Items where Subject is "computational biology"

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Number of items at this level: 255.

A

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.

B

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

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

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)

C

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

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

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)

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

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., 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, 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

D

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, 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)

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

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.

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)

F

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 (Unpublished)

G

Garrels, J. I. (August 1979) 2 Dimensional Gel Electrophoresis and Computer Analysis of Proteins Synthesized by Clonal Cell Lines. Journal of Biological Chemistry, 254 (16). pp. 7961-7977. ISSN 0021-9258 (Print)0021-9258 (Linking)

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (November 2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking) (Public Dataset)

Gillis, J., Ballouz, S., Pavlidis, P. (January 2014) Bias tradeoffs in the creation and analysis of protein-protein interaction networks. Journal of Proteomics, 100. pp. 44-54.

Gillis, J., Pavlidis, P. (2013) Cross-validation calculation from "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (2012) Exceptional Edges matrices from "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (2012) Gene Ontology matrices (with descriptions, IDs, etc) from "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (2012) Gene lists from Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (March 2012) "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. PLoS Computational Biology, 8 (3). ISSN 1553-734X

Gingeras, T. R., Roberts, R. J. (1980) Steps toward computer analysis of nucleotide sequences. Science, 209 (4463). pp. 1322-1328. ISSN 00368075 (ISSN)

Guerler, Aysam, Baker, Dannon, van den Beek, Marius, Gruening, Bjoern, Bouvier, Dave, Coraor, Nate, Shank, Stephen, Zehr, Jordan, Schatz, Michael, Nekrutenko, Anton (March 2021) Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. BioRxiv. (Unpublished)

Guigó, R., Flicek, P., Abril, J. F., Reymond, A., Lagarde, J., Denoeud, F., Antonarakis, S., Ashburner, M., Bajic, V. B., Birney, E., Castelo, R., Eyras, E., Ucla, C., Gingeras, T. R., Harrow, J., Hubbard, T., Lewis, S. E., Reese, M. G. (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology, 7 Supp. S2.1-31. ISSN 14656914 (ISSN)

Gulko, B., Hubisz, M. J., Gronau, I., Siepel, A. (March 2015) A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nature Genetics, 47 (3). pp. 276-283. ISSN 1061-4036

Gulko, Brad, Siepel, Adam (May 2018) How Much Information is Provided by Human Epigenomic Data? An Evolutionary View. BioRxiv. (Unpublished)

Guo, Y., Ding, X., Shen, Y., Lyon, G. J., Wang, K. (September 2015) SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Sci Rep, 5. p. 14283. ISSN 2045-2322 (Electronic)2045-2322 (Linking)

Günay, Cengiz, Smolinski, Tomasz G, Lytton, William W, Morse, Thomas M, Gleeson, Padraig, Crook, Sharon, Steuber, Volker, Silver, Angus, Voicu, Horatiu, Andrews, Peter, Bokil, Hemant, Maniar, Hiren, Loader, Catherine, Mehta, Samar, Kleinfeld, David, Thomson, David, Mitra, Partha P., Aaron, Gloster, Fellous, Jean-Marc (2008) Computational Intelligence in Electrophysiology: Trends and Open Problems. In: Applications of Computational Intelligence in Biology. Studies in Computational Intelligence, 122 . Springer Berlin Heidelberg, pp. 325-359. ISBN 978-3-540-78533-0

H

Haas, Brian, Dobin, Alex, Stransky, Nicolas, Li, Bo, Yang, Xiao, Tickle, Timothy, Bankapur, Asma, Ganote, Carrie, Doak, Thomas, Pochet, Nathalie, Sun, Jing, Wu, Catherine, Gingeras, Thomas, Regev, Aviv (March 2017) STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. BioRxiv. (Unpublished)

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T., Kraus, W. L. (May 2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145 (4). pp. 622-34. ISSN 0092-8674

Hammell, M. (September 2010) Computational methods to identify miRNA targets. Seminars in Cell & Developmental Biology, 21 (7). pp. 738-44. ISSN 1084-9521

Hangya, B., Pi, H. J., Kvitsiani, D., Ranade, S. P., Kepecs, A. (February 2014) From circuit motifs to computations: mapping the behavioral repertoire of cortical interneurons. Current Opinion in Neurobiology, 26c. pp. 117-124. ISSN 0959-4388

Harris, James Arthur, Reed, Howard Sprague (May 1921) Inter-periodic correlation in the analysis of growth. Biological Bulletin, The, 40 (5). pp. 243-258.

Harris, Reginald Gordon (June 1935) Mathematics in biology. The Scientific Monthly, 40 (6). pp. 504-510.

Herrero, J., Muffato, M., Beal, K., Fitzgerald, S., Gordon, L., Pignatelli, M., Vilella, A. J., Searle, S. M., Amode, R., Brent, S., Spooner, W., Kulesha, E., Yates, A., Flicek, P. (February 2016) Ensembl comparative genomics resources. Database : the journal of biological databases and curation, 2016. ISSN 17580463 (ISSN)

Herz, A. V. M., Gollisch, T., Machens, C. K., Jaeger, D. (2006) Modeling single-neuron dynamics and computations: A balance of detail and abstraction. Science, 314 (5796). pp. 80-85. ISSN 00368075

How, J. J., Navlakha, S. (August 2018) Evidence of Rentian Scaling of Functional Modules in Diverse Biological Networks. Neural Comput, 30 (8). pp. 2210-2244. ISSN 0899-7667

Hubisz, M. J., Williams, A. L., Siepel, A. (August 2020) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet, 16 (8). e1008895. ISSN 1553-7390 (Print)1553-7390

Hubisz, Melissa, Williams, Amy, Siepel, Adam (June 2019) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. BioRxiv. (Unpublished)

Hutton, Elizabeth, Vakoc, Christopher, Siepel, Adam (December 2019) ACE: A Probabilistic Model for Characterizing Gene-Level Essentiality in CRISPR Screens. BioRxiv.

