Items where Subject is "bioinformatics > quantitative biology"

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Authors | Item Type
Jump to: A | B | C | D | E | F | G | H | K | L | M | N | P | R | S | T | V | Y | Z
Number of items at this level: 54.


Andrews, P. , Saar, S., Wang, H., Valente, D., Serkhane, J., Tchernichovsky, O., Golani, I., Mitra, P. P. (2006) Multimedia signal processing for behavioral quantification in neuroscience. In: International Multimedia Conference: Proceedings of the 14th annual ACM international conference on Multimedia , Santa Barbara, CA.

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. (2012) Talk from Mickey Atwal at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Atwal, G. S., Bialek, W (2004) Ambiguous model learning made unambiguous with 1/f priors. NIPS.


Bakker, B. L. G., DeWitt, M. A., Ji, C. R., Mishchenko, Y. (2005) Restoring the equivalence between the light-front and manifestly covariant formalisms. Physical Review D, 72 (7). ISSN 1550-7998

Beach, D., Stillman, B., Watson, J. D. (1991) Cold Spring Harbor Symposia on Quantitative Biology - Foreword. Cold Spring Harbor Symposia on Quantitative Biology, 56. R21-R22. ISSN 00917451 (ISSN)

Bohland, J. W., Bokil, H., Allen, C. B., Mitra, P. P. (2009) The brain atlas concordance problem: quantitative comparison of anatomical parcellations. PLoS ONE, 4 (9). e7200. ISSN 1932-6203 (Electronic)

Bohland, J. W., Bokil, H., Pathak, S. D., Lee, C. K., Ng, L., Lau, C., Kuan, C., Hawrylycz, M., Mitra, P. P. (2010) Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy. Methods, 50 (2). pp. 105-112.

Bohland, J. W., Bullock, D., Guenther, F. H. (2010) Neural representations and mechanisms for the performance of simple speech sequences. Journal of Cognitive Neuroscience, 22 (7). pp. 1504-1529.

Bokil, H., Pesaran, B., Andersen, R. A., Mitra, P. P. (2005) A framework for detection and classification of events in neural activity. arXiv.

Bokil, H. S., Pesaran, B., Andersen, R. A., Mitra, P. P. (2006) A method for detection and classification of events in neural activity. IEEE Trans Biomed Eng, 53 (8). pp. 1678-87. ISSN 0018-9294 (Print)

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)


Chen, B. L., Chklovskii, D. B. (2006) Placement and routing optimization in the brain. In: International Symposium on Physical Design Proceedings of the 2006 International Symposium on Physical Design, San Jose, CA.

Chen, B. L., Hall, D. H., Chklovskii, D. B. (2006) Wiring optimization can relate neuronal structure and function. Proc Natl Acad Sci U S A, 103 (12). pp. 4723-8. ISSN 0027-8424 (Print)

Clark, D. A., Mitra, P. P., Wang, S. S. H. (2001) Scalable architecture in mammalian brains. Nature, 411 (6834). pp. 189-193. ISSN 00280836 (ISSN)


Das, D., Zhang, M. Q., Korenberg, M. J. (2007) Predictive models in gene regulation. In: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp. 95-110.

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, Ö, Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., Van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L. , Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novère, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C., Bader, G. D. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28 (9). pp. 935-942.

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.


Eguchi, J., Yan, Q. W., Schones, D. E., Karnal, M., Hsu, C. H., Zhang, M. Q., Crawford, G. E., Rosen, E. D. (2008) Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metabolism, 7 (1). pp. 86-94. ISSN 1550-4131

Encinas, J. M., Vaahtokari, A., Enikolopov, G. N. (2006) Fluoxetine targets early progenitor cells in the adult brain. Proc Natl Acad Sci U S A, 103 (21). pp. 8233-8. ISSN 0027-8424 (Print)

Erlich, Y., Gordon, A., Brand, M., Hannon, G. J., Mitra, P. P. (2010) Compressed genotyping. IEEE Transactions on Information Theory, 56 (2). pp. 706-723.


Feher, O., Wang, H., Saar, S., Mitra, P. P., Tchernichovski, O. (2009) De novo establishment of wild-type song culture in the zebra finch. Nature, 459 (7246). pp. 564-568. ISSN 0028-0836


Grange, P., Bohland, J. W., Hawrylycz, M., Mitra, P. P. (2012) Brain Gene Expression Analysis: a MATLAB toolbox for the analysis of brain-wide gene-expression data. arXiv. (Unpublished)


Hurwitz, B. L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S. A., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant Journal, 63 (6). pp. 990-1003.


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

Kinney, J. B. (2014) Estimation of probability densities using scale-free field theories. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 90 (1). Article no. 011301. ISSN 15502376

Kinney, J. B., Atwal, G. S. (2014) Parametric Inference in the Large Data Limit Using Maximally Informative Models. Neural Comput, 26 (4). pp. 637-653. ISSN 0899-7667

Kinney, J. B., Atwal, G. S. (2014) Reply to Reshef et al.: Falsifiability or bust. Proceedings of the National Academy of Sciences of the United States of America, 111 (33). E3364. ISSN 10916490 (ISSN)

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


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)

Luo,  W., Woolf, P. J. (2010) Reconstructing transcriptional regulatory networks using three-way mutual information and Bayesian networks. In: Methods Mol Biol. Springer Science+Business Media, pp. 401-18. ISBN 1940-6029 (Electronic) 1064-3745 (Linking)


Menon, M., Schroeder, J. B., Riske, F. (2005) Evaluation of Depth Filtration for the Clarification of Perfusion Mammalian Cell Culture Harvest. In: ACS National Conference 229, San Diego, CA..

