The National Center for Biotechnology Information's Protein Clusters Database (2009)
Klimke, William, Agarwala, Richa, Badretdin, Azat, Chetvernin, Slava, Ciufo, Stacy, Fedorov, Boris, ...
Rapid increases in DNA sequencing capabilities have led to a vast increase in the data generated from prokaryotic genomic studies, which has been a boon to scientists studying micro-organism...
Kochan, Kelli J, Amaral, M Elisabete J, Agarwala, Richa, Schäffer, Alejandro A, Riggs, Penny K
Abstract Background Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification...
Genome Analysis, Ro A. Schäffer, Edward Stallknecht Rice, William Cook, Richa Agarwala
rh tsp map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control
Database indexing for production MegaBLAST searches (2008)
Morgulis, Aleksandr, Coulouris, George, Raytselis, Yan, Madden, Thomas L., Agarwala, Richa, Schäffer, Alejandro A.
Initial sequence and comparative analysis of the cat genome (2007)
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
COBALT: constraint-based alignment tool for multiple protein sequences (2007)
Papadopoulos, Jason S., Agarwala, Richa
Motivation: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have...
rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control (2007)
Schäffer, Alejandro A., Rice, Edward Stallknecht, Cook, William, Agarwala, Richa
Summary: rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the...
COBALT: COnstraint Based ALignment Tool for Multiple Protein Sequences (2007)
Papadopoulos, Jason S., Agarwala, Richa
Motivation: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have...
COBALT: COnstraint Based ALignment Tool for Multiple Protein Sequences (2007)
Papadopoulos, Jason S., Agarwala, Richa
Motivation: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have...
rh_tsp_map 3.0: End-to-end radiation hybrid mapping with improved speed and quality control (2007)
Schäffer, Alejandro A., Rice, Edward Stallknecht, Cook, William, Agarwala, Richa
Summary: rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the...
rh_tsp_map 3.0: End-to-end radiation hybrid mapping with improved speed and quality control (2007)
Schäffer, Alejandro A., Rice, Edward Stallknecht, Cook, William, Agarwala, Richa
Summary: rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the...
Improved BLAST searches using longer words for protein seeding (2007)
Shiryev, Sergey A., Papadopoulos, Jason S., Schäffer, Alejandro A., Agarwala, Richa
Motivation: The blastp and tblastn modules of BLAST are widely used methods for searching protein queries against protein and nucleotide databases, respectively. One heuristic used in BLAST is to...
Gertz, E Michael, Yu, Yi-Kuo, Agarwala, Richa, Schäffer, Alejandro A, Altschul, Stephen F
Abstract Background TBLASTN is a mode of operation for BLAST that aligns protein sequences to a nucleotide database translated in all six frames. We present the first description of the modern...
Yu, Yi-Kuo, Gertz, E. Michael, Agarwala, Richa, Schäffer, Alejandro A., Altschul, Stephen F.
Protein sequence database search programs may be evaluated both for their retrieval accuracy—the ability to separate meaningful from chance similarities—and for the accuracy of their statistical...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Robinson, Gene E, Gibbs, Richard A, Worley, Kim C, Evans, Jay D, Maleszka, Ryszard, ...
Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes,...
Novel Gene Acquisition on Carnivore Y Chromosomes (2006)
William J. Murphy, Terje Raudsepp, Richa Agarwala, Alejandro A. Schäffer, Roscoe Stanyon, ...
Despite its importance in harboring genes critical for spermatogenesis and male-specific functions, the Y chromosome has been largely excluded as a priority in recent mammalian genome sequencing...
Novel Gene Acquisition on Carnivore Y Chromosomes (2006)
William J. Murphy, Terje Raudsepp, Richa Agarwala, Alejandro A. Schaffer, Roscoe Stanyon, ...
Despite its importance in harboring genes critical for spermatogenesis and male-specific functions, the Y chromosome has been largely excluded as a priority in recent mammalian genome sequencing...
