Arjun Bhutkar, Susan Russo, Temple F. Smith, William M. Gelbart
Genome scale synteny analysis, the analysis of relative gene-order conservation between species, can provide key insights into evolutionary chromosomal dynamics, rearrangement rates between species,...
Michael F. Lin, Joseph W. Carlson, Madeline A. Crosby, Beverley B. Matthews, Charles Yu, Kenneth H. Wan, ...
the protein-coding gene catalog of
VectorBase: a data resource for invertebrate vector genomics (2009)
Lawson, Daniel, Arensburger, Peter, Atkinson, Peter, Besansky, Nora J., Bruggner, Robert V., Butler, Ryan, ...
VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a...
Curvature dependence of viral protein structures on encapsidated nanoemulsion droplets (2008)
Chang, Connie B., Knobler, Charles M., Gelbart, William M., Mason, Thomas G.
Virus-like particles are biomimetic delivery vehicles that cloak nanoscale cores inside coatings of viral capsid proteins, offering the potential for protecting their contents and targeting them to...
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007)
Alexander Stark, Michael F. Lin, Pouya Kheradpour, Jakob S. Pedersen, Leopold Parts, Joseph W. Carlson, ...
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007)
Lin, Michael F, Kheradpour, Pouya, Pedersen, Jakob S, Parts, Leopold, Carlson, Joseph W, ...
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12...
Lobo, Neil F, Campbell, Kathy S, Thaner, Daniel, DeBruyn, Becky, Koo, Hean, Gelbart, William M, ...
Abstract Background Aedes aegypti is the principal vector of yellow fever and dengue viruses throughout the tropical world. To provide a set of manually curated and annotated sequences from the Ae....
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes (2007)
Lin, Michael F., Carlson, Joseph W., Crosby, Madeline A., Matthews, Beverley B., Yu, Charles, Park, Soo, ...
The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have...
Genome-scale analysis of positionally relocated genes (2007)
Bhutkar, Arjun, Russo, Susan M., Smith, Temple F., Gelbart, William M.
During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the...
FlyBase: genomes by the dozen (2007)
Crosby, Madeline A., Goodman, Joshua L., Strelets, Victor B., Zhang, Peili, Gelbart, William M.
FlyBase (http://flybase.org/) is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied...
VectorBase: a home for invertebrate vectors of human pathogens (2007)
Lawson, Daniel, Arensburger, Peter, Atkinson, Peter, Besansky, Nora J., Bruggner, Robert V., Butler, Ryan, ...
VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing...
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,...
Performance Predictions for Composite Materials (2006)
Gelbart, William M., Feng, Shechao, Reiss, Howard, Kivelson, Daniel
This project has initiated and brought to completion several novel microscopic approaches to the prediction of material response to applied stress. In a series of several papers we worked out a...
doi:10.1093/nar/gkl827 FlyBase: genomes by the dozen (2006)
Madeline A. Crosby, Joshua L. Goodman, Victor B. Strelets, Peili Zhang, William M. Gelbart, The Flybase Consortium
FlyBase
VectorBase: a home for invertebrate vectors of human pathogens (2006)
Lawson, Daniel, Arensburger, Peter, Atkinson, Peter, Besansky, Nora J., Bruggner, Robert V., Butler, Ryan, ...
VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing...
VectorBase: a home for invertebrate vectors of human pathogens (2006)
Lawson, Daniel, Arensburger, Peter, Atkinson, Peter, Besansky, Nora J., Bruggner, Robert V., Butler, Ryan, ...
VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing...
Dynamics of DNA Ejection From Bacteriophage (2005)
Inamdar, Mandar M., Gelbart, William M., Phillips, Rob
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The...
The effect of genome length on ejection forces in bacteriophage lambda (2005)
Grayson, Paul, Evilevitch, Alex, Inamdar, Mandar M., Purohit, Prashant K., Gelbart, William M., Knobler, Charles M., ...
A variety of viruses tightly pack their genetic material into protein capsids that are barely large enough to enclose the genome. In particular, in bacteriophages, forces as high as 60 pN are...