I

Ireland, William, Kinney, Justin (May 2016) MPAthic: Quantitative Modeling of Sequence-Function Relationships for massively parallel assays. BioRxiv. (Unpublished)

J

Jiang, B., Zhang, M. Q., Zhang, X. (November 2007) OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics, 23 (21). pp. 2823-8. ISSN 1460-2059 (Electronic)

Joo, Hannah R, Liang, Hexin, Chung, Jason E, Geaghan-Breiner, Charlotte, Fan, Jiang Lan, Nachman, Benjamin P, Kepecs, Adam, Frank, Loren M (August 2021) Rats use memory confidence to guide decisions. Current Biology. ISSN 0960-9822

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Kannan, N., Neuwald, A. F. (September 2005) Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? J Mol Biol, 351 (5). pp. 956-72. ISSN 0022-2836 (Print)

Kato, M., Hata, N., Banerjee, N., Futcher, B., Zhang, M. Q. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology, 5 (8). ISSN 1465-6914

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D., Guigo, R., Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J., Weng, Z., White, K. P., Hardison, R. C. (August 2014) Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America, 111 (33). E3366-E3366. ISSN 10916490 (ISSN)

Kendall, J., Krasnitz, A. (July 2014) Computational methods for DNA copy-number analysis of tumors. Methods in Molecular Biology, 1176. pp. 243-59. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Kepecs, A., Mainen, Z. F. (May 2012) A computational framework for the study of confidence in humans and animals. Philos Trans R Soc Lond B Biol Sci, 367 (1594). pp. 1322-37. ISSN 1471-2970 (Electronic)0962-8436 (Linking)

Kinney, J. B. (June 2014) Mutual information: a universal measure of statistical dependence. Biomedical Computation Review, 10 (2). p. 33.

Kinney, J. B., Atwal, G. S. (March 2014) Equitability, mutual information, and the maximal information coefficient. Proceedings of the National Academy of Sciences of the United States of America, 111 (9). pp. 3354-9. ISSN 0027-8424

Kinney, J. B., Atwal, G. S. (2013) Parametric inference in the large data limit using maximally informative models. Arxiv. (Unpublished)

Kinney, J. B., Atwal, G. S. (May 2014) Reply to Murrell et al.: Noise matters. Proceedings of the National Academy of Sciences of the United States of America, 111 (21). E2161. ISSN 10916490

Kinney, J. B., Murugan, A., Callan, C. G., Cox, E. C. (May 2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proceedings of the National Academy of Sciences of the United States of America, 107 (20). pp. 9158-9163. ISSN 0027-8424

Kirchner, M., Renard, B. Y., Kothe, U., Pappin, D. J., Hamprecht, F. A., Steen, H., Steen, J. A. J. (January 2010) Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinformatics, 26 (1). pp. 77-83. ISSN 1367-4803

Kirsche, Melanie, Das, Arun, Schatz, Michael C (May 2021) Sapling: accelerating suffix array queries with learned data models. Bioinformatics, 37 (6). pp. 744-749. ISSN 1367-4803

Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Aganezov, Sergey, Schatz, Michael (May 2021) Jasmine: Population-scale structural variant comparison and analysis. BioRxiv. (Unpublished)

Knott, S. R., Maceli, A. R., Erard, N., Chang, K., Marran, K., Zhou, X., Gordon, A., El Demerdash, O., Wagenblast, E., Kim, S., Fellmann, C., Hannon, G. J. (December 2014) A Computational Algorithm to Predict shRNA Potency. Mol Cell, 56 (6). pp. 796-807. ISSN 1097-2765

Koo, P. K., Ploenzke, Matt (June 2019) Improving Convolutional Network Interpretability with Exponential Activations. In: ICML Workshop for Computational Biology, Long Beach, CA.

Koo, Peter K., Eddy, Sean R. (2019) Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks. bioRxiv. p. 362756. (Unpublished)

Koo, Peter K., Ploenzke, Matt (2019) Improving Convolutional Network Interpretability with Exponential Activations. bioRxiv. p. 650804. (Unpublished)

Koo, Peter K., Qian, Sharon, Kaplun, Gal, Volf, Verena, Kalimeris, Dimitris (2019) Robust Neural Networks are More Interpretable for Genomics. bioRxiv. p. 657437. (Unpublished)

Koo, Peter K., Qian, Sharon, Volf, Verena, Kalimeris, Dimitris (June 2019) Robust Neural Networks are More Interpretable for Genomics. In: ICML Workshop for Computational Biology, Long Beach, CA.

Koo, Peter, Ploenzke, Matt (June 2020) Improving representations of genomic sequence motifs in convolutional networks with exponential activations. BioRxiv. (Unpublished)

Koo, Peter K, Eddy, Sean R (December 2019) Representation learning of genomic sequence motifs with convolutional neural networks. PLoS Computational Biology, 15 (12). e1007560. ISSN 1553-734X

Koulakov, A. A., Chklovskii, D. B. (June 2002) Direction of motion maps in the visual cortex: a wire length minimization approach. Neurocomputing, 44. pp. 489-494. ISSN 0925-2312

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