Items where Subject is "bioinformatics > genomics and proteomics > computers > computer software"

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Number of items at this level: 117.

A

Aboukhalil, R., Fendler, B., Atwal, G. S. (2013) Kerfuffle: a web tool for multi-species gene colocalization analysis. BMC Bioinformatics, 14. ISSN 1471-2105

Adorjan, P., Barna, G., Erdi, P., Grobler, T., Kepecs, A., Lengyel, M., Ventriglia, F. (1996) Multicompartmental modeling of hippocampal pyramidal cells and interneurons with the GENESIS software tool. Neurobiology, 4 (3). pp. 247-249. ISSN 12168068 (ISSN)

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)

B

Ballouz, S., Liu, J. Y., George, R. A., Bains, N., Liu, A., Oti, M., Gaeta, B., Fatkin, D., Wouters, M. A. (2013) Gentrepid V2.0: a web server for candidate disease gene prediction. BMC Bioinformatics, 14. ISSN 1471-2105

Bieri, T., Blasiar, D., Ozersky, P., Antoshechkin, I., Bastiani, C., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., Fiedler, T. J., Girard, L. R., Han, M., Harris, T. W., Kishore, R., Lee, R., McKay, S. J., Müller, H- M., Nakamura, C., Petcherski, A., Rangarajan, A., Rogers, A., Schindelman, G., Schwarz, E. M., Spooner, W., Tuli, M. A., Van Auken, K., Wang, D., Wang, X., Williams, G., Durbin, R., Stein, L. D., Sternberg, P. W., Spieth, J. (2007) WormBase: new content and better access. Nucleic Acids Res, 35 (Databa). D506-D510. ISSN 0305-1048

Bokil, H. S., Andrews, P., Kulkarni, J. E., Mehta, S., Mitra, P. P. (2010) Chronux: A platform for analyzing neural signals. Journal of Neuroscience Methods, 10 (Supp 1). pp. 146-151.

Bokil, H. S., Purpura, K., Schoffelen, J. M., Thomson, D., Mitra, P. P. (2007) Comparing spectra and coherences for groups of unequal size. J Neurosci Methods, 159 (2). pp. 337-45. ISSN 0165-0270 (Print)

Bray, D., Le Novere, N., Lowe, L. (2010) COMPUTATIONAL CELL BIOLOGY. In: Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on Computational Cell Biology, February 10–February 13, 2010, Wellcome Trust Hixton Conference Center UK.

C

Canaran, P., Stein, L. D., Ware, D. H. (2006) Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics, 22 (7). pp. 885-6. ISSN 1367-4803 (Print)

Coghlan, A., Fiedler, T. J., McKay, S. J., Flicek, P., Harris, T. W., Blasiar, D., Stein, L. D. (2008) nGASP - the nematode genome annotation assessment project. Bmc Bioinformatics, 9 (1). p. 549.

Cokol, M., Weinstein, Z. B., Yilancioglu, K., Tasan, M., Doak, A., Cansever, D., Mutlu, B., Li, S., Rodriguez-Esteban, R., Akhmedov, M., Guvenek, A., Cokol, M., Cetiner, S., Giaever, G., Iossifov, I., Nislow, C., Shoichet, B., Roth, F. P. (2014) Large-Scale Identification and Analysis of Suppressive Drug Interactions. Chemistry & Biology, 21 (4). pp. 541-551. ISSN 1074-5521

Cowley, B. R., Kaufman, M. T., Butler, Z. S., Churchland, M. M., Ryu, S. I., Shenoy, K. V., Yu, B. M. (2013) DataHigh: Graphical user interface for visualizing and interacting with high-dimensional neural activity. Journal of Neural Engineering, 10 (6). ISSN 17412560 (ISSN)

D

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)

Dedhia, N. N., McCombie, W. R. (1998) Kaleidaseq: A Web-based tool to monitor data flow in a high throughput sequencing facility. Genome Research, 8 (3). pp. 313-318. ISSN 10889051 (ISSN)

de la Bastide, M., McCombie, W. R. (2007) Assembling genomic DNA sequences with PHRAP. Current Protocols in Bioinformatics (Unit 1). ISSN 1934-340X (Electronic)1934-3396 (Linking)

F

Faith, J. J., Olson, A. J., Gardner, T. S., Sachidanandam, R. (2007) Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context. BMC Bioinformatics, 8. p. 344. ISSN 1471-2105

G

Gajer, P., Schatz, M., Salzberg, S. L. (2004) Automated correction of genome sequence errors. Nucleic Acids Research, 32 (2). pp. 562-569. ISSN 03051048 (ISSN)

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)

Gessler, D. D., Schiltz, G. S., May, G. D., Avraham, S., Town, C. D., Grant, D., Nelson, R. T. (2009) SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services. BMC Bioinformatics, 10. p. 309.