E Michael Gertz, Yi-kuo Yu, Richa Agarwala, Ro A Schäffer, Stephen F Altschul, Alejandro A Schäffer, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
compositional similarity (2006)
Yi-kuo Yu, E. Michael Gertz, Richa Agarwala, Ro A. Schäffer, Stephen F. Altschul
Retrieval accuracy, statistical significance and
WindowMasker: window-based masker for sequenced genomes (2006)
Morgulis, Aleksandr, Gertz, E. Michael, Schäffer, Alejandro A., Agarwala, Richa
Motivation: Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database....
Fyfe, John C., Menotti-Raymond, Marilyn, David, Victor A., Brichta, Lars, Schäffer, Alejandro A., Agarwala, Richa, ...
The leading genetic cause of infant mortality is spinal muscular atrophy (SMA), a clinically and genetically heterogeneous group of disorders. Previously we described a domestic cat model of...
Yu, Yi-Kuo, Gertz, E. Michael, Agarwala, Richa, Schäffer, Alejandro A., Altschul, Stephen F.
Protein sequence database search programs may be evaluated both for their retrieval accuracy—the ability to separate meaningful from chance similarities—and for the accuracy of their statistical...
Fyfe, John C., Menotti-Raymond, Marilyn, David, Victor A., Brichta, Lars, Schäffer, Alejandro A., Agarwala, Richa, ...
The leading genetic cause of infant mortality is spinal muscular atrophy (SMA), a clinically and genetically heterogeneous group of disorders. Previously we described a domestic cat model of...
Yu, Yi-Kuo, Gertz, E. Michael, Agarwala, Richa, Schäffer, Alejandro A., Altschul, Stephen F.
Protein sequence database search programs may be evaluated both for their retrieval accuracy—the ability to separate meaningful from chance similarities—and for the accuracy of their statistical...
WindowMasker: window-based masker for sequenced genomes (2005)
Genome Analysis, R Morgulis, E. Michael Gertz, Ro A. Schäffer, Richa Agarwala
doi:10.1093/bioinformatics/bti774
WindowMasker: window based masker for sequenced genomes (2005)
Morgulis, Aleksandr, Gertz, E. Michael, Schäffer, Alejandro A., Agarwala, Richa
Motivation: Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database....
Towards a Complete North American Anabaptist Genealogy II: Analysis of Inbreeding (2001)
Agarwala, Richa., Schaffer, Alejandro A., Tomlin, James F.
Human Biology - Volume 73, Number 4, August 2001
A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy (2000)
Agarwala, Richa, Applegate, David L., Maglott, Donna, Schuler, Gregory D., Schäffer, Alejandro A.
The Sox10Dom Mouse: Modeling the Genetic Variation of Waardenburg-Shah (WS4) Syndrome (1999)
Southard-Smith, E. Michelle, Angrist, Misha, Ellison, Jane S., Agarwala, Richa, Baxevanis, Andreas D., Chakravarti, Aravinda, ...
Agarwala, Richa, Biesecker, Leslie G., Hopkins, Katherine A., Francomano, Clair A., Schaffer, Alejandro A.
Richa Agarwala, Serafim Batzoglou, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena
We consider the problem of determining the threedimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill [3], which...
Richa Agarwala, Serafim Batzoglou, Scott E. Decatur, Sridhar Hannenhalli, Martin Farach, S. Muthukrishnan, ...
We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill [7], which...
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics) (1997)
Richa Agarwala, Vineet Bafna, Martin Farach, Babu Narayanan, Mike Paterson, Mikkel Thorup
We consider the problem of fitting an n \Theta n distance matrix D by a tree metric T . Let " be the distance to the closest tree metric under the L1 norm, that is, " = min T fk T \Gamma D...
Richa Agarwala, Serafim Batzoglou, Vlado Dancik, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, ...
We consider the problem of determining the threedimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill [3], which...
Richa Agarwala, Serafim Batzoglou, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan
Richa Agarwala y Serafim Batzoglou z Vlado Danc'ik x Scott E. Decatur -- Martin Farach k Sridhar Hannenhalli S. Muthukrishnan yy Steven Skiena zz A long standing problem in molecular biology is...
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics) (1996)
Richa Agarwala, Vineet Bafna, Martin Farach, Mike Paterson, Mikkel Thorup
. We consider the problem of fitting an n \Theta n distance matrix D by a tree metric T . Let " be the distance to the closest tree metric under the L1 norm, that is, " = minT fk T \Gamma D...
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics) (1995)
Richa Agarwala, Vineet Bafna, Martin Farach, Babu Narayanan, Mike Paterson, Mikkel Thorup
We consider the problem of fitting an n \Theta n distance matrix D by a tree metric T . Let " be the distance to the closest tree metric, that is, " = min T fk T; D k1 g. First we present...
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics) (1995)
Richa Agarwala, Vineet Bafna, Martin Farach, Babu Narayanan, Mike Paterson, Mikkel Thorup
We consider the problem of fitting an n \Theta n distance matrix D by a tree metric T . Let " be the distance to the closest tree metric, that is, " = min T fk T; D k1 g. First we present...
Algorithms for weighted multidimensional search and perfect phylogeny / (1994)
Typescript (photocopy).
A Faster Algorithm for the Perfect Phylogeny Problem when the Number of Characters is Fixed (1994)
We present an algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of characters is fixed. This algorithm...
A Faster Algorithm for the Perfect Phylogeny Problem when the Number of Characters is Fixed (1994)
Richa Agarwala, David Fernández-Baca, David Fern
We present an algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of characters is fixed. This algorithm...
Weighted Search in the Plane (1994)
Richa Agarwala, David Fernández-Baca, David Fern'andez-baca
We present a simple two-dimensional weighted version of Megiddo's multidimensional search technique. This speeds up algorithms for certain convex optimization problems in the plane. Keywords:...
Richa Agarwala, David Fernández-Baca, Fern Andez-baca
. We present a polynomial-time algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of possible states...
Weighted Multidimensional Search and its Application to Convex Optimization (1993)
Richa Agarwala, David Fernández-Baca, David Fern
We present a weighted version of Megiddo's multidimensional search technique and use it to obtain faster algorithms for certain convex optimization problems in R d , for fixed d. This leads to...
Richa Agarwala, David Fernández-Baca, David Fern
We present a polynomial-time algorithm for determining whether a set of species, described by the characters they exhibit, has a phylogenetic tree, assuming the maximum number of possible states for...
Richa Agarwala, David Fernández-Baca, David Fern'andez-baca
We present a polynomial-time algorithm for determining whether a set of species, described by the characters they exhibit, has a phylogenetic tree, assuming the maximum number of possible states for...
Weighted multidimensional search and its applications to convex optimization (1992)
Richa Agarwala, Richa Agarwala, David Fern, David Fern
We present a weighted version of Megiddo's multidimensional search technique and use it to obtain faster algorithms for certain convex optimization problems in R
Parametric minimum spanning trees in outerplanar graphs /--by Richa Agarwala. (1991)
Typescript (photocopy)
Sequence variations in the public human genome data reflect a bottlenecked population history
Marth, Gabor, Schuler, Greg, Yeh, Raymond, Davenport, Ruth, Agarwala, Richa, Church, Deanna, ...
Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving...
A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy
Agarwala, Richa, Applegate, David L., Maglott, Donna, Schuler, Gregory D., Schäffer, Alejandro A.
This paper describes a fast and scalable strategy for constructing a radiation hybrid (RH) map from data on different RH panels. The maps on each panel are then integrated to produce a single RH map...
A Novel Nemaline Myopathy in the Amish Caused by a Mutation in Troponin T1
Johnston, Jennifer J., Kelley, Richard I., Crawford, Thomas O., Morton, D. Holmes, Agarwala, Richa, Koch, Thorsten, ...
The nemaline myopathies are characterized by weakness and eosinophilic, rodlike (nemaline) inclusions in muscle fibers. Amish nemaline myopathy is a form of nemaline myopathy common among the Old...
Protein Database Searches Using Compositionally Adjusted Substitution Matrices
Altschul, Stephen F., Wootton, John C., Gertz, E. Michael, Agarwala, Richa, Morgulis, Aleksandr, Schäffer, Alejandro A., ...
Almost all protein database search methods use amino acid substitution matrices for scoring, optimizing, and assessing the statistical significance of sequence alignments. Much care and effort has...
Novel Gene Acquisition on Carnivore Y Chromosomes
Murphy, William J, Wilkerson, Alison J. Pearks, Raudsepp, Terje, Agarwala, Richa, Schäffer, Alejandro A, Stanyon, Roscoe, ...
Despite its importance in harboring genes critical for spermatogenesis and male-specific functions, the Y chromosome has been largely excluded as a priority in recent mammalian genome sequencing...
Sequence variations in the public human genome data reflect a bottlenecked population history
Marth, Gabor, Schuler, Greg, Yeh, Raymond, Davenport, Ruth, Agarwala, Richa, Church, Deanna, ...
Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving...
A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy
Agarwala, Richa, Applegate, David L., Maglott, Donna, Schuler, Gregory D., Schäffer, Alejandro A.
This paper describes a fast and scalable strategy for constructing a radiation hybrid (RH) map from data on different RH panels. The maps on each panel are then integrated to produce a single RH map...
A Novel Nemaline Myopathy in the Amish Caused by a Mutation in Troponin T1
Johnston, Jennifer J., Kelley, Richard I., Crawford, Thomas O., Morton, D. Holmes, Agarwala, Richa, Koch, Thorsten, ...
The nemaline myopathies are characterized by weakness and eosinophilic, rodlike (nemaline) inclusions in muscle fibers. Amish nemaline myopathy is a form of nemaline myopathy common among the Old...
Novel Gene Acquisition on Carnivore Y Chromosomes
Murphy, William J, Pearks Wilkerson, Alison J, Raudsepp, Terje, Agarwala, Richa, Schäffer, Alejandro A, Stanyon, Roscoe, ...
Despite its importance in harboring genes critical for spermatogenesis and male-specific functions, the Y chromosome has been largely excluded as a priority in recent mammalian genome sequencing...
Yu, Yi-Kuo, Gertz, E. Michael, Agarwala, Richa, Schäffer, Alejandro A., Altschul, Stephen F.
Protein sequence database search programs may be evaluated both for their retrieval accuracy—the ability to separate meaningful from chance similarities—and for the accuracy of their statistical...
Fyfe, John C., Menotti-Raymond, Marilyn, David, Victor A., Brichta, Lars, Schäffer, Alejandro A., Agarwala, Richa, ...
The leading genetic cause of infant mortality is spinal muscular atrophy (SMA), a clinically and genetically heterogeneous group of disorders. Previously we described a domestic cat model of...
Initial sequence and comparative analysis of the cat genome
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, Clamp, Michele, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
PSI-BLAST pseudocounts and the minimum description length principle
Altschul, Stephen F., Gertz, E. Michael, Agarwala, Richa, Schäffer, Alejandro A., Yu, Yi-Kuo
Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search...
Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
Church, Deanna M., Goodstadt, Leo, Hillier, LaDeana W., Zody, Michael C., Goldstein, Steve, She, Xinwe, ...
A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled...
The National Center for Biotechnology Information's Protein Clusters Database
Klimke, William, Agarwala, Richa, Badretdin, Azat, Chetvernin, Slava, Ciufo, Stacy, Fedorov, Boris, ...
Rapid increases in DNA sequencing capabilities have led to a vast increase in the data generated from prokaryotic genomic studies, which has been a boon to scientists studying micro-organism...
Database indexing for production MegaBLAST searches
Morgulis, Aleksandr, Coulouris, George, Raytselis, Yan, Madden, Thomas L., Agarwala, Richa, Schäffer, Alejandro A.
Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that...