Lembong, Jessica, Nir Yakoby, and Stanislav Y Shvartsman. (2008) 2008. “Spatial Regulation of BMP Signaling by Patterned Receptor Expression.”. Tissue Eng Part A 14 (9): 1469-77. Reference Link
Persikov, Anton, V, Robert Osada, and Mona Singh. (2009) 2009. “Predicting DNA Recognition by Cys2His2 Zinc Finger Proteins.”. Bioinformatics 25 (1): 22-9. Reference Link
Huttenhower, Curtis, Sajid O Mehmood, and Olga G Troyanskaya. 2009. “Graphle: Interactive Exploration of Large, Dense Graphs.”. BMC Bioinformatics 10: 417. Reference Link
Ghersi, Dario, and Mona Singh. 2013. “Disentangling Function from Topology to Infer the Network Properties of Disease Genes.”. BMC Syst Biol 7: 5. Reference Link
Reguly, Teresa, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, et al. 2006. “Comprehensive Curation and Analysis of Global Interaction Networks in Saccharomyces Cerevisiae.”. J Biol 5 (4): 11. Reference Link
Lenz, Derrick H, Kenny C Mok, Brendan N Lilley, Rahul Kulkarni V, Ned S Wingreen, and Bonnie L Bassler. (2004) 2004. “The Small RNA Chaperone Hfq and Multiple Small RNAs Control Quorum Sensing in Vibrio Harveyi and Vibrio Cholerae.”. Cell 118 (1): 69-82. Reference Link
Banks, Eric, Elena Nabieva, Bernard Chazelle, and Mona Singh. (2008) 2008. “Organization of Physical Interactomes As Uncovered by Network Schemas.”. PLoS Comput Biol 4 (10): e1000203. Reference Link
Zhou, Jian, and Olga G Troyanskaya. (2014) 2014. “Global Quantitative Modeling of Chromatin Factor Interactions.”. PLoS Comput Biol 10 (3): e1003525. Reference Link
Myers, Chad L, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, and Olga G Troyanskaya. 2005. “Discovery of Biological Networks from Diverse Functional Genomic Data.”. Genome Biol 6 (13): R114. Reference Link
Huttenhower, Curtis, and Olga G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.”. Comput Syst Bioinformatics Conf, 341-51. Reference Link
Huttenhower, Curtis, Mark Schroeder, Maria D Chikina, and Olga G Troyanskaya. (2008) 2008. “The Sleipnir Library for Computational Functional Genomics.”. Bioinformatics 24 (13): 1559-61. Reference Link
Lee, Young-suk, Arjun Krishnan, Qian Zhu, and Olga G Troyanskaya. (2013) 2013. “Ontology-Aware Classification of Tissue and Cell-Type Signals in Gene Expression Profiles across Platforms and Technologies.”. Bioinformatics 29 (23): 3036-44. Reference Link
Troyanskaya, Olga. (2007) 2007. “‘Getting Started in. ’: A Series Not to Miss.”. PLoS Comput Biol 3 (10): 1841. Reference Link
Huttenhower, Curtis, Tsheko Mutungu, Natasha Indik, Woongcheol Yang, Mark Schroeder, Joshua J Forman, Olga G Troyanskaya, and Hilary A Coller. (2009) 2009. “Detailing Regulatory Networks through Large Scale Data Integration.”. Bioinformatics 25 (24): 3267-74. Reference Link
Barutcuoglu, Zafer, Edoardo M Airoldi, Vanessa Dumeaux, Robert E Schapire, and Olga G Troyanskaya. (2009) 2009. “Aneuploidy Prediction and Tumor Classification With Heterogeneous Hidden Conditional Random Fields.”. Bioinformatics 25 (10): 1307-13. Reference Link
Pritykin, Yuri, and Mona Singh. 2013. “Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks.”. PLoS Comput Biol 9 (10): e1003243. Reference Link
Andolfatto, Peter, Dan Davison, Deniz Erezyilmaz, Tina T Hu, Joshua Mast, Tomoko Sunayama-Morita, and David L Stern. (2011) 2011. “Multiplexed Shotgun Genotyping for Rapid and Efficient Genetic Mapping.”. Genome Res 21 (4): 610-7. Reference Link
Guan, Yuanfang, Chad L Myers, Rong Lu, Ihor R Lemischka, Carol J Bult, and Olga G Troyanskaya. 2008. “A Genomewide Functional Network for the Laboratory Mouse.”. PLoS Comput Biol 4 (9): e1000165. Reference Link