Mishchenko, Y. (2006) Remedy for the fermion sign problem in the diffusion Monte Carlo method for few fermions with antisymmetric diffusion process. Phys Rev E Stat Nonlin Soft Matter Phys, 73 (2 Pt 2). 026706. ISSN 1539-3755 (Print)

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

Mitra, P. P., Khammash, M. (2006) Special issue on "Control biology - Emerging field of life science that connects biology and control". Asian Journal of Control, 8 (3). III-IV. ISSN 1561-8625


Neuwald, A. F., Liu, J. S. (2004) Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. BMC Bioinformatics, 5. p. 157. ISSN 1471-2105 (Electronic)


Pang, A., Smith, A. D., Nuin, P. A. S., Tillier, E. R. (2005) SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics, 6. ISSN 1471-2105

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


Russnes, H. G., Vollan, H. K. M., Lingjærde, O. C., Krasnitz, A., Lundin, P., Naume, B., Sørlie, T., Borgen, E., Rye, I. H., Langerød, A., Chin, S. F., Teschendorff, A. E., Stephens, P. J., Månér, S., Schlichting, E., Baumbusch, L. O., Kåresen, R., Stratton, M. P., Wigler, M. H., Caldas, C., Zetterberg, A., Hicks, J. B., Børresen-Dale, A. L. (2010) Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Science Translational Medicine, 2 (38).


Schatz, M. C. (2015) Biological data sciences in genome research. Genome Res, 25 (10). pp. 1417-22. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Schatz, M. C. (2010) The missing graphical user interface for genomics. Genome Biology, 11 (8). p. 128. ISSN 14656914 (ISSN)

Shadlen, M. N., Hanks, T. D., Churchland, A. K., Kiani, R., Yang, T. J. (2007) The Speed and Accuracy of a Simple Perceptual Decision: A Mathematical Primer. In: Bayesian Brain: Probabilistic Approaches to Neural Coding (Computational Neuroscience). M. I. T. Press, Cambridge, MA, pp. 209-238. ISBN ISBN-10: 0-262-51601-2

Shepherd, G. M. G., Stepanyants, A., Bureau, I., Chklovskii, D., Svoboda, K. (2005) Geometric and functional organization of cortical circuits. Nature Neuroscience, 8 (6). pp. 782-790. ISSN 1097-6256

Stepanyants, A., Chklovskii, D. B. (2005) Neurogeometry and potential synaptic connectivity. Trends in Neurosciences, 28 (7). pp. 387-394. ISSN 0166-2236

Stillman, B. (1993) Cold Spring Harbor Symposia on Quantitative Biology - Foreword. Cold Spring Harbor Symposia on Quantitative Biology, 58. R19-R20. ISSN 00917451 (ISSN)

Stillman, B., Stewart, D. (2006) Regulatory RNAs. Cold Spring Harb Symp Quant Biol, 71. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)


Tchernichovski, O., Mitra, P. P. (2002) Towards quantification of vocal imitation in the zebra finch. Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology, 188 (11-12). pp. 867-878. ISSN 03407594 (ISSN)


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


Yilancioglu, K., Weinstein, Z. B., Meydan, C., Akhmetov, A., Toprak, I., Durmaz, A., Iossifov, I., Kazan, H., Roth, F. P., Cokol, M. (2014) Target-independent prediction of drug synergies using only drug lipophilicity. Journal of Chemical Information and Modeling, 54 (8). pp. 2286-2293. ISSN 15499596


Zhang, C., Lu, X., Zhang, X. (2006) Significance of gene ranking for classification of microarray samples. IEEE/ACM Trans Comput Biol Bioinform, 3 (3). pp. 312-20. ISSN 1545-5963 (Print)

Zhang, C. L., Hastings, M. L., Krainer, A. R., Zhang, M. Q. (2007) Dual-specificity splice sites function alternatively as 5 ' and 3 ' splice sites. Proceedings of the National Academy of Sciences of the United States of America, 104 (38). pp. 15028-15033. ISSN 0027-8424

Zhang, J., Jiang, B., Li, M., Tromp, J., Zhang, X. G., Zhang, M. Q. (2007) Computing exact P-values for DNA motifs. Bioinformatics, 23 (5). pp. 531-537. ISSN 1367-4803

Zhang, M. Q. (2007) Computational analyses of eukaryotic promoters. Bmc Bioinformatics, 8 Supp (6). S3. ISSN 1471-2105 (Electronic)

Zhao, Xi., Xuan, Z. Y., Zhang, M. Q. (2007) Boosting with stumps for predicting transcription start sites. Genome Biol, 8 (2). R17. ISSN 1465-6914 (Electronic)

This list was generated on Mon Mar 27 19:47:56 2017 EDT.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving