Items where Subject is "computational biology"

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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)

Ahmed, Omar, Rossi, Massimiliano, Kovaka, Sam, Schatz, Michael C, Gagie, Travis, Boucher, Christina, Langmead, Ben (June 2021) Pan-genomic Matching Statistics for Targeted Nanopore Sequencing. iScience. p. 102696. ISSN 2589-0042

Al-Jouie, A., Esfandiari, M., Ramakrishnan, S., Roshan, U. (September 2015) Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test. BMC Res Notes, 8. p. 436. ISSN 1756-0500 (Electronic)1756-0500 (Linking)

Andersen, J. N., Del Vecchio, R. L., Kannan, N., Gergel, J., Neuwald, A. F., Tonks, N.K. (January 2005) Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources. Methods, 35 (1). pp. 90-114. ISSN 1046-2023 (Print)

Antoniotti, M., Policriti, A., Ugel, N., Mishra, B. (2003) Model building and model checking for biochemical processes. Cell Biochemistry and Biophysics, 38 (3). pp. 271-286. ISSN 1085-9195

Arbiza, L., Gottipati, S., Siepel, A., Keinan, A. (June 2014) Contrasting X-linked and autosomal diversity across 14 human populations. Am J Hum Genet, 94 (6). pp. 827-44. ISSN 0002-9297

Arbiza, L., Gronau, I., Aksoy, B. A., Hubisz, M. J., Gulko, B., Keinan, A., Siepel, A. (July 2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet, 45 (7). pp. 723-9. ISSN 1061-4036

Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel MD, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong (July 2018) KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology, 36 (7). pp. 566-569. ISSN 1087-0156

Asari, H., Pearlmutter, B. A., Zador, A. M. (July 2006) Sparse representations for the cocktail party problem. Journal of Neuroscience, 26 (28). pp. 7477-7490. ISSN 02706474

Asari, H., Zador, A. M. (August 2009) Long-Lasting Context Dependence Constrains Neural Encoding Models in Rodent Auditory Cortex. J Neurophysiol, 102 (5). pp. 2638-56.

Atwal, G. S. (May 2006) Clustering problems in biological networks. Journal of Classification, 23. pp. 349-352. ISSN 0176-4268 (print) 1432-1343 (Online)

Atwal, G. S., Kinney, J. B. (March 2016) Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments. Journal of Statistical Physics, 162 (5). pp. 1203-1243. ISSN 00224715

Atwal, G. S. (2007) Correlations in Complex Disease Association Studies. Society for Industrial and Applied Mathematics.

Atwal, Gurinder Singh (2014) Statistical mechanics of multistable perception. BioRxiv.

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Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Banerjee, Arkarup, Egger, Robert, Long, Michael A (June 2021) Using focal cooling to link neural dynamics and behavior. Neuron. ISSN 0896-6273

Banerjee, Samik, Magee, Lucas, Wang, Dingkang, Li, Xu, Huo, Bing-Xing, Jayakumar, Jaikishan, Matho, Katherine, Lin, Meng-Kuan, Ram, Keerthi, Sivaprakasam, Mohanasankar, Huang, Josh, Wang, Yusu, Mitra, Partha P (October 2020) Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder-decoder deep networks. Nature Machine Intelligence, 2 (10). 585-+. ISSN 2522-5839

Baslan, Timour, Kovaka, Sam, Sedlazeck, Fritz J, Zhang, Yanming, Wappel, Robert, Tian, Sha, Lowe, Scott W, Goodwin, Sara, Schatz, Michael C (September 2021) High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Research. ISSN 0305-1048

Bejerano, G., Siepel, A. C., Kent, W. J., Haussler, D. (July 2005) Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods, 2 (7). pp. 535-45. ISSN 1548-7091 (Print)1548-7091

