Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote, W Ucuacggccagc
• ab-initio prediction (does not require homolog), • single structure prediction. Partition function and base pair binding probabilities (McCaskill,1990). UCUCAAACCAGA • evaluate the ensemble...
Research Sequencing a Genome by Walking with Clone-End Sequences: A Mathematical Analysis (2009)
Serafim Batzoglou, Bonnie Berger, Jill Mesirov, Eric S. L
One approach to sequencing a large genome is (1) to sequence a collection of nonoverlapping “seeds ” chosen from a genomic library of large-insert clones [such as bacterial artificial chromosomes...
Categories and Subject Descriptors (2009)
Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen
A method is presented that uses β-strand interactions at both the sequence and the atomic level, to predict the betastructural motifs in protein sequences. A program called Wrap-and-Pack implements...
Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. L
We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of...
IsoRankN: spectral methods for global alignment of multiple protein networks (2009)
Liao, Chung-Shou, Lu, Kanghao, Baym, Michael, Singh, Rohit, Berger, Bonnie
Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is...
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures (2009)
Waldispühl, Jerome, Devadas, Srinivas, Berger, Bonnie, Clote, Peter
The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as...
Abstract Chapter 7 Improved Algorithms for Protein Motif Recognition (2008)
The identification of protein sequences that fold into certain known three-dimensional (3D) structures, or motifs, is evaluated through a probabilistic analysis of their one-dimensional (1D)...
ChainTweak: Sampling from the Neighbourhood of a Protein Conformation (2008)
When searching for an optimal protein structure, it is often necessary to generate a set of structures similar, e.g., within 4˚A Root Mean Square Deviation (RMSD), to some base structure. Current...
LTHREADER: PREDICTION OF LIGAND-RECEPTOR INTERACTIONS USING LOCALIZED THREADING (2008)
Vinay Pulim, Jadwiga Bienkowska, Bonnie Berger
Identification of ligand-receptor interactions is important for drug design and the treatment of diseases. Difficulties in detecting these interactions using high-throughput experimental techniques...
Computational genomics: Mapping, comparison, and annotation of genomes (2008)
Bonnie Berger, Arthur C. Smith, Serafim Batzoglou, Serafim Batzoglou
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer...
Rohit Singh, Jinbo Xu, Bonnie Berger, Rohit Singh, Jinbo Xu, Bonnie Berger
This paper presents a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and...
1. Formal Problem Definition (2008)
This document provides some supplementary information for:
Abstract. This article studies the protein side-chain packing problem using the tree-decomposition of a protein structure. To obtain fast and accurate protein side-chain packing, protein structures...
R. Singh, B. Berger, Rohit Singh, Bonnie Berger
When searching for an optimal protein structure, it is often necessary to generate a set of structures similar, e.g., within 4˚A Root Mean Square Deviation (RMSD), to some base structure. Current...
STRUCT2NET: INTEGRATING STRUCTURE INTO PROTEIN-PROTEIN INTERACTION PREDICTION ROHIT SINGH ∗ (2008)
This paper presents a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and...
Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008)
Matthew Menke, Bonnie Berger, Lenore Cowen
Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many...
Pulim, Vinay, Bienkowska, Jadwiga, Berger, Bonnie
Identification of extracellular ligand–receptor interactions is important for drug design and the treatment of diseases. Difficulties in detecting these interactions using high-throughput...
Optimal contact map alignment of protein-protein interfaces (2008)
Pulim, Vinay, Berger, Bonnie, Bienkowska, Jadwiga
The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order...
Local Topology of Silica Networks (2007)
Linn Hobbs, C. Esther Jesurum, Vinay Pulim, Bonnie Berger
Model-building algorithms based on self-assembly according to local rules have been devised which permit rapid assembly of vertex-sharing tetrahedral network structures. These have been applied to...
MIT{LCS Technical Memo #TM-527 Local Rule Switching Mechanism for Viral Shell Geometry (2007)
In a previous paper [Berger et al., PNAS 91 7732, 1994], a theory of virus shell formation was proposed in which shell assembly is directed by local interactions of the coat and sca olding subunits....
