Items where Subject is "quantitative biology"

Paper

Adams, R. M., Kinney, J. B., Walczak, A. M., Mora, T. (December 2018) Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy. Cell Syst, 8 (1). pp. 86-93. ISSN 2405-4712 (Print)2405-4712

Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M, Lippman, Zachary B (October 2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382 (6668). pp. 315-320. ISSN 0036-8075

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

Bakker, B. L. G., DeWitt, M. A., Ji, C. R., Mishchenko, Y. (October 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. (September 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. (February 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. (April 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. (August 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. (January 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. (April 2006) Placement and routing optimization in the brain. Proceedings of the 2006 international symposium on Physical design, 2006. pp. 136-141.

Chen, B. L., Hall, D. H., Chklovskii, D. B. (March 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)

Daruwalla, Kyle, Lipasti, Mikko (May 2024) Information bottleneck-based Hebbian learning rule naturally ties working memory and synaptic updates. Frontiers in Computational Neuroscience, 18. p. 1240348. ISSN 1662-5188

Das, D., Zhang, M. Q. (2007) Predictive models in gene regulation. Methods Mol Biol, 377. pp. 95-110. ISSN 978-1-59745-390-5

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.

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. (May 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. (February 2010) Compressed genotyping. IEEE Transactions on Information Theory, 56 (2). pp. 706-723.

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

Franchin, Cinzia, Cesaro, Luca, Salvi, Mauro, Millioni, Renato, Iori, Elisabetta, Cifani, Paolo, James, Peter, Arrigoni, Giorgio, Pinna, Lorenzo (June 2015) Quantitative analysis of a phosphoproteome readily altered by the protein kinase CK2 inhibitor quinalizarin in HEK-293T cells. BBA: Proteins and Proteomics, 1854 (6). pp. 609-623. ISSN 1570-9639

Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, C. R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R. J. C., Megraw, M., Meyers, B. C., Murray, J. A. H., Provart, N. J., Rhee, S., Smith, R., Spalding, E. P., Taylor, C., Teal, T. K., Torii, K. U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., Brady, S. M. (December 2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol, 175 (4). pp. 1499-1509. ISSN 0032-0889

Grange, P., Bohland, J. W., Hawrylycz, M., Mitra, P. P. (November 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

Khan, Omar, Giles, Josephine R, McDonald, Sierra, Manne, Sasikanth, Ngiow, Shin Foong, Patel, Kunal P, Werner, Michael T, Huang, Alexander C, Alexander, Katherine A, Wu, Jennifer E, Attanasio, John, Yan, Patrick, George, Sangeeth M, Bengsch, Bertram, Staupe, Ryan P, Donahue, Greg, Xu, Wei, Amaravadi, Ravi K, Xu, Xiaowei, Karakousis, Giorgos C, Mitchell, Tara C, Schuchter, Lynn M, Kaye, Jonathan, Berger, Shelley L, Wherry, E John (June 2019) TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature, 571 (7764). pp. 211-218. ISSN 0028-0836

Kinney, J. B. (July 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. (January 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. (August 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)

Kinney, J. B., McCandlish, D. M. (May 2019) Massively Parallel Assays and Quantitative Sequence-Function Relationships. Annu Rev Genomics Hum Genet, 20. pp. 99-127. ISSN 1527-8204

Krapivsky, P. L., Ben-Naim, E., Grosse, I. R. (February 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. Proceedings of the Eighth Workshop on Mining and Learning with Graphs . pp. 78-85.

McCandlish, D. M., Lang, G.I. (July 2020) Evolution of Epistasis: Small Populations Go Their Separate Ways. Journal of Molecular Evolution, 88 (5). pp. 418-420.

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

Mitra, P. P., Khammash, M. (September 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

Navlakha, S., Bar-Joseph, Z. (January 2015) Distributed information processing in biological and computational systems. Communications of the ACM, 58 (1). pp. 94-102. ISSN 00010782 (ISSN)

Neuwald, A. F., Liu, J. S. (October 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. (September 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

Posfai, Anna, McCandlish, David M, Kinney, Justin B (May 2024) Symmetry, gauge freedoms, and the interpretability of sequence-function relationships. bioRxiv. (Submitted)

Posfai, Anna, Zhou, Juannan, McCandlish, David M, Kinney, Justin B (May 2024) Gauge fixing for sequence-function relationships. bioRxiv.

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. (June 2010) Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Science Translational Medicine, 2 (38).

Sarkar, Anirban, Tang, Ziqi, Zhao, Chris, Koo, Peter (May 2024) Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion. bioRxiv. (Submitted)

Schatz, M. C. (October 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)

Seitz, EE, McCandlish, DM, Kinney, JB, Koo, PK (June 2024) Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. Nature Machine Intelligence, 6 (6). pp. 701-713. ISSN 2522-5839 (Public Dataset)

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

Soyk, S., Benoit, M., Lippman, Z. B. (September 2020) New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation. Annu Rev Genet, 54. pp. 287-307. ISSN 0066-4197

Stepanyants, A., Chklovskii, D. B. (July 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)

Tang, Ziqi, Koo, Peter K (March 2024) Evaluating the representational power of pre-trained DNA language models for regulatory genomics. bioRxiv. (Public Dataset) (Submitted)

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)

Thompson, Mike, Martin, Mariano, Olmo, Trinidad Sanmartin, Rajesh, Chandana, Koo, Peter, Bolognesi, Benedetta, Lehner, Ben (July 2024) Interpretably deep learning amyloid nucleation by massive experimental quantification of random sequences. bioRxiv. (Submitted)

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

Wiberg, Akira, Lucey, Maria A, Kleeman, Sam, Kang, Youngjoo, Ng, Mike, Furniss, Dominic (August 2023) Genetic correlations between migraine and carpal tunnel syndrome. Plastic and Reconstructive Surgery. ISSN 0032-1052

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

Yu, Yiyang, Muthukumar, Shivani, Koo, Peter K (January 2024) EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. bioRxiv. (Submitted)

Zhai, Jingjing, Gokaslan, Aaron, Schiff, Yair, Berthel, Ana, Liu, Zong-Yan, Miller, Zachary R, Scheben, Armin, Stitzer, Michelle C, Romay, M Cinta, Buckler, Edward S, Kuleshov, Volodymyr (June 2024) Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. bioRxiv. (Public Dataset) (Submitted)

Zhang, C., Lu, X., Zhang, X. (July 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. (September 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. (March 2007) Computing exact P-values for DNA motifs. Bioinformatics, 23 (5). pp. 531-537. ISSN 1367-4803

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

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

Zhou, Juannan, Wong, Mandy S, Chen, Wei-Chia, Krainer, Adrian R, Kinney, Justin B, McCandlish, David M (September 2022) Higher-order epistasis and phenotypic prediction. Proceedings of the National Academy of Sciences of USA, 119 (39). e2204233119. ISSN 0027-8424

Book Section

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)

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

Conference or Workshop Item

Andrews, P. , Saar, S., Wang, H., Valente, D., Serkhane, J., Tchernichovsky, O., Golani, I., Mitra, P. P. (October 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.

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.

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

Video

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