Structural Polymorphism of the Cytoskeleton: A Model of Linker-Assisted Filament Aggregation (2005)
Borukhov, Itamar, Bruinsma, Robijn F., Gelbart, William M., Liu, Andrea J.
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker...
Effect of Mono- and Multivalent Salts on Angle-dependent Attractions between Charged Rods (2003)
Lee, Kun-Chun, Borukhov, Itamar, Gelbart, William M., Liu, Andrea J., Stevens, Mark J.
Using molecular dynamics simulations we examine the effective interactions between two like-charged rods as a function of angle and separation. In particular, we determine how the competing...
What drives the translocation of stiff chains? (2003)
Zandi, Roya, Reguera, David, Rudnick, Joseph, Gelbart, William M.
We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the...
Viral self-assembly as a thermodynamic process (2003)
Bruinsma, Robijn F., Gelbart, William M., Reguera, D., Rudnick, Joseph, Zandy, Roya
The protein shells, or capsids, of nearly all spherelike viruses adopt icosahedral symmetry. In the present Letter, we propose a statistical thermodynamic model for viral self-assembly. We find that...
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review (2002)
Misra, Sima, Crosby, Madeline A, Mungall, Christopher J, Matthews, Beverley B, Campbell, Kathryn S, Hradecky, Pavel, ...
Abstract Background The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78%...
Viral self-assembly as a thermodynamic process (2002)
Bruinsma, Robijn F., Gelbart, William M., Reguera, David, Rudnick, Joseph, Zandi, Roya
The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that...
Elastically Driven Linker Aggregation between Two Semiflexible Polyelectrolytes (2001)
Borukhov, Itamar, Bruinsma, Robijn F., Gelbart, William M., Liu, Andrea J.
Spontaneous patterning of quantum dots at the air-water interface (1999)
Sear, Richard P., Chung, Sung-Wook, Markovich, Gil, Gelbart, William M., Heath, James R.
Nanoparticles deposited at the air-water interface are observed to form circular domains at low density and stripes at higher density. We interpret these patterns as equilibrium phenomena produced by...
Array formation in nano-colloids: Theory and experiment in 2D (1998)
William M. Gelbart, Stephanie Chaneya
We discuss theoretical and experimental aspects of the array formation of nano-colloids in two-dimensional (2D) situations. In particular, we treat metal nanocrystals which have been passivated by...
Crystallization of opals from polydisperse nanoparticles (1995)
Ohara, Pamela C., Leff, Daniel V., Heath, James R., Gelbart, William M.
We report the reversible formation of crystals of nanoparticles (opals) from solutions of polydisperse gold nanocrystals. The structures are identified by transmission electron microscopy, and are...
Lambert, Olivier, Letellier, Lucienne, Gelbart, William M., Rigaud, Jean-Louis
We report a strategy for encapsulating and condensing DNA. When T5 phage binds to its membrane protein receptor, FhuA, its double stranded DNA (120,000 bp) is progressively released base pair after...
DNA packaging and ejection forces in bacteriophage
Kindt, James, Tzlil, Shelly, Ben-Shaul, Avinoam, Gelbart, William M.
We calculate the forces required to package (or, equivalently, acting to eject) DNA into (from) a bacteriophage capsid, as a function of the loaded (ejected) length, under conditions for which the...
Huet, François, Lu, Jeffrey T., Myrick, Kyl V., Baugh, L. Ryan, Crosby, Madeline A., Gelbart, William M.
With the available eukaryotic genome sequences, there are predictions of thousands of previously uncharacterized genes without known function or available mutational variant. Thus, there is an urgent...
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Misra, Sima, Crosby, Madeline A, Mungall, Christopher J, Matthews, Beverley B, Campbell, Kathryn S, Hradecky, Pavel, ...
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to...
What drives the translocation of stiff chains?
Zandi, Roya, Reguera, David, Rudnick, Joseph, Gelbart, William M.
We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian molecular dynamics simulations we investigate the mean...
Osmotic pressure inhibition of DNA ejection from phage
Evilevitch, Alex, Lavelle, Laurence, Knobler, Charles M., Raspaud, Eric, Gelbart, William M.
Bacterial viral capsids in aqueous solution can be opened in vitro by addition of their specific receptor proteins, with consequent full ejection of their genomes. We demonstrate that it is possible...
DNA-Induced Transformation in Drosophila: Evidence for Transmission without Integration*
Fox, Allen S., Duggleby, William F., Gelbart, William M., Yoon, Sei Byung
A key feature of the exosome model of transformation in Drosophila melanogaster is that the DNA segments responsible for the phenomenon are not integrated into the linear structure of the...
DNA-Induced Transformation in Drosophila: Genetic Analysis of Transformed Stocks
Fox, Allen S., Yoon, Sei Byung, Gelbart, William M.
The exosome model of transformation in Drosophila melanogaster proposes that DNA fragments enter the cells of treated individuals and become firmly associated with their homologous chromosome...
Origin of icosahedral symmetry in viruses
Zandi, Roya, Reguera, David, Bruinsma, Robijn F., Gelbart, William M., Rudnick, Joseph
With few exceptions, the shells (capsids) of sphere-like viruses have the symmetry of an icosahedron and are composed of coat proteins (subunits) assembled in special motifs, the T-number structures....
Structural polymorphism of the cytoskeleton: A model of linker-assisted filament aggregation
Borukhov, Itamar, Bruinsma, Robijn F., Gelbart, William M., Liu, Andrea J.
The phase behavior of charged rods in the presence of interrod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker...
Forces and Pressures in DNA Packaging and Release from Viral Capsids
Tzlil, Shelly, Kindt, James T., Gelbart, William M., Ben-Shaul, Avinoam
In a previous communication (Kindt et al., 2001) we reported preliminary results of Brownian dynamics simulation and analytical theory which address the packaging and ejection forces involving DNA in...
Osmotic Shock and the Strength of Viral Capsids
Cordova, Amado, Deserno, Markus, Gelbart, William M., Ben-Shaul, Avinoam
Osmotic shock is a familiar means for rupturing viral capsids and exposing their genomes intact. The necessary conditions for providing this shock involve incubation in high-concentration salt...
A Statistical-Thermodynamic Model of Viral Budding
Tzlil, Shelly, Deserno, Markus, Gelbart, William M., Ben-Shaul, Avinoam
We present a simple statistical thermodynamic model for budding of viral nucleocapsids at the cell membrane. The membrane is modeled as a flexible lipid bilayer embedding linker (spike) proteins,...
Evilevitch, Alex, Gober, James W., Phillips, Martin, Knobler, Charles M., Gelbart, William M.
The effect of external osmotic pressure on the extent of DNA ejection from bacteriophage-λ was recently investigated (Evilevitch et al., 2003). The total length of DNA ejected was measured via the...
Interactions of Zeste Mutations with Loci Exhibiting Transvection Effects in DROSOPHILA MELANOGASTER
Gelbart, William M., Wu, Chao-Ting
Zeste (1-1.0; 3A3) mutations have been known to modify the expression of two gene complexes: white (1-1.5; 3C1.5) and bithorax (3-58.8; 89E1-4) in Drosophila melanogaster. Certain mutations of these...
Shortvein, a New Component of the Decapentaplegic Gene Complex in DROSOPHILA MELANOGASTER
Segal, Daniel, Gelbart, William M.
Our laboratory has been concerned with the structure and function of the decapentaplegic gene complex (DPP-C) in Drosophila melanogaster . To define the boundaries of the complex, we have studied the...
The Effects of Chromosomal Rearrangements on the zeste-white Interaction in Drosophila melanogaster
Smolik-Utlaut, Sarah M., Gelbart, William M.
Three gene systems have been shown to exhibit proximity-dependent phenotypes in Drosophila melanogaster: bithorax (BX-C), decapentaplegic (DPP-C) and white (w). In structurally homozygous genotypes,...
Molecular and Recombinational Mapping of Mutations in the Ace Locus of Drosophila melanogaster
Nagoshi, Rodney N., Gelbart, William M.
The Ace locus in Drosophila melanogaster is known to be the structural gene for acetylcholinesterase. Ace is located in a region of chromosome arm 3R which has been subjected to intensive genetic and...
