Sridhar, Srinath, Schwartz, Russell
Abstract Background Many common inference problems in computational genetics depend on inferring aspects of the evolutionary history of a data set given a set of observed modern sequences. Detailed...
Efficient stochastic sampling of first-passage times for fracturing bond networks (2008)
Misra, Navodit, Schwartz, Russell
Models of reaction chemistry based on the stochastic simulation algorithm (SSA) have become a crucial tool for simulating complicated biological reaction networks due to their ability to handle...
Direct maximum parsimony phylogeny reconstruction from genotype data (2007)
Sridhar, Srinath, Lam, Fumei, Blelloch, Guy E, Ravi, R, Schwartz, Russell
Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population...
A comparative genomics approach to identifying the plasticity transcriptome (2007)
Pfenning, Andreas R, Schwartz, Russell, Barth, Alison L
Abstract Background Neuronal activity regulates gene expression to control learning and memory, homeostasis of neuronal function, and pathological disease states such as epilepsy. A great deal of...
Local Rules Modeling of Nucleation-Limited Virus Capsid Assembly (2001)
Russell Schwartz, Peter E. Prevelige, Bonnie Berger
We describe an application of computer modeling to the study of the kinetics of virus capsid (protein shell) assembly. We examine two proposed models of the source of nucleation-limited growth, an...
Local Rules Modeling of Nucleation-Limited Virus Capsid Assembly MIT-LCS-TM-584 (2000)
Russell Schwartz, Peter E. Prevelige, Bonnie Berger
We describe an application of computer modeling to the study of the kinetics of virus capsid (protein shell) assembly. We examine two proposed models of the source of nucleation-limited growth, an...
Area Exam: The Limitations of DNA Computing (1998)
This report addresses the theoretical and practical limitations of DNA computing. The discussion focuses on the work of Adleman [1], Winfree [42], and Hagiya et al. [21]. However, we also cover...
Local Rules Modeling of Nucleation-Limited Virus Capsid Assembly (1998)
Russell Schwartz, Peter E. Prevelige, Bonnie Berger
We describe an application of computer modeling to the study of the kinetics of virus capsid (protein shell) assembly. We examine two proposed models of the source of nucleation-limited growth, an...
Local Rules Modeling of Nucleation-Limited Virus Capsid Assembly (1998)
Russell Schwartz, Peter E. Prevelige, Bonnie Berger
We describe an application of computer modeling to the study of the kinetics of virus capsid (protein shell) assembly. We examine two proposed models of the source of nucleation-limited growth, an...
Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies
Halldórsson, Bjarni V., Bafna, Vineet, Lippert, Ross, Schwartz, Russell, De La Vega, Francisco M., Clark, Andrew G., ...
It is widely hoped that the study of sequence variation in the human genome will provide a means of elucidating the genetic component of complex diseases and variable drug responses. A major...
Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies
Halldórsson, Bjarni V., Bafna, Vineet, Lippert, Ross, Schwartz, Russell, De La Vega, Francisco M., Clark, Andrew G., ...
It is widely hoped that the study of sequence variation in the human genome will provide a means of elucidating the genetic component of complex diseases and variable drug responses. A major...
Simulation Study of the Contribution of Oligomer/Oligomer Binding to Capsid Assembly Kinetics
Zhang, Tiequan, Schwartz, Russell
The process by which hundreds of identical capsid proteins self-assemble into icosahedral structures is complex and poorly understood. Establishing constraints on the assembly pathways is crucial to...
Direct maximum parsimony phylogeny reconstruction from genotype data
Sridhar, Srinath, Lam, Fumei, Blelloch, Guy E, Ravi, R, Schwartz, Russell
Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure
Schwartz, Russell, King, Jonathan
Patterns of alternation of hydrophobic and polar residues are a profound aspect of amino acid sequences, but a feature not easily interpreted for soluble proteins. Here we report statistics of...
Schwartz, Russell, Istrail, Sorin, King, Jonathan
Patterns of hydrophobic and hydrophilic residues play a major role in protein folding and function. Long, predominantly hydrophobic strings of 20–22 amino acids each are associated with...