Belkhatir, Zehor, Pavon, Michele, Mathews, James C, Pouryahya, Maryam, Deasy, Joseph O, Norton, Larry, Tannenbaum, Allen R (March 2021) Stochastic Norton-Simon-Massague Tumor Growth Modeling: Controlled and Mixed-Effect Uncontrolled Analysis. IEEE Transactions on Control Systems Technology, 29 (2). pp. 704-717. ISSN 1063-6536

Benoit, Matthias, Drost, Hajk-Georg (April 2021) A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. Methods in Molecular Biology, 2250. pp. 1-14. ISSN 1064-3745

Berlow, N. E., Rikhi, R., Geltzeiler, M., Abraham, J., Svalina, M. N., Davis, L. E., Wise, E., Mancini, M., Noujaim, J., Mansoor, A., Quist, M. J., Matlock, K. L., Goros, M. W., Hernandez, B. S., Doung, Y. C., Thway, K., Tsukahara, T., Nishio, J., Huang, E. T., Airhart, S., Bult, C. J., Gandour-Edwards, R., Maki, R. G., Jones, R. L., Michalek, J. E., Milovancev, M., Ghosh, S., Pal, R., Keller, C. (June 2019) Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma. BMC Cancer, 19 (1). p. 593. ISSN 1471-2407 (Public Dataset)

Bhattacharya, Nicholas, Thomas, Neil, Rao, Roshan, Dauparas, Justas, Koo, Peter K, Baker, David, Song, Yun S, Ovchinnikov, Sergey (2022) Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 27. pp. 34-45. ISSN 2335-6936

Biderman, Dan, Whiteway, Matthew R, Hurwitz, Cole, Greenspan, Nicholas, Lee, Robert S, Vishnubhotla, Ankit, Warren, Richard, Pedraja, Federico, Noone, Dillon, Schartner, Michael M, Huntenburg, Julia M, Khanal, Anup, Meijer, Guido T, Noel, Jean-Paul, Pan-Vazquez, Alejandro, Socha, Karolina Z, Urai, Anne E, International Brain Laboratory, Cunningham, John P, Sawtell, Nathaniel B, Paninski, Liam (July 2024) Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling and cloud-native open-source tools. Nature Methods, 21 (7). pp. 1316-1328. ISSN 1548-7091

Birol, I., Champ, M., Cant, J. (September 2010) GENOME INFORMATICS. In: Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on GENOME INFORMATICS, September 15–September 19, 2010, Wellcome Conference Center.

Brown, E. N., Kass, R. E., Mitra, P. P. (May 2004) Multiple neural spike train data analysis: state-of-the-art and future challenges. Nature Neuroscience, 7 (5). pp. 456-461. ISSN 1097-6256

Browning, Michael, Carter, Cameron S, Chatham, Christopher, Den Ouden, Hanneke, Gillan, Claire M, Baker, Justin T, Chekroud, Adam M, Cools, Roshan, Dayan, Peter, Gold, James, Goldstein, Rita Z, Hartley, Catherine A, Kepecs, Adam, Lawson, Rebecca P, Mourao-Miranda, Janaina, Phillips, Mary L, Pizzagalli, Diego A, Powers, Albert, Rindskopf, David, Roiser, Jonathan P, Schmack, Katharina, Schiller, Daniela, Sebold, Miriam, Stephan, Klaas Enno, Frank, Michael J, Huys, Quentin, Paulus, Martin (July 2020) Realizing the Clinical Potential of Computational Psychiatry: Report From the Banbury Center Meeting, February 2019. Biological Psychiatry, 88 (2). e5-e10. ISSN 0006-3223

Bulsara, A. R., Zador, A. M. (1996) Threshold detection of wideband signals: A noise-induced maximum in the mutual information. Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 54 (3). R2185-R2188. ISSN 1063651X (ISSN)

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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)

Carter, J. A., Preall, J. B., Atwal, G. S. (October 2019) Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire. Cell Syst, 9 (5). pp. 475-482. ISSN 2405-4712 (Public Dataset)