A New Mutant Controlling Mitotic Chromosome Disjunction in DROSOPHILA MELANOGASTER
A new mutant, mit (mitotic loss inducer), is described. The mutant is recessive and maternal in action, producing gynandromorphs and haplo-4 mosaics among the progeny of homozygous mit females....
Spontaneous Unequal Exchange in the Rosy Region of DROSOPHILA MELANOGASTER
Gelbart, William M., Chovnick, Arthur
A selective system for recovery of exchanges between trans mutations at adjacent loci, l(3)S12 and rosy, is described. In addition to the expected cross-over and conversion classes, two exceptional...
Hilliker, Arthur J., Clark, Stephen H., Chovnick, Arthur, Gelbart, William M.
This report describes the genetic analysis of a region of the third chromosome of Drosophila melanogaster extending from 87D2–4 to 87E12–F1, an interval of 23 or 24 polytene chromosome bands....
Gelbart, William M., McCarron, Margaret, Pandey, Janardan, Chovnick, Arthur
Experiments are described that provide an opportunity to estimate the genetic limits of the structural (amino acid coding) portion of the rosy locus (3:52.0) in Drosophila melanogaster, which...
Li, Jinghong, Li, Willis X., Gelbart, William M.
The Dpp signaling pathway is essential for many developmental processes in Drosophila and its activity is tightly regulated. To identify additional regulators of Dpp signaling, we conducted a genetic...
Mohr, Stephanie E, Gelbart, William M
Understanding the function of each gene in the genome of a model organism such as Drosophila melanogaster is an important goal. The development of improved methods for uncovering the mutant...
Lambert, Olivier, Letellier, Lucienne, Gelbart, William M., Rigaud, Jean-Louis
We report a strategy for encapsulating and condensing DNA. When T5 phage binds to its membrane protein receptor, FhuA, its double stranded DNA (120,000 bp) is progressively released base pair after...
DNA packaging and ejection forces in bacteriophage
Kindt, James, Tzlil, Shelly, Ben-Shaul, Avinoam, Gelbart, William M.
We calculate the forces required to package (or, equivalently, acting to eject) DNA into (from) a bacteriophage capsid, as a function of the loaded (ejected) length, under conditions for which the...
Huet, François, Lu, Jeffrey T., Myrick, Kyl V., Baugh, L. Ryan, Crosby, Madeline A., Gelbart, William M.
With the available eukaryotic genome sequences, there are predictions of thousands of previously uncharacterized genes without known function or available mutational variant. Thus, there is an urgent...
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Misra, Sima, Crosby, Madeline A, Mungall, Christopher J, Matthews, Beverley B, Campbell, Kathryn S, Hradecky, Pavel, ...
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to...
What drives the translocation of stiff chains?
Zandi, Roya, Reguera, David, Rudnick, Joseph, Gelbart, William M.
We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian molecular dynamics simulations we investigate the mean...
Osmotic pressure inhibition of DNA ejection from phage
Evilevitch, Alex, Lavelle, Laurence, Knobler, Charles M., Raspaud, Eric, Gelbart, William M.
Bacterial viral capsids in aqueous solution can be opened in vitro by addition of their specific receptor proteins, with consequent full ejection of their genomes. We demonstrate that it is possible...
DNA-Induced Transformation in Drosophila: Evidence for Transmission without Integration*
Fox, Allen S., Duggleby, William F., Gelbart, William M., Yoon, Sei Byung
A key feature of the exosome model of transformation in Drosophila melanogaster is that the DNA segments responsible for the phenomenon are not integrated into the linear structure of the...
DNA-Induced Transformation in Drosophila: Genetic Analysis of Transformed Stocks
Fox, Allen S., Yoon, Sei Byung, Gelbart, William M.
The exosome model of transformation in Drosophila melanogaster proposes that DNA fragments enter the cells of treated individuals and become firmly associated with their homologous chromosome...
Origin of icosahedral symmetry in viruses
Zandi, Roya, Reguera, David, Bruinsma, Robijn F., Gelbart, William M., Rudnick, Joseph
With few exceptions, the shells (capsids) of sphere-like viruses have the symmetry of an icosahedron and are composed of coat proteins (subunits) assembled in special motifs, the T-number structures....