Automated real time constant-specificity surveillance for disease outbreaks (2007)
Wieland, Shannon C, Brownstein, John S, Berger, Bonnie, Mandl, Kenneth D
Abstract Background For real time surveillance, detection of abnormal disease patterns is based on a difference between patterns observed, and those predicted by models of historical data. The...
Accurate Detection of Arbitrarily-Shaped Spatial Disease Clusters (2007)
Shannon Wieland, John Brownstein, Bonnie Berger, Kenneth Mandl
Accurate Detection of Arbitrarily-Shaped Spatial Disease Clusters (2007)
Shannon Wieland, John Brownstein, Bonnie Berger, Kenneth Mandl
Accurate Detection of Arbitrarily-Shaped Spatial Disease Clusters (2007)
Shannon Wieland, John Brownstein, Bonnie Berger, Kenneth Mandl
Accurate Detection of Arbitrarily-Shaped Spatial Disease Clusters (2007)
Shannon Wieland, John Brownstein, Bonnie Berger, Kenneth Mandl
Open Access Freely available online through the Protein Science Open Access option. (2007)
Vinay Pulim, Jadwiga Bienkowska, Bonnie Berger
alerting service Notes Receive free email alerts when new articles cite this article- sign up in the box at the top right corner of the article or click here Advance online articles have been peer...
Probabilistic modeling of systematic errors in two-hybrid experiments (2007)
We describe a novel probabilistic approach to estimating errors in two-hybrid (2H) experiments. Such experiments are frequently used to elucidate protein-protein interaction networks in a...
A parameterized algorithm for protein structure alignment (2006)
Jinbo Xu, Feng Jiao, Bonnie Berger
Abstract. This paper proposes a parameterized algorithm for aligning two protein structures, in the case where one protein structure is represented by a contact map graph and the other by a contact...
Fast and accurate algorithms for protein side-chain packing (2006)
This paper studies the protein side-chain packing problem using the tree-decomposition of a protein structure. To obtain fast and accurate protein side-chain packing, protein structures are modeled...
A parameterized algorithm for protein structure alignment (2006)
Abstract. This paper proposes a parameterized algorithm for aligning two protein structures, in the case where one protein structure is represented by a contact map graph and the other by a contact...
transFold: a web server for predicting the structure and (2006)
J. Waldispühl, Bonnie Berger, Peter Clote, Jean-marc Steyaert
residue contacts of transmembrane beta-barrels
Waldispühl, J., Berger, Bonnie, Clote, Peter, Steyaert, Jean-Marc
Transmembrane β-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of β-barrel outer...
A tree-decomposition approach to protein structure prediction (2005)
This paper proposes a tree decomposition of protein structures, which can be used to efficiently solve two key subproblems of protein structure prediction: protein threading for backbone prediction...
Water Resources: Agricultural and Environmental Issues (2004)
DAVID PIMENTEL, BONNIE BERGER, DAVID FILIBERTO, MICHELLE NEWTON, BENJAMIN WOLFE, ELIZABETH KARABINAKIS, ...
The increasing demands placed on the global water supply threaten biodiversity and the supply of water for food production and other vital human needs. Water shortages already exist in many regions,...
Water resources, agriculture and the environment. (2004)
Pimentel, David, Berger, Bonnie, David, Filiberto, Newton, Michelle, Wolfe, Benjamin, Karabinakis, Elizabeth, ...
In this article, water utilization by individuals and especially agricultural systems is analyzed. Interrelationships exist among population growth, water use and distribution, the status of...
Water resources, agriculture and the environment. (2004)
Pimentel, David, Berger, Bonnie, David, Filiberto, Newton, Michelle, Wolfe, Benjamin, Karabinakis, Elizabeth, ...
In this article, water utilization by individuals and especially agricultural systems is analyzed. Interrelationships exist among population growth, water use and distribution, the status of...
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. L
In Kellis et al. (2003), we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genome-wide...
Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric L
In [13] we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genome-wide comparative analysis...
Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing. (2002)
Berger, Bonnie, Brady, Martin, Brown, Donna, Leighton, Tom
Channel routing plays a crucial role in the development of automated layout systems for integrated circuits. Most layout systems first place modules on a chip and then wire together terminals on...
ARACHNE: A Whole-Genome Shotgun Assembler (2002)
Batzoglou, Serafim, Jaffe, David B., Stanley, Ken, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, ...
Predicting the beta-helix fold from protein sequence data (2001)
Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger
A method is presented that uses b-strand interactions to predict the parallel right-handed b-helix super-secondary structural motif in protein sequences. A program called BetaWrap implements this...
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction (2000)
Batzoglou, Serafim, Pachter, Lior, Mesirov, Jill P., Berger, Bonnie, Lander, Eric S.
A Dictionary Based Approach for Gene Annotation (1999)
Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, ...
This paper describes a fast and fully automated dictionary based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and...
A Dictionary Based Approach for Gene Annotation (1999)
Lior Pachter, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger
L.P. and S.B. contributed equally to this work. z
A dictionary-based approach for gene annotation (1999)
Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, ...
This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and...
Sequencing a Genome by Walking with Clone-End Sequences: A Mathematical Analysis (1999)
Batzoglou, Serafim, Berger, Bonnie, Mesirov, Jill, Lander, Eric S.
Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing, (1998)
Berger, Bonnie, Brady, Martin, Brown, Donna, Leighton, Tom
Channel routing plays an important role in the development of automated layout systems for integrated circuits. Many layout systems first place modules on a chip and then wire together terminals on...
Simulating (log(c) n)-wise Independence in NC. (1998)
We develop a general framework for removing randomness from randomized NC algorithms whose analysis uses only polyalgorithmic independence. Previously no techniques were known to determine those RNC...
Efficient NC Algorithms for Set Cover Applications to Learning and Geometry. (1998)
Berger, Bonnie, Rompel, John, Shor, Peter W.
In this paper we give NC approximation algorithms for the unweighted and weighted set cover problems. Our algorithms use a linear number of processors and give a cover that has at most log n times...
Near-linear time construction of sparse neighborhood covers (1998)
Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
Abstract. This paper introduces a near-linear time sequential algorithm for constructing a sparse neighborhood cover. This implies analogous improvements (from quadratic to near-linear time) for any...
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, 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...
Recent Developments in Computational Gene Recognition (1998)
Serafim Batzoglou, Bonnie Berger, Daniel J. Kleitman, Eric S. Lander, Eric S. L, Lior Pachter
. We survey recent mathematical and computational work in the field of gene recognition, focusing on the techniques that have been developed to tackle the problem of identifying protein coding...
Reconstructing a Three-Dimensional Model with Arbitrary Errors (1996)
Bonnie Berger, Jon Kleinberg, Tom Leighton
A number of current technologies allow for the determination of inter-atomic distance information in structures such as proteins and RNA. Thus, the reconstruction of a three-dimensional set of points...
Fast Distributed Network Decompositions and Covers (1996)
Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
This paper presents deterministic sublinear-time distributed algorithms for network decomposition and for constructing a sparse neighborhood cover of a network. The latter construction leads to...
Local rules switching mechanism for viral shell geometry (1995)
In a previous paper [Berger et al., PNAS 91 7732, 1994], a theory of virus shell formation was proposed in which shell assembly is directed by local interactions of the coat and scaffolding subunits....
On the mathematics of virus shell assembly (1995)
A local rule theory is developed which shows that the self-assembly of icosahedral virus shells may depend on only the lower-level interactions of a protein subunit with its neighbors, i.e. local...
On the mathematics of virus shell assembly (1995)
A local rule theory is developed which shows that the self-assembly of icosahedral virus shells may depend on only the lower-level interactions of a protein subunit with its neighbors, i.e. local...
Scheduling with Concurrency-Based Constraints (1995)
This paper considers scheduling problems with timing constraints of the forms: ! (precedence), (no later than), and : = (concurrence). Scheduling unit-time jobs subject to ! and : = constraints, and...