Ju, Wenjun, Casey S Greene, Felix Eichinger, Viji Nair, Jeffrey B Hodgin, Markus Bitzer, Young-suk Lee, et al. (2013) 2013. “Defining Cell-Type Specificity at the Transcriptional Level in Human Disease.”. Genome Res 23 (11): 1862-73. Reference Link
Lu, Wenyun, Bryson D Bennett, and Joshua D Rabinowitz. (2008) 2008. “Analytical Strategies for LC-MS-Based Targeted Metabolomics.”. J Chromatogr B Analyt Technol Biomed Life Sci 871 (2): 236-42. Reference Link
Hong, Joung-Woo, David A Hendrix, and Michael S Levine. (2008) 2008. “Shadow Enhancers As a Source of Evolutionary Novelty.”. Science 321 (5894): 1314. Reference Link
Hendrix, David, Michael Levine, and Weiyang Shi. 2010. “MiRTRAP, a Computational Method for the Systematic Identification of MiRNAs from High Throughput Sequencing Data.”. Genome Biol 11 (4): R39. Reference Link
Diehn, Maximilian, Ramona Bhattacharya, David Botstein, and Patrick O Brown. (2006) 2006. “Genome-Scale Identification of Membrane-Associated Human MRNAs.”. PLoS Genet 2 (1): e11. Reference Link
Persikov, Anton, V, Elizabeth F Rowland, Benjamin L Oakes, Mona Singh, and Marcus B Noyes. (2014) 2014. “Deep Sequencing of Large Library Selections Allows Computational Discovery of Diverse Sets of Zinc Fingers That Bind Common Targets.”. Nucleic Acids Res 42 (3): 1497-508. Reference Link
Chikina, Maria D, and Olga G Troyanskaya. 2011. “Accurate Quantification of Functional Analogy Among Close Homologs.”. PLoS Comput Biol 7 (2): e1001074. Reference Link
Butte, Atul J, Indra Neil Sarkar, Marco Ramoni, Yves Lussier, and Olga Troyanskaya. 2009. “Selected Proceedings of the First Summit on Translational Bioinformatics 2008.”. BMC Bioinformatics 10 Suppl 2: I1. Reference Link
Zhen, Ying, and Peter Andolfatto. 2012. “Methods to Detect Selection on Noncoding DNA.”. Methods Mol Biol 856: 141-59. Reference Link
Costanzo, Michael, Anastasia Baryshnikova, Jeremy Bellay, Yungil Kim, Eric D Spear, Carolyn S Sevier, Huiming Ding, et al. (2010) 2010. “The Genetic Landscape of a Cell.”. Science 327 (5964): 425-31. Reference Link
Markstein, Michele, and Michael Levine. (2002) 2002. “Decoding Cis-Regulatory DNAs in the Drosophila Genome.”. Curr Opin Genet Dev 12 (5): 601-6. Reference Link
Gorenshteyn, Dmitriy, Elena Zaslavsky, Miguel Fribourg, Christopher Y Park, Aaron K Wong, Alicja Tadych, Boris M Hartmann, et al. (2015) 2015. “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”. Immunity 43 (3): 605-14. Reference Link
Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael J Berry. (2014) 2014. “Searching for Collective Behavior in a Large Network of Sensory Neurons.”. PLoS Comput Biol 10 (1): e1003408. Reference Link
Markowetz, Florian, Klaas W Mulder, Edoardo M Airoldi, Ihor R Lemischka, and Olga G Troyanskaya. 2010. “Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells.”. PLoS Comput Biol 6 (12): e1001034. Reference Link
Consortium, Gene Ontology. (2010) 2010. “The Gene Ontology in 2010: Extensions and Refinements.”. Nucleic Acids Res 38 (Database issue). Reference Link
Erives, Albert, and Michael Levine. (2004) 2004. “Coordinate Enhancers Share Common Organizational Features in the Drosophila Genome.”. Proc Natl Acad Sci U S A 101 (11): 3851-6. Reference Link
Zhou, Jian, Christopher Y Park, Chandra L Theesfeld, Aaron K Wong, Yuan Yuan, Claudia Scheckel, John J Fak, et al. (2019) 2019. “Whole-Genome Deep-Learning Analysis Identifies Contribution of Noncoding Mutations to Autism Risk.”. Nat Genet 51 (6): 973-80. doi:10.1038/s41588-019-0420-0. Reference Link