Structural polymorphism of the cytoskeleton: A model of linker-assisted filament aggregation
Borukhov, Itamar, Bruinsma, Robijn F., Gelbart, William M., Liu, Andrea J.
The phase behavior of charged rods in the presence of interrod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker...
Interactions of Zeste Mutations with Loci Exhibiting Transvection Effects in DROSOPHILA MELANOGASTER
Gelbart, William M., Wu, Chao-Ting
Zeste (1-1.0; 3A3) mutations have been known to modify the expression of two gene complexes: white (1-1.5; 3C1.5) and bithorax (3-58.8; 89E1-4) in Drosophila melanogaster. Certain mutations of these...
Shortvein, a New Component of the Decapentaplegic Gene Complex in DROSOPHILA MELANOGASTER
Segal, Daniel, Gelbart, William M.
Our laboratory has been concerned with the structure and function of the decapentaplegic gene complex (DPP-C) in Drosophila melanogaster . To define the boundaries of the complex, we have studied the...
The Effects of Chromosomal Rearrangements on the zeste-white Interaction in Drosophila melanogaster
Smolik-Utlaut, Sarah M., Gelbart, William M.
Three gene systems have been shown to exhibit proximity-dependent phenotypes in Drosophila melanogaster: bithorax (BX-C), decapentaplegic (DPP-C) and white (w). In structurally homozygous genotypes,...
Molecular and Recombinational Mapping of Mutations in the Ace Locus of Drosophila melanogaster
Nagoshi, Rodney N., Gelbart, William M.
The Ace locus in Drosophila melanogaster is known to be the structural gene for acetylcholinesterase. Ace is located in a region of chromosome arm 3R which has been subjected to intensive genetic and...
A New Mutant Controlling Mitotic Chromosome Disjunction in DROSOPHILA MELANOGASTER
A new mutant, mit (mitotic loss inducer), is described. The mutant is recessive and maternal in action, producing gynandromorphs and haplo-4 mosaics among the progeny of homozygous mit females....
Spontaneous Unequal Exchange in the Rosy Region of DROSOPHILA MELANOGASTER
Gelbart, William M., Chovnick, Arthur
A selective system for recovery of exchanges between trans mutations at adjacent loci, l(3)S12 and rosy, is described. In addition to the expected cross-over and conversion classes, two exceptional...
Hilliker, Arthur J., Clark, Stephen H., Chovnick, Arthur, Gelbart, William M.
This report describes the genetic analysis of a region of the third chromosome of Drosophila melanogaster extending from 87D2–4 to 87E12–F1, an interval of 23 or 24 polytene chromosome bands....
Gelbart, William M., McCarron, Margaret, Pandey, Janardan, Chovnick, Arthur
Experiments are described that provide an opportunity to estimate the genetic limits of the structural (amino acid coding) portion of the rosy locus (3:52.0) in Drosophila melanogaster, which...
Forces and Pressures in DNA Packaging and Release from Viral Capsids
Tzlil, Shelly, Kindt, James T., Gelbart, William M., Ben-Shaul, Avinoam
In a previous communication (Kindt et al., 2001) we reported preliminary results of Brownian dynamics simulation and analytical theory which address the packaging and ejection forces involving DNA in...
Osmotic Shock and the Strength of Viral Capsids
Cordova, Amado, Deserno, Markus, Gelbart, William M., Ben-Shaul, Avinoam
Osmotic shock is a familiar means for rupturing viral capsids and exposing their genomes intact. The necessary conditions for providing this shock involve incubation in high-concentration salt...
A Statistical-Thermodynamic Model of Viral Budding
Tzlil, Shelly, Deserno, Markus, Gelbart, William M., Ben-Shaul, Avinoam
We present a simple statistical thermodynamic model for budding of viral nucleocapsids at the cell membrane. The membrane is modeled as a flexible lipid bilayer embedding linker (spike) proteins,...
Evilevitch, Alex, Gober, James W., Phillips, Martin, Knobler, Charles M., Gelbart, William M.
The effect of external osmotic pressure on the extent of DNA ejection from bacteriophage-λ was recently investigated (Evilevitch et al., 2003). The total length of DNA ejected was measured via the...
