Items where Subject is "computers"

Paper

Aboukhalil, R., Fendler, B., Atwal, G. S. (January 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)

Biffi, C., de Marvao, A., Attard, M. I., Dawes, T. J. W., Whiffin, N., Bai, W., Shi, W., Francis, C., Meyer, H., Buchan, R., Cook, S. A., Rueckert, D., O'Regan, D. P. (January 2018) Three-dimensional cardiovascular imaging-genetics: a mass univariate framework. Bioinformatics, 34 (1). pp. 97-103. ISSN 1367-4803

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

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)

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)

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)

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)

Goodman, L. (September 1997) More BLAST for the buck. Genome Research, 7 (9). pp. 858-9. ISSN 1088-9051

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)

Hutton, Elizabeth R, Vakoc, Christopher R, Siepel, Adam (September 2021) ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens. Genome Biology, 22 (1). p. 278. ISSN 1474-760X

Kel, A. E., Kel-Margoulis, O. V., Farnham, P. J., Bartley, S. M., Wingender, E., Zhang, M. Q. (May 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

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

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

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

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

Renton, Angela I, Dao, Thuy T, Johnstone, Tom, Civier, Oren, Sullivan, Ryan P, White, David J, Lyons, Paris, Slade, Benjamin M, Abbott, David F, Amos, Toluwani J, Bollmann, Saskia, Botting, Andy, Campbell, Megan EJ, Chang, Jeryn, Close, Thomas G, Doerig, Monika, Eckstein, Korbinian, Egan, Gary F, Evas, Stefanie, Flandin, Guillaume, Garner, Kelly G, Garrido, Marta I, Ghosh, Satrajit S, Grignard, Martin, Halchenko, Yaroslav O, Hannan, Anthony J, Heinsfeld, Anibal S, Huber, Laurentius, Hughes, Matthew E, Kaczmarzyk, Jakub R, Kasper, Lars, Kuhlmann, Levin, Lou, Kexin, Mantilla-Ramos, Yorguin-Jose, Mattingley, Jason B, Meier, Michael L, Morris, Jo, Narayanan, Akshaiy, Pestilli, Franco, Puce, Aina, Ribeiro, Fernanda L, Rogasch, Nigel C, Rorden, Chris, Schira, Mark M, Shaw, Thomas B, Sowman, Paul F, Spitz, Gershon, Stewart, Ashley W, Ye, Xincheng, Zhu, Judy D, Narayanan, Aswin, Bollmann, Steffen (May 2024) Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods, 21 (2). pp. 804-808. ISSN 1548-7091

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. (July 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., 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., 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. (February 1993) Existence of a flat phase in red cell membrane skeletons. Science, 259 (5097). pp. 952-5. ISSN 0036-8075

Siepel, A. (July 2019) Challenges in funding and developing genomic software: roots and remedies. Genome Biol, 20 (1). p. 147. ISSN 1474-7596

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

Sun, G., Krasnitz, A. (2019) Statistically Supported Identification of Tumor Subtypes. Methods Mol Biol, 1878. pp. 209-216. ISSN 1064-3745

Book Section

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

Conference or Workshop Item

Lyon, Gholson J. (November 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)

Video

Schatz, M. C. (November 2012) Talk from Mike Schatz at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Dataset

Gillis, J., Pavlidis, P. (2011) Figure data from "The role of indirect connections in gene networks in predicting function" Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) Gene Ontology matrices from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) Gene lists from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) Network data from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011)Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]