Items where Subject is "bioinformatics > computational biology"

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Al-Jouie, A., Esfandiari, M., Ramakrishnan, S., Roshan, U. (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. (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. (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. (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet, 45 (7). pp. 723-9. ISSN 1061-4036

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

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

Atwal, G. S. (2006) Clustering problems in biological networks. In: Network data analysis and data mining: Applications in Biology, Computer Science, Intrusion Detection and other areas, Piscataway, NJ.

Atwal, G. S., Kinney, J. B. (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. UNSPECIFIED.

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


Bejerano, G., Siepel, A. C., Kent, W. J., Haussler, D. (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

Birol, I., Champ, M., Cant, J. (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. (2004) Multiple neural spike train data analysis: state-of-the-art and future challenges. Nature Neuroscience, 7 (5). pp. 456-461. ISSN 1097-6256

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)


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

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. (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. (2015) Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus). Proc Biol Sci, 282 (1815). ISSN 1471-2954 (Electronic)0962-8452 (Linking)

Churchland, A. K., Abbott, L. F. (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. (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


Daruwala, R. S., Rudra, A., Ostrer, H., Lucito, R., Wigler, M. H., Mishra, B. (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. (2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol, 2. pp. 2006-2029. ISSN 1744-4292 (Electronic)

Das, D., Banerjee, N., Zhang, M. Q. (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. (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)

Davuluri, R. V., Grosse, I., Zhang, M. Q. (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. (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. (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 (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.


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.


Garrels, J. I. (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. (2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Gillis, J., Ballouz, S., Pavlidis, P. (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. (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)

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. (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

Guo, Y., Ding, X., Shen, Y., Lyon, G. J., Wang, K. (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


Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T., Kraus, W. L. (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. (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. (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 (1921) Inter-periodic correlation in the analysis of growth. Biological Bulletin, The, 40 (5). pp. 243-258.

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. (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


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


Kannan, N., Neuwald, A. F. (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. (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. (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. (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. (2004) Mutual information: a universal measure of statistical dependence. Biomedical Computation Review, 10 (2). p. 33.

Kinney, J. B., Atwal, G. S. (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. (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. (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. (2010) Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinformatics, 26 (1). pp. 77-83. ISSN 1367-4803

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. (2014) A Computational Algorithm to Predict shRNA Potency. Mol Cell, 56 (6). pp. 796-807. ISSN 1097-2765

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

Koulakov, A. A., Chklovskii, D. B. (2001) Orientation preference patterns in mammalian visual cortex: A wire length minimization approach. Neuron, 29 (2). pp. 519-527. ISSN 0896-6273

Koulakov, A. A., Hromadka, T., Zador, A. M. (2009) Correlated Connectivity and the Distribution of Firing Rates in the Neocortex. J Neurosci, 29 (12). pp. 3685-3694. ISSN 0270-6474

Koulakov, A. A., Rinberg, D. A., Tsigankov, D. N. (2005) How to find decision makers in neural networks. Biological Cybernetics, 94 (1). pp. 86-88. ISSN 03401200

Krapivsky, P. L., Ben-Naim, E., Grosse, I. R. (2004) Stable distributions in stochastic fragmentation. Journal of Physics a-Mathematical and General, 37 (8). pp. 2863-2880. ISSN 0305-4470

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)

Kundeti, V. K., Rajasekaran, S., Dinh, H., Vaughn, M. W., Thapar, V. (2010) Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs. BMC Bioinformatics, 11. Artical number 560.

Kupferman, R., Mitra, P. P., Hohenberg, P. C., Wang, S. S. H. (1997) Analytical calculation of intracellular calcium wave characteristics. Biophysical Journal, 72 (6). pp. 2430-2444. ISSN 00063495 (ISSN)


Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A. A., Pfeffer, S., Rice, A., Kamphorst, A. O., Landthaler, M., Lin, C., Socci, N. D., Hermida, L., Fulci, V., Chiaretti, S., Foa, R., Schliwka, J., Fuchs, U., Novosel, A., Muller, R. U., Schermer, B., Bissels, U., Inman, J., Phan, Q., Chien, M. C., Weir, D. B., Choksi, R., De Vita, G., Frezzetti, D., Trompeter, H. I., Hornung, V., Teng, G., Hartmann, G., Palkovits, M., Di Lauro, R., Wernet, P., Macino, G., Rogler, C. E., Nagle, J. W., Ju, J. Y., Papavasiliou, F. N., Benzing, T., Lichter, P., Tam, W., Brownstein, M. J., Bosio, A., Borkhardt, A., Russo, J. J., Sander, C., Zavolan, M., Tuschl, T. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129 (7). pp. 1401-1414. ISSN 0092-8674