Gillis, J., Mistry, M., Pavlidis, P. (2010) Gene function analysis in complex data sets using ErmineJ. Nature Protocols, 5 (6). pp. 1148-1159. ISSN 17502799 (ISSN)

Gillis, J., Pavlidis, P. (2011) The impact of multifunctional genes on guilt "by association "analysis. PLoS One, 6 (2). ISSN 19326203 (ISSN)

Gillis, J., Pavlidis, P. (2009) A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics, 10. p. 306. ISSN 14712105 (ISSN)

Gillis, J., Pavlidis, P. (2011) The role of indirect connections in gene networks in predicting function. Bioinformatics, 27 (13). pp. 1860-1866. ISSN 13674803 (ISSN)

Gingeras, T. R. (1983) Computers and DNA sequences: A natural combination. In: Statistical analysis of DNA sequence data. M. Dekker, New York, pp. 15-44. ISBN 9780824770327

Gingeras, T. R., Milazzo, J. P., Roberts, R. J. (1978) A computer assisted method for the determination of restriction enzyme recognition sites. Nucleic Acids Research, 5 (11). pp. 4105-4128. ISSN 03051048 (ISSN)

Gingeras, T. R., Milazzo, J. P., Sciaky, D., Roberts, R. J. (1979) Computer programs for the assembly of DNA sequences. Nucleic Acids Research, 7 (2). pp. 529-45. ISSN 0305-1048 (Print)0305-1048

Gingeras, T. R., Rice, P., Roberts, R. J. (1982) A semi-automated method for the reading of nucleic acid sequencing gels. Nucleic Acids Research, 10 (1). pp. 103-114. ISSN 03051048 (ISSN)

Gingeras, T. R., Roberts, R. J. (1981) Computer assisted methods for nucleic acid sequencing. In: Genetic Engineering: Principles and Methods. Plenum Press, pp. 319-338. ISBN 9780306439193

Girard, L. R., Fiedler, T. J., Harris, T. W., Carvalho, F., Antoshechkin, I., Han, M., Sternberg, P.l W., Stein, L. D., Chalfie, M. (2007) WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res, 35 (Databa). D472-D475. ISSN 0305-1048

Gordon, D., Finch, S. J., Jacobs, A. L., Mendell, N. R., Single, R. M., Marr, T. G. (1997) Association of posterior p-values of S.A.G.E. SIBPAL proportion-IBD and Haseman-Elston statistics for ACTHR112. Genetic Epidemiology, 14 (6). pp. 629-34. ISSN 0741-0395 (Print)

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)

Gurtowski, J., Schatz, M. C., Langmead, B. (2012) Genotyping in the cloud with crossbow. Current Protocols in Bioinformatics. 15.3. ISSN 1934-340X (Electronic)1934-3396 (Linking)

H

Hannon, G. J., Jentoft, J. E. (1985) MOLECULAR DESIGNER: An interactive program for the display of protein structure on the IBM-PC. Computer Applications in the Biosciences, 1 (3). pp. 177-181. ISSN 02667061 (ISSN)

Harris, T. W., Stein, L. D. (2006) WormBase: methods for data mining and comparative genomics. In: C. elegans: methods and applications. Methods Mol Biol, 351 . Humana Press, Totowa, NJ, pp. 31-50. ISBN 1064-3745 (Print)

Haw, R., Hermjakob, H., D'Eustachio, P., Stein, L. D. (2011) Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics, 11 (18). pp. 3598-3613. ISSN 16159853 (ISSN)

Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T. S., Harte, R. A., Hsu, F., Hillman-Jackson, J., Kuhn, R. M., Pedersen, J. S., Pohl, A., Raney, B. J., Rosenbloom, K. R., Siepel, A., Smith, K. E., Sugnet, C. W., Sultan-Qurraie, A., Thomas, D. J., Trumbower, H., Weber, R. J., Weirauch, M., Zweig, A. S., Haussler, D., Kent, W. J. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res, 34 (Databa). D590-8. ISSN 0305-1048