Carter, J. A., Preall, J. B., Grigaityte, K., Goldfless, S. J., Jeffery, E., Briggs, A. W., Vigneault, F., Atwal, G. S. (July 2019) Single T Cell Sequencing Demonstrates the Functional Role alpha beta TCR Pairing in Cell Lineage and Antigen Specificity. Frontiers in Immunology, 10. Article Number:1516. ISSN 1664-3224

Celniker, S., Clark, A., Ponting, C., Weinstock, G. (May 2010) THE BIOLOGY OF GENOMES. In: 2010 meeting of THE BIOLOGY OF GENOMES, May 11–May 15, 2010, Cold Spring Harbor Laboratory.

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)

Chandrasekhar, A., Navlakha, S. (May 2019) Neural arbors are Pareto optimal. Proc Biol Sci, 286 (1902). p. 20182727. ISSN 0962-8452 (Public Dataset)

Chandrasekhar, Arjun, Marshall, James AR, Austin, Cortnea, Navlakha, Saket, Gordon, Deborah M (October 2021) Better tired than lost: Turtle ant trail networks favor coherence over short edges. PLoS Computational Biology, 17 (10). e1009523. ISSN 1553-7358

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

Chang, W. I., Lawler, E. L. (October 1994) Sublinear Approximate String-Matching and Biological Applications. Algorithmica, 12 (4-5). pp. 327-344. ISSN 0178-4617

Chen, Wei-Chia, Zhou, Juannan, McCandlish, David M (October 2024) Density estimation for ordinal biological sequences and its applications. Physical Review E, 110 (4). ISSN 2470-0045

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)

Chen, Y., McElvain, L. E., Tolpygo, A. S., Ferrante, D., Friedman, B., Mitra, P. P., Karten, H. J., Freund, Y., Kleinfeld, D. (March 2019) An active texture-based digital atlas enables automated mapping of structures and markers across brains. Nat Methods, 16 (4). pp. 341-350. ISSN 1548-7091

Chen, Shuonan, Loper, Jackson, Chen, Xiaoyin, Vaughan, Alex, Zador, Anthony M, Paninski, Liam (March 2021) BARcode DEmixing through Non-negative Spatial Regression (BarDensr). PLoS Computational Biology, 17 (3). e1008256. ISSN 1553-734X

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason, Kinney, Justin, McCandlish, David (December 2020) Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer. BioRxiv. (Unpublished)

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason M, Kinney, Justin B, McCandlish, David M (October 2021) Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer. Proceedings of the National Academy of Sciences of USA, 118 (40). ISSN 1091-6490

Cheng, H., Gottlieb, L., Marchi, E., Kleyner, R., Bhardwaj, P., Rope, A. F., Rosenheck, S., Moutton, S., Philippe, C., Eyaid, W., Alkuraya, F. S., Toribio, J., Mena, R., Prada, C. E., Stessman, H., Bernier, R., Wermuth, M., Kauffmann, B., Blaumeiser, B., Kooy, R. F., Baralle, D., Mancini, G. M. S., Conway, S. J., Xia, F., Chen, Z., Meng, L., Mihajlovic, L., Marmorstein, R., Lyon, G. J. (May 2019) Phenotypic and biochemical analysis of an international cohort of individuals with variants in NAA10 and NAA15. Hum Mol Genet, 28 (17). pp. 2900-2919. ISSN 0964-6906

Cheng, J., Sedlazek, F., Altmuller, J., Nolte, A. W. (September 2015) Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus). Proc Biol Sci, 282 (1815). ISSN 1471-2954 (Electronic)0962-8452 (Linking)

Chorbadjiev, L., Kendall, J., Alexander, J., Zhygulin, V., Song, J., Wigler, M., Krasnitz, A. (May 2020) Integrated Computational Pipeline for Single-Cell Genomic Profiling. JCO Clinical Cancer Informatics, 4. pp. 464-471.