Latour, L. L., Kleinberg, R. L., Mitra, P. P., Sotak, C. H. (1995) Pore-Size Distributions and Tortuosity in Heterogeneous Porous Media. Journal of Magnetic Resonance, Series A, 112 (1). pp. 83-91. ISSN 10641858 (ISSN)

Latour, L. L., Mitra, P. P., Kleinberg, R. L., Sotak, C. H. (1993) Time-Dependent Diffusion Coefficient of Fluids in Porous Media as a Probe of Surface-to-Volume Ratio. Journal of Magnetic Resonance, Series A, 101 (3). pp. 342-346. ISSN 10641858 (ISSN)

Latour, L. L., Svoboda, K., Mitra, P. P., Sotak, C. H. (1994) Time-dependent diffusion of water in a biological model system. Proc Natl Acad Sci U S A, 91 (4). pp. 1229-33. ISSN 0027-8424

Lee, J. S. M., Katari, G., Sachidanandam, R. (2005) GObar: a gene ontology based analysis and visualization tool for gene sets. BMC Bioinformatics, 6. p. 189. ISSN 1471-2105 (Electronic)

Levy, Dan, Pachter, Lior (2011) The neighbor-net algorithm. Advances in Applied Mathematics, 47 (2). pp. 240-258. ISSN 0196-8858

Li, J., Zhang, M. Q., Zhang, X. (2006) A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. American Journal of Human Genetics, 79 (4). pp. 628-639. ISSN 00029297

Lin, J., Schatz, M. C. (2010) Design patterns for efficient graph algorithms in MapReduce. 8th Workshop on Mining and Learning with Graphs, MLG'10 . MLG, pp. 78-85. ISBN 9781450302142 (ISBN)

Lin, J. M., Bohland, J. W., Andrews, P., Burns, G. A., Allen, C. B., Mitra, P. P. (2008) An analysis of the abstracts presented at the annual meetings of the Society for Neuroscience from 2001 to 2006. PLoS ONE, 3 (4). e2052. ISSN 1932-6203 (Electronic)

Lin, Jimmy, Schatz, Michael C. (2010) Design Patterns for Efficient Graph Algorithms in MapReduce. In: Eighth Workshop on Mining and Learning with Graphs, July 24th-25th 2010, Washington D.C..

Liu-Sullivan, N., Zhang, J., Bakleh, A., Marchica, J., Li, J., Siolas, D., Laquerre, S., Degenhardt, Y. Y., Wooster, R., Chang, K., Hannon, G. J., Powers, S. (2011) Pooled shRNA screen for sensitizers to inhibition of the mitotic regulator polo-like kinase (PLK1). Oncotarget, 2 (12). pp. 1254-64. ISSN 1949-2553 (Electronic) 1949-2553 (Linking)

Lucito, R., West, J., Reiner, A., Alexander, J., Esposito, D., Mishra, B., Powers, S., Norton, L., Wigler, M. H. (2000) Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations. Genome Research, 10 (11). pp. 1726-1736. ISSN 1088-9051

Lyon, Gholson J. (2013) Cambridge HealthTech Institute Clinical Genomics Podcast: Highlights from the Upcoming Clinical Exome Sequencing Conference. [Audio]

Lyon, Gholson J. (2014) Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module. Journal Club. (Unpublished)


Maass, W., Zador, A. M. (1999) Dynamic stochastic synapses as computational units. Neural Computation, 11 (4). pp. 903-917. ISSN 08997667 (ISSN)

Machens, C. K., Zador, A. M. (2003) Auditory modeling gets an edge. Journal of Neurophysiology, 90 (6). pp. 3581-3582. ISSN 0022-3077

Maniar, H. D., Mitra, P. P. (2005) The concentration problem for vector fields. In: 5th International Conference on Bioelectromagnetism & Symposium on Noninvasive Functional Source Imaging, Minneapolis.