Hladish, T., Gopalan, V., Liang, C., Qiu, W., Yang, P., Stoltzfus, A. (2007) Bio :: NEXUS: a Perl API for the NEXUS format for comparative biological data. Bmc Bioinformatics, 8. p. 191. ISSN 1471-2105

J

Jin, Y., Tam, O. H., Paniagua, E., Hammell, M. (2015) TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 31 (22). pp. 3593-3599. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

K

Katari, M.t S., Balija, V., Wilson, R. K., Martienssen, R. A., McCombie, W. R. (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Research, 15 (4). pp. 496-504. ISSN 10889051 (ISSN)

Kel, A. E., Kel-Margoulis, O. V., Farnham, P. J., Bartley, S. M., Wingender, E., Zhang, M. Q. (2001) Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology, 309 (1). pp. 99-120. ISSN 0022-2836

Kelley, D. R., Schatz, M. C., Salzberg, S. L. (2010) Quake: Quality-aware detection and correction of sequencing errors. Genome Biology, 11 (11). ISSN 1474-7596

Kepecs, A., Wang, X. J. (2000) Analysis of complex bursting in cortical pyramidal neuron models. Neurocomputing, 32-33. pp. 181-187. ISSN 09252312 (ISSN)

L

Langmead, B., Schatz, M. C., Lin, J., Pop, M., Salzberg, S. L. (2009) Searching for SNPs with cloud computing. Genome Biology, 10 (11). ISSN 14747596 (ISSN)

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)

Li, W. T., Bernaola-Galvan, P., Haghighi, F., Grosse, I. (2002) Applications of recursive segmentation to the analysis of DNA sequences. Computers & Chemistry, 26 (5). pp. 491-510. ISSN 0097-8485

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)

Long, D. D., Grosse, I., Marx, K. A. (2004) Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis. Biophysical Chemistry, 110 (1-2). pp. 25-38. ISSN 0301-4622

Lyon, Gholson J. (2012) Implementation of Variant Calling Algorithms in Clinical Genome Sequencing. In: Bio-IT Europe The Road to the Clinic: Applying Genomics in a Clinical Setting , Oct 10th 2012, Vienna, Austria. (Unpublished)

Lyon, Gholson J. (2012) Software Considerations for Processing, Analyzing and Interpreting Exome & Genome Sequence Data in Clinical Settings. In: World Genome Data Analysis Summit: Pre Conference Workshop, Nov 27th 2012, San Francisco. (Unpublished)

M

Machens, C. K. (2002) Adaptive sampling by information maximization. Physical Review Letters, 88 (22). ISSN 0031-9007

Majoros, W. H., Campbell, M. S., Holt, C., DeNardo, E., Ware, D., Allen, A. S., Yandell, M., Reddy, T. E. (2016) High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

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

McKay, S. J., Vergara, I. A., Stajich, J. E. (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics, Chapte. Unit 9 12. ISSN 1934-340X (Electronic) 1934-3396 (Linking)

Menges, F., Narzisi, G., Mishra, B. (2011) TotalReCaller: improved accuracy and performance via integrated alignment and base-calling. Bioinformatics, 27 (17). pp. 2330-2337. ISSN 1367-4803

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. (2009) Technical perspective: Where biology meets computing. Communications of the ACM, 52 (3). p. 96.

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

Monardo, P. J., Boutell, T., Garrels, J. I., Latter, G. I. (1994) A distributed system for two-dimensional gel analysis. Comput Appl Biosci, 10 (2). pp. 137-43.

N

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)

Navin, N. E., Grubor, V., Hicks, J. B., Leibu, E., Thomas, E., Troge, J., Riggs, M., Lundin, P., Månér, S., Sebat, J., Zetterberg, A., Wigler, M. H. (2006) PROBER: oligonucleotide FISH probe design software. Bioinformatics, 22 (19). pp. 2437-8. ISSN 1460-2059 (Electronic)

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

Niedworok, C. J., Brown, A. P., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M., Margrie, T. W. (2016) aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nat Commun, 7. p. 11879. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

O

Olson, A., Sheth, N., Lee, J., Hannon, G. J., Sachidanandam, R. (2005) Rnai codex - a comprehensive RNAi resource. Briefings in Bioinformatics, 6 (1). pp. 104-106. ISSN 1467-5463

