Yip, Kevin Y, Kim, Philip M, McDermott, Drew, Gerstein, Mark
Abstract Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy:...
Application Note An Integrated System for Studying Residue Coevolution in Proteins (2008)
Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew Mcdermott
Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not...
Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz, Mark Gerstein
Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular networks...
An integrated system for studying residue coevolution in proteins (2008)
Yip, Kevin Y., Patel, Prianka, Kim, Philip M., Engelman, Donald M., McDermott, Drew, Gerstein, Mark
Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not...
Kim, Philip M., Lam, Hugo Y.K., Urban, Alexander E., Korbel, Jan O., Affourtit, Jason, Grubert, Fabian, ...
Segmental duplications (SDs) are operationally defined as >1 kb stretches of duplicated DNA with high sequence identity. They arise from copy number variants (CNVs) fixed in the population. To...
Copy Number Variants and Segmental Duplications Show Different Formation Signatures (2007)
Kim, Philip M., Korbel, Jan O., Chen, Xueying, Gerstein, Mark B.
In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These...
Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology (2007)
Lu, Long J., Sboner, Andrea, Huang, Yuanpeng J., Lu, Hao Xin, Gianoulis, Tara A., Yip, Kevin Y., ...
Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation...
Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has...
Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifinov, Mark Gerstein
It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has...
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome (2007)
Korbel, Jan O., Urban, Alexander Eckehart, Affourtit, Jason P., Godwin, Brian, Grubert, Fabian, Simons, Jan Fredrik, ...
Yip, Kevin Y., Yu, Haiyuan, Kim, Philip M., Schultz, Martin, Gerstein, Mark
Summary: Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular...
Limitations of Quantitative Gene Regulation Models: A Case Study (2003)
Understanding the relationship between network structure and behavior is fundamental to the field of computational and systems biology. A particularly important distinction is the extent to which...
Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data (2003)
The availability of parallel, high-throughput biological experiments that simultaneously monitor thousands of cellular observables provides an opportunity for investigating cellular behavior in a...
Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data
The availability of parallel, high-throughput biological experiments that simultaneously monitor thousands of cellular observables provides an opportunity for investigating cellular behavior in a...
Limitations of Quantitative Gene Regulation Models: A Case Study
Understanding the relationship between network structure and behavior is fundamental to the field of computational and systems biology. A particularly important distinction is the extent to which...
Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data
The availability of parallel, high-throughput biological experiments that simultaneously monitor thousands of cellular observables provides an opportunity for investigating cellular behavior in a...
Limitations of Quantitative Gene Regulation Models: A Case Study
Understanding the relationship between network structure and behavior is fundamental to the field of computational and systems biology. A particularly important distinction is the extent to which...
Yu, Haiyuan, Kim, Philip M, Sprecher, Emmett, Trifonov, Valery, Gerstein, Mark
It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has...
The role of disorder in interaction networks: a structural analysis
Kim, Philip M, Sboner, Andrea, Xia, Yu, Gerstein, Mark
Recent studies have emphasized the value of including structural information into the topological analysis of protein networks. Here, we utilized structural information to investigate the role of...
Kim, Philip M., Korbel, Jan O., Gerstein, Mark B.
Because of recent advances in genotyping and sequencing, human genetic variation and adaptive evolution in the primate lineage have become major research foci. Here, we examine the relationship...
High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution
Hasin, Yehudit, Olender, Tsviya, Khen, Miriam, Gonzaga-Jauregui, Claudia, Kim, Philip M., Urban, Alexander Eckehart, ...
Olfactory receptors (ORs), which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected...
Kim, Philip M., Lam, Hugo Y.K., Urban, Alexander E., Korbel, Jan O., Affourtit, Jason, Grubert, Fabian, ...
Segmental duplications (SDs) are operationally defined as >1 kb stretches of duplicated DNA with high sequence identity. They arise from copy number variants (CNVs) fixed in the population. To...
Tonikian, Raffi, Xin, Xiaofeng, Toret, Christopher P., Gfeller, David, Landgraf, Christiane, Panni, Simona, ...
A genome-scale specificity and interaction map for yeast SH3 domain-containing proteins reveal how family members show selective binding to target proteins and predicts the dynamic localization of...