Near-Linear Cost Sequential and Distributed Constructions of Sparse Neighborhood Covers (1993)
Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
This paper introduces the first near-linear (specifically, O(E log n + n log 2 n)) time algorithm for constructing a sparse neighborhood cover in sequential and distributed environments. This...
Near-Linear Cost Sequential and Distributed Constructions of Sparse Neighborhood Covers (1993)
Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
This paper introduces the first near-linear (specifically, O(E log n + n log 2 n)) time algorithm for constructing a sparse neighborhood cover in sequential and distributed environments. This...
Low-Diameter Graph Decomposition is in NC (1992)
Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
We obtain the first NC algorithm for the low-diameter graph decomposition problem on arbitrary graphs. Our algorithm runs in O(log 5 (n)) time, and uses O(n 2 ) processors. 1 Introduction For an...
The applicability of values clarification to cardiac patient education / (1974)
Berger, Bonnie., Raettig, Vilma.
Thesis (M.S.)--Loma Linda University, 1974.
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains
Singh, Mona, Berger, Bonnie, Kim, Peter S., Berger, James M., Cochran, Andrea G.
The recent rapid growth of protein sequence databases is outpacing the capacity of researchers to biochemically and structurally characterize new proteins. Accordingly, new methods for recognition of...
Bradley, Phil, Cowen, Lenore, Menke, Matthew, King, Jonathan, Berger, Bonnie
The amino acid sequence rules that specify β-sheet structure in proteins remain obscure. A subclass of β-sheet proteins, parallel β-helices, represent a processive folding of the chain into an...
trilogy: Discovery of sequence–structure patterns across diverse proteins
Bradley, Philip, Kim, Peter S., Berger, Bonnie
We describe a new computer program, trilogy, for the automated discovery of sequence–structure patterns in proteins. trilogy implements a pattern discovery algorithm that begins with an exhaustive...
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction
Batzoglou, Serafim, Pachter, Lior, Mesirov, Jill P., Berger, Bonnie, Lander, Eric S.
We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of...
msari: Multiple sequence alignments for statistical detection of RNA secondary structure
Coventry, Alex, Kleitman, Daniel J., Berger, Bonnie
We present a highly accurate method for identifying genes with conserved RNA secondary structure by searching multiple sequence alignments of a large set of candidate orthologs for correlated...
ARACHNE: A Whole-Genome Shotgun Assembler
Batzoglou, Serafim, Jaffe, David B., Stanley, Ken, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, ...
We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive...
Waldispühl, J., Berger, Bonnie, Clote, Peter, Steyaert, Jean-Marc
Transmembrane β-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of β-barrel outer...
Junker, Mirco, Schuster, Christopher C., McDonnell, Andrew V., Sorg, Kelli A., Finn, Mary C., Berger, Bonnie, ...
Many virulence factors secreted from pathogenic Gram-negative bacteria are autotransporter proteins. The final step of autotransporter secretion is C → N-terminal threading of the passenger domain...
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains
Singh, Mona, Berger, Bonnie, Kim, Peter S., Berger, James M., Cochran, Andrea G.
The recent rapid growth of protein sequence databases is outpacing the capacity of researchers to biochemically and structurally characterize new proteins. Accordingly, new methods for recognition of...
Bradley, Phil, Cowen, Lenore, Menke, Matthew, King, Jonathan, Berger, Bonnie
The amino acid sequence rules that specify β-sheet structure in proteins remain obscure. A subclass of β-sheet proteins, parallel β-helices, represent a processive folding of the chain into an...
trilogy: Discovery of sequence–structure patterns across diverse proteins
Bradley, Philip, Kim, Peter S., Berger, Bonnie
We describe a new computer program, trilogy, for the automated discovery of sequence–structure patterns in proteins. trilogy implements a pattern discovery algorithm that begins with an exhaustive...
ARACHNE: A Whole-Genome Shotgun Assembler
Batzoglou, Serafim, Jaffe, David B., Stanley, Ken, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, ...