Li, Jinghong, Li, Willis X., Gelbart, William M.
The Dpp signaling pathway is essential for many developmental processes in Drosophila and its activity is tightly regulated. To identify additional regulators of Dpp signaling, we conducted a genetic...
Mohr, Stephanie E, Gelbart, William M
Understanding the function of each gene in the genome of a model organism such as Drosophila melanogaster is an important goal. The development of improved methods for uncovering the mutant...
Crosby, Madeline A., Goodman, Joshua L., Strelets, Victor B., Zhang, Peili, Gelbart, William M.
FlyBase () is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied species in this family,...
VectorBase: a home for invertebrate vectors of human pathogens
Lawson, Daniel, Arensburger, Peter, Atkinson, Peter, Besansky, Nora J., Bruggner, Robert V., Butler, Ryan, ...
VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for...
Dynamics of DNA Ejection from Bacteriophage
Inamdar, Mandar M., Gelbart, William M., Phillips, Rob
The ejection of DNA from a bacterial virus (i.e., phage) into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The...
Lobo, Neil F, Campbell, Kathy S, Thaner, Daniel, DeBruyn, Becky, Koo, Hean, Gelbart, William M, ...
In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using...
Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study
Bhutkar, Arjun, Gelbart, William M, Smith, Temple F
A simple, fast, and biologically-inspired computational approach to infer genome-scale rearrangement phylogeny and ancestral gene order has been developed and applied to eight Drosophila genomes,...
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
Lin, Michael F., Carlson, Joseph W., Crosby, Madeline A., Matthews, Beverley B., Yu, Charles, Park, Soo, ...
The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have...
Genome-scale analysis of positionally relocated genes
Bhutkar, Arjun, Russo, Susan M., Smith, Temple F., Gelbart, William M.
During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the...
Schaeffer, Stephen W., Bhutkar, Arjun, McAllister, Bryant F., Matsuda, Muneo, Matzkin, Luciano M., O'Grady, Patrick M., ...
The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of...
Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes
Bhutkar, Arjun, Schaeffer, Stephen W., Russo, Susan M., Xu, Mu, Smith, Temple F., Gelbart, William M.
The availability of 12 complete genomes of various species of genus Drosophila provides a unique opportunity to analyze genome-scale chromosomal rearrangements among a group of closely related...
Effects of Salt Concentrations and Bending Energy on the Extent of Ejection of Phage Genomes
Evilevitch, Alex, Fang, Li Tai, Yoffe, Aron M., Castelnovo, Martin, Rau, Donald C., Parsegian, V. Adrian, ...
Recent work has shown that pressures inside dsDNA phage capsids can be as high as many tens of atmospheres; it is this pressure that is responsible for initiation of the delivery of phage genomes to...
Packaging of a Polymer by a Viral Capsid: The Interplay between Polymer Length and Capsid Size
Hu, Yufang, Zandi, Roya, Anavitarte, Adriana, Knobler, Charles M., Gelbart, William M.
We report a study of the in vitro self-assembly of virus-like particles formed by the capsid protein of cowpea chlorotic mottle virus and the anionic polymer poly(styrene sulfonate) (PSS) for five...
Predicting the sizes of large RNA molecules
Yoffe, Aron M., Prinsen, Peter, Gopal, Ajaykumar, Knobler, Charles M., Gelbart, William M., Ben-Shaul, Avinoam
We present a theory of the dependence on sequence of the three-dimensional size of large single-stranded (ss) RNA molecules. The work is motivated by the fact that the genomes of many viruses are...
VectorBase: a data resource for invertebrate vector genomics
Lawson, Daniel, Arensburger, Peter, Atkinson, Peter, Besansky, Nora J., Bruggner, Robert V., Butler, Ryan, ...
VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a...
Myrick, Kyl V., Huet, François, Mohr, Stephanie E., Álvarez-García, Inés, Lu, Jeffrey T., Smith, Mark A., ...
Whole genome sequencing of the model organisms has created increased demand for efficient tools to facilitate the genome annotation efforts. Accordingly, we report the further implementations and...