Christie, Karen R, Shuai Weng, Rama Balakrishnan, Maria C Costanzo, Kara Dolinski, Selina S Dwight, Stacia R Engel, et al. (2004) 2004. “Saccharomyces Genome Database (SGD) Provides Tools to Identify and Analyze Sequences from Saccharomyces Cerevisiae and Related Sequences from Other Organisms.”. Nucleic Acids Res 32 (Database issue). Reference Link
Stathopoulos, Angelike, and Michael Levine. (2005) 2005. “Localized Repressors Delineate the Neurogenic Ectoderm in the Early Drosophila Embryo.”. Dev Biol 280 (2): 482-93. Reference Link
Hong, Eurie L, Rama Balakrishnan, Qing Dong, Karen R Christie, Julie Park, Gail Binkley, Maria C Costanzo, et al. (2008) 2008. “Gene Ontology Annotations at SGD: New Data Sources and Annotation Methods.”. Nucleic Acids Res 36 (Database issue). Reference Link
Myers, Chad L, and Olga G Troyanskaya. (2007) 2007. “Context-Sensitive Data Integration and Prediction of Biological Networks.”. Bioinformatics 23 (17): 2322-30. Reference Link
Chen, Kathleen M, Evan M Cofer, Jian Zhou, and Olga G Troyanskaya. (2019) 2019. “Selene: A PyTorch-Based Deep Learning Library for Sequence Data.”. Nat Methods 16 (4): 315-18. doi:10.1038/s41592-019-0360-8. Reference Link
Engel, Stacia R, Rama Balakrishnan, Gail Binkley, Karen R Christie, Maria C Costanzo, Selina S Dwight, Dianna G Fisk, et al. (2010) 2010. “Saccharomyces Genome Database Provides Mutant Phenotype Data.”. Nucleic Acids Res 38 (Database issue). Reference Link
Bialek, William, and David Botstein. (2004) 2004. “Introductory Science and Mathematics Education for 21st-Century Biologists.”. Science 303 (5659): 788-90. Reference Link
Liang, Yu, Maximilian Diehn, Nathan Watson, Andrew W Bollen, Ken D Aldape, Kelly Nicholas, Kathleen R Lamborn, et al. (2005) 2005. “Gene Expression Profiling Reveals Molecularly and Clinically Distinct Subtypes of Glioblastoma Multiforme.”. Proc Natl Acad Sci U S A 102 (16): 5814-9. Reference Link
Cande, Jessica Doran, Yury Goltsev, and Michael S Levine. (2009) 2009. “Conservation of Enhancer Location in Divergent Insects.”. Proc Natl Acad Sci U S A 106 (34): 14414-9. Reference Link
Zhou, Jian, Ignacio E Schor, Victoria Yao, Chandra L Theesfeld, Raquel Marco-Ferreres, Alicja Tadych, Eileen E M Furlong, and Olga G Troyanskaya. (2019) 2019. “Accurate Genome-Wide Predictions of Spatio-Temporal Gene Expression During Embryonic Development.”. PLoS Genet 15 (9): e1008382. doi:10.1371/journal.pgen.1008382. Reference Link
Tkačik, Gašper, Thomas Gregor, and William Bialek. 2008. “The Role of Input Noise in Transcriptional Regulation.”. PLoS One 3 (7): e2774. Reference Link
Pop, Ana, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N Benfey, and Olga G Troyanskaya. 2010. “Integrated Functional Networks of Process, Tissue, and Developmental Stage Specific Interactions in Arabidopsis Thaliana.”. BMC Syst Biol 4: 180. Reference Link
Park, Christopher Y, Aaron K Wong, Casey S Greene, Jessica Rowland, Yuanfang Guan, Lars A Bongo, Rebecca Burdine, and Olga G Troyanskaya. 2013. “Functional Knowledge Transfer for High-Accuracy Prediction of under-Studied Biological Processes.”. PLoS Comput Biol 9 (3): e1002957. Reference Link
Kanodia, Jitendra S, Yoosik Kim, Raju Tomer, Zia Khan, Kwanghun Chung, John D Storey, Hang Lu, Philipp J Keller, and Stanislav Y Shvartsman. (2011) 2011. “A Computational Statistics Approach for Estimating the Spatial Range of Morphogen Gradients.”. Development 138 (22): 4867-74. Reference Link
Botstein, David. (2006) 2006. “Willing to Do the Math: An Interview With David Botstein. Interview by Jane Gitschier.”. PLoS Genet 2 (5): e79. Reference Link