Churchland, A. K., Abbott, L. F. (February 2016) Conceptual and technical advances define a key moment for theoretical neuroscience. Nat Neurosci, 19 (3). pp. 348-9. ISSN 1546-1726 (Electronic)1097-6256 (Linking)

Cifani, Paolo, Li, Zhi, Luo, Danmeng, Grivainis, Mark, Intlekofer, Andrew M, Fenyö, David, Kentsis, Alex (April 2021) Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. Journal of Proteome Research, 20 (4). pp. 1835-1848. ISSN 1535-3893

Ciubotaru, Mihai, Ionita, Elena, Koo, Peter (2023) RAG DNA recombinase mechanism investigated by single molecule assays; novel reaction mechanism derived from thermodynamics and statistical analysis. In: 25th International Analytical Ultracentrifugation Conference, July 10-15, 2022, Lethbridge, AB, Canada.

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

Conn, A., Chandrasekhar, A., Rongen, M. V., Leyser, O., Chory, J., Navlakha, S. (September 2019) Network trade-offs and homeostasis in Arabidopsis shoot architectures. PLoS Comput Biol, 15 (9). e1007325. ISSN 1553-734x (Public Dataset)

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., Lis, J. T. (December 2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet, 46 (12). pp. 1311-20. ISSN 1061-4036

Couto, Joao, Musall, Simon, Sun, Xiaonan R, Khanal, Anup, Gluf, Steven, Saxena, Shreya, Kinsella, Ian, Abe, Taiga, Cunningham, John P, Paninski, Liam, Churchland, Anne K (June 2021) Chronic, cortex-wide imaging of specific cell populations during behavior. Nature Protocols. ISSN 1754-2189

Cowley, Benjamin R, Smith, Matthew A, Kohn, Adam, Yu, Byron M (December 2016) Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex. PLoS Computational Biology, 12 (12). e1005185. ISSN 1553-734X

Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E, Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C, Buchanan, Alex, van Baren, Marijke J, Spangler, Ryan, Rollins, M Rick, Spellman, Paul T, Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A, Caloian, Cristian, Watson, John D, Uhrig, Sebastian, Haas, Brian J, Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, SMC-RNA Challenge Participants, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C, Stuart, Joshua M, Ellrott, Kyle (August 2021) A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Cell Systems, 12 (8). 827-838.e5. ISSN 2405-4712

Crow, M., Gillis, J. (August 2018) Co-expression in Single-Cell Analysis: Saving Grace or Original Sin? Trends Genet, 34 (11). pp. 823-831. ISSN 0168-9525 (Print)0168-9525

Crow, M., Gillis, J. (June 2019) Single cell RNA-sequencing: replicability of cell types. Current Opinion in Neurobiology, 56. pp. 69-77. ISSN 09594388 (ISSN)

Crow, M., Lim, N., Ballouz, S., Pavlidis, P., Gillis, J. (March 2019) Predictability of human differential gene expression. Proc Natl Acad Sci U S A. ISSN 0027-8424

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (February 2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9 (1). p. 884. ISSN 2041-1723

Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (November 2020) Coexpression reveals conserved mechanisms of transcriptional cell identity. BioRxiv. (Unpublished)

Czégel, Dániel, Giaffar, Hamza, Csillag, Márton, Futó, Bálint, Szathmáry, Eörs (June 2021) Novelty and imitation within the brain: a Darwinian neurodynamic approach to combinatorial problems. Scientific reports, 11 (1). p. 12513. ISSN 2045-2322

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

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Dachet, Fabien, Brown, James B, Valyi-Nagy, Tibor, Narayan, Kunwar D, Serafini, Anna, Boley, Nathan, Gingeras, Thomas R, Celniker, Susan E, Mohapatra, Gayatry, Loeb, Jeffrey A (March 2021) Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Scientific Reports, 11 (1). p. 6078. ISSN 2045-2322