Marcus, S., Lee, H., Schatz, M. C. (2014) SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics, 30 (24). pp. 3476-3483. ISSN 1367-4803

Martinez, M. J., Smith, A. D., Li, B. L., Zhang, M. Q., Harrod, K. S. (2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics, 23 (1). pp. 21-29. ISSN 1367-4803

Masse, N. Y., Turner, G. C., Jefferis, G. S. X. E. (2009) Olfactory Information Processing in Drosophila. Current Biology, 19 (16). R700-R713. ISSN 0960-9822

McKay, S. J., Skidmore, E. J., LaRose, C. J., Mercer, A. W., Noutsos, C. (2013) Cloud Computing with iPlant Atmosphere. Curr Protoc Bioinformatics, 43. 9 15 1-20. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Menon, R. K., Bhat, G. P., Schatz, M. C. (2011) Rapid parallel genome indexing with MapReduce. 2nd International Workshop on MapReduce and Its Applications, MapReduce'11, Co-located with 20th International ACM Symposium on High-Performance Parallel and Distributed Computing, HPDC 2011 . ACM, pp. 51-58. ISBN 9781450307000 (ISBN)

Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D., Antin, P. (2016) The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences. PLoS Biol, 14 (1). e1002342. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Mishra, B. (2002) A symbolic approach to modeling cellular behavior. In: High Performance Computing — HiPC 2002. Lecture Notes in Computer Science, 2552 . Springer, pp. 725-732. ISBN 0302-9743

Mitra, P. P. (2007) NIH Conference on Knowledge Environments for Biomedical Research (December 11-12, 2006). Neuroinformatics, 5 (2). pp. 139-140. ISSN 1539-2791

Mitra, P. P., Bokil, H. S. (2007) Observed Brain Dynamics. Oxford University Press, p. 408.

Mitra, P. P., Maniar, H. (2006) Concentration maximization and local basis expansions (LBEX) for linear inverse problems. IEEE Trans Biomed Eng, 53 (9). pp. 1775-82. ISSN 0018-9294 (Print)

Mohammed, J., Flynt, A. S., Siepel, A., Lai, E. C. (2013) The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA, 19 (9). pp. 1295-308. ISSN 1355-8382

Moret, Bernard, Siepel, Adam, Tang, Jijun, Liu, Tao (2002) Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2452 . Springer Berlin Heidelberg, pp. 521-536. ISBN 978-3-540-44211-0


Narzisi, G., Mishra, B., Schatz, M. C. (2014) On algorithmic complexity of biomolecular sequence assembly problem. In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer, pp. 183-195. ISBN 16113349 - ISSN978-331907952-3

Natschlger, T., Maass, W., Zador, A. M. (2001) Efficient temporal processing with biologically realistic dynamic synapses. Network: Computation in Neural Systems, 12 (1). pp. 75-87.

Nattestad, M., Schatz, M. C. (2016) Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics, 32 (19). pp. 3021-3023. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Navlakha, S., Schatz, M. C., Kingsford, C. (2009) Revealing biological modules via graph summarization. Journal of Computational Biology, 16 (2). pp. 253-264. ISSN 10665277 (ISSN)

Neuwald, A. F., Poleksic, A. (2000) PSI-BLAST searches using hidden Markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. Nucleic Acids Research, 28 (18). pp. 3570-3580. ISSN 0305-1048

Neuwald, A. F. (2006) Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine. Nucleic Acids Res, 34 (18). pp. 5280-90. ISSN 1362-4962 (Electronic)

Neuwald, A. F. (2006) Bayesian shadows of molecular mechanisms cast in the light of evolution. Trends Biochem Sci, 31 (7). pp. 374-82. ISSN 0968-0004 (Print)


Pavlidis, P., Gillis, J. (2012) Progress and challenges in the computational prediction of gene function using networks. F1000 Research, 1. ISSN 20461402 (ISSN)

Pavlidis, P., Gillis, J. (2013) Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update. F1000 Research, 2. p. 230. ISSN 20461402 (ISSN)

Pedersen, J. S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E. S., Kent, J., Miller, W., Haussler, D. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol, 2 (4). e33. ISSN 1553-734x

Poleksic, A. (2000) Groups acting on quasiconvex spaces and translation numbers. Proceedings of the American Mathematical Society, 128 (11). pp. 3177-3183. ISSN 0002-9939


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