MacCallum, Iain, Przybylski, Dariusz, Gnerre, Sante, Burton, Joshua, Shlyakhter, Ilya, Gnirke, Andreas, ...
Abstract We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes...
Assisted assembly: how to improve a de novogenome assembly by using related species (2009)
Gnerre, Sante, Lander, Eric S, Lindblad-Toh, Kerstin, Jaffe, David B
Abstract We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an...
Assisted assembly: how to improve a de novo genome assembly by using related species (2009)
Gnerre, Sante, Lander, Eric S., Lindbald-Toh, Kerstin, Jaffe, David B.
We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting...
Methods Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2 (2008)
David B. Jaffe, Jonathan Butler, Sante Gnerre, Evan Mauceli, Kerstin Lindblad-toh, Jill P. Mesirov, ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
Quality scores and SNP detection in sequencing-by-synthesis systems (2008)
Brockman, William, Alvarez, Pablo, Young, Sarah, Garber, Manuel, Giannoukos, Georgia, Lee, William L., ...
Promising new sequencing technologies, based on sequencing-by-synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We...
ALLPATHS: De novo assembly of whole-genome shotgun microreads (2008)
Butler, Jonathan, MacCallum, Iain, Kleber, Michael, Shlyakhter, Ilya A., Belmonte, Matthew K., Lander, Eric S., ...
New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial,...
Functorial Structure of Units in a Tensor Product (2007)
. The behavior of units in a tensor product of rings is studied, as one factor varies. For example, let k be an algebraically closed field. Let A and B be reduced rings containing k, having connected...
Numerical Results on the Asymptotic Rate of Binary Codes (2007)
Barg And David, A. Barg, David B. Jaffe
. We compute upper bounds on the maximal size of a binary linear code of length n 1000, dimension k, and distance d For each value of d, the bound is found by solving the Delsarte linear programming...
A Sextic Surface Cannot Have 66 Nodes (2007)
David B. Jaffe, Daniel Ruberman
this paper, we complete the story by showing that S cannot have 66 nodes.
Coherent functors, with application to torsion in the Picard group (2007)
Let A be a commutative noetherian ring. We investigate a class of functors from #commutative A-algebras# to #sets#, which we call coherent. When such a functor F in fact takes its values in #abelian...
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis (2006)
Kahmann, Regine, Bölker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J, ...
Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi (2005)
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2 (2003)
Jaffe, David B., Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, Lindblad-Toh, Kerstin, Mesirov, Jill P., ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
ARACHNE: A Whole-Genome Shotgun Assembler (2002)
Batzoglou, Serafim, Jaffe, David B., Stanley, Ken, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, ...
Binary Linear Codes: New Results on Nonexistence (1996)
ly, a constraint is a relation of the form a 1 v 1 + · · · +a n v n k, where v 1 , . . . , v n are variables, a 1 , . . . , a n # Q , k # Z, and is either #, #, or =. Constraints are represented...
New results on binary linear codes (1995)
This research announcement describes in very rough terms methods and a computer language under development, which can be used to prove the nonexistence of binary linear codes. Over a hundred new...
A sextic surface cannot have 66 nodes (1995)
Jaffe, David B., Ruberman, Daniel
Let S be a surface in complex projective 3-space, having only nodes as singularities. Suppose that S has degree 6. We show that the maximum number of nodes which S can have is 65. An abbreviated...
On sextic surfaces having only nodes (preliminary report) (1994)
Let S be a surface in CP^3, having only nodes as singularities. Let pi: S~ --> S be a minimal resolution of singularities. A set N of nodes on S is EVEN if there exists a divisor Q on S~ such that 2Q...
Applications of iterated curve blowup to set-theoretic complete intersections in P3 (1994)
Let S, T be surfaces in P3. Suppose that S intersect T is set-theoretically a smooth curve C of degree d and genus g. Suppose that S and T have no common singular points. Then if C is not a complete...
Coherent functors, with application to torsion in the Picard group (1994)
Let A be a commutative noetherian ring. Call a functor --> coherent if it can be built up (via iterated finite limits) from functors of the form B \mapsto M tensor_A B, where M is a f.g. A-module....
Functorial structure of units in a tensor product (1994)
We study the units in a tensor product of rings. For example, let k be an algebraically closed field. Let A and B be reduced rings containing k, having connected spectra. Let u \in A tensor_k B be a...
Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
Jaffe, David B., Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, Lindblad-Toh, Kerstin, Mesirov, Jill P., ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
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...
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...
Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
Jaffe, David B., Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, Lindblad-Toh, Kerstin, Mesirov, Jill P., ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
Oxidative modification of M-type K+ channels as a mechanism of cytoprotective neuronal silencing
Gamper, Nikita, Zaika, Oleg, Li, Yang, Martin, Pamela, Hernandez, Ciria C, Perez, Michael R, ...
Voltage-gated K+ channels of the Kv7 family underlie the neuronal M current that regulates action potential firing. Suppression of M current increases excitability and its enhancement can silence...
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Passive electrotonic properties of rat hippocampal CA3 interneurones
Chitwood, Raymond A, Hubbard, Aida, Jaffe, David B
The linear membrane responses of CA3 interneurones were determined with the use of whole-cell patch recording methods. The mean input resistance (RN) for all cells in this study was 526 ± 16 MΩ and...
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Butler, Jonathan, MacCallum, Iain, Kleber, Michael, Shlyakhter, Ilya A., Belmonte, Matthew K., Lander, Eric S., ...
New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial,...
Quality scores and SNP detection in sequencing-by-synthesis systems
Brockman, William, Alvarez, Pablo, Young, Sarah, Garber, Manuel, Giannoukos, Georgia, Lee, William L., ...
Promising new sequencing technologies, based on sequencing-by-synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We...
Assisted assembly: how to improve a de novo genome assembly by using related species
Gnerre, Sante, Lander, Eric S, Lindblad-Toh, Kerstin, Jaffe, David B
A method is described for improving low sequence coverage genome assemblies