P

Paz, I., Akerman, M., Dror, I., Kosti, I., Mandel-Gutfreund, Y. (2010) SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Research, 38 (S2). W281-W285. ISSN 03051048 (ISSN)

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., Siepel, A. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res, 20 (1). pp. 110-21. ISSN 1088-9051

Pologruto, T. A., Sabatini, B. L., Svoboda, K. (2003) ScanImage: flexible software for operating laser scanning microscopes. Biomedical Engineering Online, 2. p. 13. ISSN 1475-925X (Electronic)

Posfai, J., Roberts, R. J. (1992) Finding errors in DNA sequences. Proc Natl Acad Sci U S A, 89 (10). pp. 4698-702. ISSN 0027-8424 (Print)0027-8424 (Linking)

R

Raposo, D., Kaufman, M. T., Churchland, A. K. (2014) Datasets from "Raposo, David and Kaufman, Matthew T. and Churchland, Anne K. (2014) A category-free neural population supports evolving demands during decision-making. Nature Neuroscience". [Experiment]

Raposo, D., Kaufman, M. T., Churchland, A. K. (2014) Matlab code for running the PAIRS and Variance Alignment Analyses from "Raposo, David and Kaufman, Matthew T. and Churchland, Anne K. (2014) A category-free neural population supports evolving demands during decision-making. Nature Neuroscience". [Experiment]

Rasmussen, M. D., Hubisz, M. J., Gronau, I., Siepel, A. (2014) Genome-wide inference of ancestral recombination graphs. PLoS Genetics, 10 (5). e1004342. ISSN 15537390 (ISSN)

Rodriguez-Esteban, R., Iossifov, I. (2009) Figure mining for biomedical research. Bioinformatics, 25 (16). pp. 2082-2084.

S

Schatz, M. C. (2009) CloudBurst: Highly sensitive read mapping with MapReduce. Bioinformatics, 25 (11). pp. 1363-1369. ISSN 13674803 (ISSN)

Schatz, M. C., Langmead, B. (2013) THE DNA DATA DELUGE FAST, EFFICIENT GENOME-SEQUENCING MACHINES ARE SPEWING OUT MORE DATA THAN GENETICISTS CAN ANALYZE. IEEE Spectrum, 50 (7). pp. 28-33. ISSN 0018-9235

Schatz, M. C., Langmead, B., Salzberg, S. L. (2010) Cloud computing and the DNA data race. Nature Biotechnology, 28 (7). pp. 691-693.

Schatz, M. C., Phillippy, A. M., Gajer, P., DeSantis, T. Z., Andersen, G. L., Ravel, J. (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Applied and Environmental Microbiology, 76 (16). pp. 5636-5638. ISSN 00992240 (ISSN)

Schatz, M. C., Phillippy, A. M., Shneiderman, B., Salzberg, S. L. (2007) Hawkeye: An interactive visual analytics tool for genome assemblies. Genome Biology, 8 (3). ISSN 14747596 (ISSN)

Schatz, M. C., Phillippy, A. M., Sommer, D. D., Delcher, A. L., Puiu, D., Narzisi, G., Salzberg, S. L., Pop, M. (2013) Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics, 14 (2). pp. 213-224. ISSN 14675463

Schatz, M. C., Trapnell, C., Delcher, A. L., Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. Bmc Bioinformatics, 8. ISSN 14712105 (ISSN)

Schmidt, Christoph F., Svoboda, Karel, Lei, Ning, Petsche, Irena B., Berman, Lonny E., Safinya, Cyrus R., Grest, Gary S. (1993) Existence of a flat phase in red cell membrane skeletons. Science, 259 (5097). pp. 952-5. ISSN 0036-8075

Schones, D. E., Smith, A. D., Zhang, M. Q. (2007) Statistical significance of cis-regulatory modules. Working Paper. Bmc Bioinformatics.

Schwarz, E. M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., Fiedler, T. J., Girard, L., Harris, T. W., Kenny, E. E., Kishore, R., Lawson, D., Lee, R., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Spooner, W., Tuli, M. A., Van Auken, K., Wang, D., Durbin, R., Spieth, J., Stein, L. D., Sternberg, P. W. (2006) WormBase: better software, richer content. Nucl. Acids Res., 34 (suppl_). D475-478.

Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W., Sobral, B. (2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17 (1). pp. 83-94. ISSN 1367-4803 (Print)1367-4803

Siepel, A. C., Halpern, A. L., Macken, C., Korber, B. T. (1995) A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses, 11 (11). pp. 1413-6. ISSN 0889-2229 (Print)0889-2229

Siepel, A. C., Steenhuis, T. S., Rose, C. W., Parlange, J. Y., McIsaac, G. F. (2002) A simplified hillslope erosion model with vegetation elements for practical applications. Journal of Hydrology, 258 (1-4). pp. 111-121.

Siepel, A. C., Tolopko, A. N., Farmer, A. D., Steadman, P. A., Schilkey, F. D., Perry, B. D., Beavis, W. D. (2001) An integration platform for heterogeneous bioinformatics software components. IBM Systems Journal, 40 (2). pp. 570-591.

Smith, A. D., Chung, W. Y., Hodges, E., Kendall, Jude T., Hannon, G. J., Hicks, J. B., Xuan, Z., Zhang, M. Q. (2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25 (21). pp. 2841-2842.

Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., Wilkinson, M. D., Birney, E. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Research, 12 (10). pp. 1611-8. ISSN 10889051 (ISSN)

Stein, L. D. (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet, 9 (9). pp. 678-688.

Stein, L. D. (2007) Unix survival guide. Curr Protoc Bioinformatics, Append. Appendix 1C.

Stein, L. D. (2001) Using Perl to facilitate biological analysis. In: Bioinformatics: a practical guide to the analysis of genes and proteins. Methods of Biochemical Analysis, 43 . Wiley, New York, pp. 413-49. ISBN 0076-6941 (Print)

Stein, L. D. (2007) X Window System survival guide. Curr Protoc Bioinformatics, Append. Appendix 1D.

Stein, L. D., Cartinhour, S., Thierry-Mieg, D., Thierry-Mieg, J. (1998) JADE: an approach for interconnecting bioinformatics databases. Gene, 209 (1-2). GC39-GC43.

Stein, L. D., Mungall, C., Shu, S. Q., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., Lewis, S. (2002) The Generic Genome Browser: A building block for a model organism system database. Genome Research, 12 (10). pp. 1599-1610. ISSN 1088-9051

Sumazin, P., Chen, G., Hata, N., Smith, A. D., Zhang, T., Zhang, M. Q. (2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)

T

Teng, M., Love, M. I., Davis, C. A., Djebali, S., Dobin, A., Graveley, B. R., Li, S., Mason, C. E., Olson, S., Pervouchine, D., Sloan, C. A., Wei, X., Zhan, L., Irizarry, R. A. (2016) A benchmark for RNA-seq quantification pipelines. Genome Biol, 17 (1). p. 74. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Thorisson, G. A., Smith, A. V., Krishnan, L., Stein, L. D. (2005) The International HapMap Project Web site. Genome Res, 15 (11). pp. 1592-3. ISSN 1088-9051 (Print)

Tolonen, A. C., Albeanu, D. F., Corbett, J. F., Handley, H., Henson, C., Malik, P. (2002) Optimized in situ construction of oligomers on an array surface. Nucleic Acids Research, 30 (20). e107. ISSN 0305-1048

Trapnell, C., Schatz, M. C. (2009) Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Computing, 35 (8-9). pp. 429-440. ISSN 01678191 (ISSN)

Tvarusko, W., Bentele, M., Misteli, Tom, Rudolf, R., Kaether, C., Spector, David L., Gerdes, H. H., Eils, R. (1999) Time-resolved analysis and visualization of dynamic processes in living cells. Proceedings of the National Academy of Sciences of the United States of America, 96 (14). pp. 7950-5. ISSN 0027-8424

V

Vastrik, I., D'Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., Stein, L. D. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol, 8 (3). R39. ISSN 1474-760X

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., Schatz, M. C. (2017) GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics. ISSN 1367-4803

W

Wang, J., Smith, P. J., Krainer, A. R., Zhang, M. Q. (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res, 33 (16). pp. 5053-62. ISSN 1362-4962 (Electronic)

Wang, L., Uilecan, I. V., Assadi, A. H., Kozmik, C. A., Spalding, E. P. (2009) HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis. Plant Physiol., 149 (4). pp. 1632-1637.

Wang, L., Van Buren, P., Ware, D. (2016) Architecting a distributed bioinformatics platform with iRODS and iPlant agave API. 2015 International Conference on Computational Science and Computational Intelligence (CSCI). pp. 420-423.

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This list was generated on Sat May 27 13:31:07 2017 EDT.
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