graphs using graph summarization. Lecture Notes in Computer Science, 7031 L (Part 1). Springer, pp. 714-729. ISBN 03029743 (ISSN); 9783642250729 (ISBN)