We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive...
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction
Batzoglou, Serafim, Pachter, Lior, Mesirov, Jill P., Berger, Bonnie, Lander, Eric S.
We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of...
msari: Multiple sequence alignments for statistical detection of RNA secondary structure
Coventry, Alex, Kleitman, Daniel J., Berger, Bonnie
We present a highly accurate method for identifying genes with conserved RNA secondary structure by searching multiple sequence alignments of a large set of candidate orthologs for correlated...
Junker, Mirco, Schuster, Christopher C., McDonnell, Andrew V., Sorg, Kelli A., Finn, Mary C., Berger, Bonnie, ...
Many virulence factors secreted from pathogenic Gram-negative bacteria are autotransporter proteins. The final step of autotransporter secretion is C → N-terminal threading of the passenger domain...
Waldispühl, J., Berger, Bonnie, Clote, Peter, Steyaert, Jean-Marc
Transmembrane β-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of β-barrel outer...
Automated real time constant-specificity surveillance for disease outbreaks
Wieland, Shannon C, Brownstein, John S, Berger, Bonnie, Mandl, Kenneth D
Density-equalizing Euclidean minimum spanning trees for the detection of all disease cluster shapes
Wieland, Shannon C., Brownstein, John S., Berger, Bonnie, Mandl, Kenneth D.
Existing disease cluster detection methods cannot detect clusters of all shapes and sizes or identify highly irregular sets that overestimate the true extent of the cluster. We introduce a...
Matt: Local Flexibility Aids Protein Multiple Structure Alignment
Menke, Matthew, Berger, Bonnie, Cowen, Lenore
Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many...
Efficient Algorithms for Probing the RNA Mutation Landscape
Waldispühl, Jérôme, Devadas, Srinivas, Berger, Bonnie, Clote, Peter
The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented. This broad range of functions is achieved through...
Optimal contact map alignment of protein–protein interfaces
Pulim, Vinay, Berger, Bonnie, Bienkowska, Jadwiga
The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order...
Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells
Wu, Erxi, Palmer, Nathan, Tian, Ze, Moseman, Annie P., Galdzicki, Michal, Wang, Xuetao, ...
Despite the growing understanding of PDGF signaling, studies of PDGF function have encountered two major obstacles: the functional redundancy of PDGFRα and PDGFRβ in vitro and their distinct roles...
Pulim, Vinay, Bienkowska, Jadwiga, Berger, Bonnie
Identification of extracellular ligand–receptor interactions is important for drug design and the treatment of diseases. Difficulties in detecting these interactions using high-throughput...
Singh, Rohit, Xu, Jinbo, Berger, Bonnie
Protein–protein interactions (PPIs) and their networks play a central role in all biological processes. Akin to the complete sequencing of genomes and their comparative analysis, complete...
BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis
Bryan, Allen W., Menke, Matthew, Cowen, Lenore J., Lindquist, Susan L., Berger, Bonnie
Amyloids and prion proteins are clinically and biologically important β-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In...
Revealing the spatial distribution of a disease while preserving privacy
Wieland, Shannon C., Cassa, Christopher A., Mandl, Kenneth D., Berger, Bonnie
Datasets describing the health status of individuals are important for medical research but must be used cautiously to protect patient privacy. For patient data containing geographical identifiers,...
IsoRankN: spectral methods for global alignment of multiple protein networks
Liao, Chung-Shou, Lu, Kanghao, Baym, Michael, Singh, Rohit, Berger, Bonnie
Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is...
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
Waldispühl, Jerome, Devadas, Srinivas, Berger, Bonnie, Clote, Peter
The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as...
Large-scale identification of genetic design strategies using local search
Lun, Desmond S, Rockwell, Graham, Guido, Nicholas J, Baym, Michael, Kelner, Jonathan A, Berger, Bonnie, ...
In the past decade, computational methods have been shown to be well suited to unraveling the complex web of metabolic reactions in biological systems. Methods based on flux–balance analysis (FBA)...