Darby, C.A., Gaddipati, R., Schatz, M.C., Langmead, B. (April 2020) Vargas: Heuristic-Free Alignment for Assessing Linear and Graph Read Aligners. Bioinformatics. ISSN 1367-4803 (Public Dataset)

Daruwala, R. S., Rudra, A., Ostrer, H., Lucito, R., Wigler, M. H., Mishra, B. (November 2004) A versatile statistical analysis algorithm to detect genome copy number variation. Proceedings of the National Academy of Sciences of the United States of America, 101 (46). pp. 16292-16297. ISSN 0027-8424

Das, Arun, Schatz, Michael C (October 2022) Sketching and sampling approaches for fast and accurate long read classification. BMC Bioinformatics, 23 (1). p. 452. ISSN 1471-2105

Das, D , Nahlé, Z , Zhang, M. Q. (June 2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol, 2. pp. 2006-2029. ISSN 1744-4292 (Electronic)

Das, D., Banerjee, N., Zhang, M. Q. (November 2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A, 101 (46). pp. 16234-9. ISSN 0027-8424 (Print)

Das, R., Dimitrova, N., Xuan, Z. Y., Rollins, R. A., Haghighi, F., Edwards, J. R., Ju, J. Y., Bestor, T. H., Zhang, M. Q. (July 2006) Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A, 103 (28). pp. 10713-6. ISSN 0027-8424 (Print)

Das, Arun, Schatz, Michael (November 2021) Sketching and sampling approaches for fast and accurate long read classification. BioRxiv. (Unpublished)

Dasgupta, Sanjoy, Meirovitch, Yaron, Zheng, Xingyu, Bush, Inle, Lichtman, Jeff W, Navlakha, Saket (September 2024) A neural algorithm for computing bipartite matchings. Proceedings of the National Academy of Sciences of the United States of America, 121 (37). e2321032121. ISSN 0027-8424 (Public Dataset)

Dasgupta, S., Sheehan, T. C., Stevens, C. F., Navlakha, S. (December 2018) A neural data structure for novelty detection. Proc Natl Acad Sci U S A, 115 (51). pp. 13093-13098. ISSN 0027-8424 (Public Dataset)

Dauparas, Justas, Wang, Haobo, Swartz, Avi, Koo, Peter, Nitzan, Mor, Ovchinnikov, Sergey (June 2019) Unified framework for modeling multivariate distributions in biological sequences. arXiv e-prints. (Unpublished)

Dauparas, Justas, Wang, Haobo, Swartz, Avi, Koo, Peter K., Nitzan, Mor, Ovchinnikov, Sergey (June 2019) Unified framework for modeling multivariate distributions in biological sequences. In: ICML Workshop for Computational Biology, Long Beach, CA.

Davuluri, R. V., Grosse, I., Zhang, M. Q. (December 2001) Computational identification of promoters and first exons in the human genome. Nature Genetics, 29 (4). pp. 412-417. ISSN 1061-4036

DeWeese, M., Zador, A. M. (1998) Asymmetric Dynamics in Optimal Variance Adaptation. Neural Computation, 10 (5). pp. 1179-1202. ISSN 08997667 (ISSN)

DeWeese, M. R., Hromádka, T., Zador, A. M. (November 2005) Reliability and representational bandwidth in the auditory cortex. Neuron, 48 (3). pp. 479-88. ISSN 0896-6273 (Print)

DeWeese, M. R., Wehr, M., Zador, A. M. (August 2003) Binary spiking in auditory cortex. Journal of Neuroscience, 23 (21). pp. 7940-7949. ISSN 0270-6474

Derkarabetian, S., Castillo, S., Koo, P. K., Ovchinnikov, S., Hedin, M. (October 2019) A demonstration of unsupervised machine learning in species delimitation. Mol Phylogenet Evol, 139. p. 106562. ISSN 1055-7903

Dimitrova, Nevenka , Atwal, Gurinder Singh “Mickey”, Vikalo, Haris, Yoon, Byung-Jun (November 2010) 9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). In: 9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), November 10–November 12, 2010, Cold Spring Harbor.

Diniz, A. L., da Silva, D. I. R., Lembke, C. G., Costa, M. D. L., Ten-Caten, F., Li, F., Vilela, R. D., Menossi, M., Ware, D., Endres, L., Souza, G. M. (November 2020) Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. Int J Mol Sci, 21 (23). p. 9124. ISSN 1422-0067

Dugourd, Aurelien, Kuppe, Christoph, Sciacovelli, Marco, Gjerga, Enio, Gabor, Attila, Emdal, Kristina B, Vieira, Vitor, Bekker-Jensen, Dorte B, Kranz, Jennifer, Bindels, Eric MJ, Costa, Ana SH, Sousa, Abel, Beltrao, Pedro, Rocha, Miguel, Olsen, Jesper V, Frezza, Christian, Kramann, Rafael, Saez-Rodriguez, Julio (January 2021) Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses. Molecular Systems Biology, 17 (1). e9730. ISSN 1744-4292

Dukler, N., Huang, Y-F., Siepel, A. (March 2020) Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data. Mol Biol Evol, 37 (7). pp. 2137-2152. ISSN 0737-4038

Dukler, Noah, Huang, Yi-Fei, Siepel, Adam (September 2019) Phylogenetic modeling of regulatory element turnover based on epigenomic data. BioRxiv. (Unpublished)

Dunn, Timothy W., Koo, Peter K. (2017) Inferring Functional Neural Connectivity with Deep Residual Convolutional Networks. bioRxiv. p. 141010. (Unpublished)

de Bézieux, Hector Roux, Street, Kelly, Fischer, Stephan, Van den Berge, Koen, Chance, Rebecca, Risso, Davide, Gillis, Jesse, Ngai, John, Purdom, Elizabeth, Dudoit, Sandrine (March 2020) Improving replicability in single-cell RNA-Seq cell type discovery with Dune. BioRxiv. (Unpublished)

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Elkin, Rena, Oh, Jung Hun, Liu, Ying L, Selenica, Pier, Weigelt, Britta, Reis-Filho, Jorge S, Zamarin, Dmitriy, Deasy, Joseph O, Norton, Larry, Levine, Arnold J, Tannenbaum, Allen R (November 2021) Geometric network analysis provides prognostic information in patients with high grade serous carcinoma of the ovary treated with immune checkpoint inhibitors. npj Genomic Medicine, 6 (1). p. 99. ISSN 2056-7944

Emek, Yuval, Navlakha, Saket (April 2022) Special Issue: Biological Distributed Algorithms 2021. Journal of Computational Biology, 29 (4). p. 305. ISSN 1557-8666

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Fahlgren, Noah, Kapoor, Muskan, Yordanova, Galabina, Papatheodorou, Irene, Waese, Jamie, Cole, Benjamin, Harrison, Peter, Ware, Doreen, Tickle, Timothy, Paten, Benedict, Burdett, Tony, Elsik, Christine G, Tuggle, Christopher K, Provart, Nicholas J (October 2022) Toward a Data Infrastructure for the Plant Cell Atlas. Plant Physiology. ISSN 1532-2548

Fang, Han, Huang, Yi-Fei, Radhakrishnan, Aditya, Siepel, Adam, Lyon, Gholson J., Schatz, Michael C. (February 2018) Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Systems, 6 (2). pp. 180-191. ISSN 2405-4712

Fang, Han, Wu, Yiyang, Narzisi, G., O'Rawe, Jason, Jimenez Barron, Laura, Rosenbaum, J., Ronemus, M., Iossifov, I., Schatz, M. C., Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med, 6 (10). p. 89.

Fischer, Stephan, Crow, Megan, Harris, Benjamin D, Gillis, Jesse (July 2021) Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Nature Protocols. ISSN 1754-2189

Fischer, Stephan, Gillis, Jesse (October 2022) Defining the extent of gene function using ROC curvature. Bioinformatics. btac692. ISSN 1367-4803

Fischer, Stephan, Gillis, Jesse (June 2021) How many markers are needed to robustly determine a cell’s type? BioRxiv. (Unpublished)

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Zhang, M. Q. (September 2002) Computational prediction of eukaryotic protein-coding genes. Nature Reviews Genetics, 3 (9). pp. 698-709. ISSN 1471-0056

Zhang, M. Q. (March 1998) Identification of human gene core promoters in silico. Genome Research, 8 (3). pp. 319-26. ISSN 1088-9051 (Print)

Zhang, M. Q. (August 1999) Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Research, 9 (8). pp. 681-8. ISSN 1088-9051 (Print)

Zhang, M. Q. (1998) A discrimination study of human core-promoters. Pacific Symposium on Biocomputing. pp. 240-51.

Zhang, M. Q., Marr, T. G. (May 1995) Alignment of molecular sequences seen as random path analysis. Journal of Theoretical Biology, 174 (2). pp. 119-29. ISSN 0022-5193 (Print)

Zhang, X. O., Gingeras, T. R., Weng, Z. (August 2019) Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome Res, 29 (9). pp. 1402-1414. ISSN 1088-9051

Zhang, Y., Song, G., Vinar, T., Green, E. D., Siepel, A., Miller, W. (August 2009) Evolutionary history reconstruction for Mammalian complex gene clusters. J Comput Biol, 16 (8). pp. 1051-70. ISSN 1066-5277

Zhang, Yu, Song, Giltae, Vinar, Tomas, Green, EricD, Siepel, Adam, Miller, Webb (2008) Reconstructing the Evolutionary History of Complex Human Gene Clusters. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science, 4955 . Springer Berlin Heidelberg, pp. 29-49. ISBN 978-3-540-78838-6

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles, Siepel, Adam (March 2021) Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells. BioRxiv. (Unpublished)

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam (August 2021) Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. ISSN 1367-4803

Zhou, J., McCandlish, D. M. (April 2020) Minimum Epistasis Interpolation for Sequence-Function Relationships. Nature Communication, 11 (1782). pp. 1-11. ISSN 2041-1723 (Public Dataset)

Zhou, Juannan, Wong, Mandy, Chen, Wei-Chia, Krainer, Adrian, Kinney, Justin, McCandlish, David (October 2020) Empirical variance component regression for sequence-function relationships. BioRxiv. (Unpublished)

Zhu, Jiening, Oh, Jung Hun, Simhal, Anish K, Elkin, Rena, Norton, Larry, Deasy, Joseph O, Tannenbaum, Allen (September 2023) Geometric graph neural networks on multi-omics data to predict cancer survival outcomes. Computers in Biology and Medicine, 163. p. 107117. ISSN 0010-4825

Ziamtsov, I., Navlakha, S. (October 2019) Machine learning approaches to improve three basic plant phenotyping tasks using 3D point clouds. Plant Physiol. ISSN 0032-0889

Ziamtsov, I, Faizi, K, Navlakha, S (September 2021) Branch-pipe: Improving graph skeletonization around branch points in 3D point clouds. Remote Sensing, 13 (19). ISSN 2072-4292

Ziamtsov, I., Navlakha, S. (March 2020) Plant 3D (P3D): A Plant Phenotyping Toolkit for 3D Point Clouds. Bioinformatics. ISSN 1367-4803 (Public Dataset)

Ziyi, Mo (January 2024) Scalable and robust deep-learning methods power evolutionary-genetic studies of biobank-scale population genomic data. PhD thesis, Cold Spring Harbor Laboratory.