Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (2009)
Langmead, Ben, Trapnell, Cole, Pop, Mihai, Salzberg, Steven L
Abstract Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more...
Review Author's personal copy Bioinformatics challenges of new (2009)
This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and education use, including for instruction at the author’s institution,...
ARDB--Antibiotic Resistance Genes Database (2009)
The treatment of infections is increasingly compromised by the ability of bacteria to develop resistance to antibiotics through mutations or through the acquisition of resistance genes. Antibiotic...
Genome assembly reborn: recent computational challenges (2009)
Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been...
2009 Langmead et Volume al. 10, Issue 3, Article R25 Open Access (2009)
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg
Software Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Arthur L. Delcher, Steven L. Salzberg, Mihai Pop
research interests include genome assembly and comparative genomics.
Methods Hierarchical Scaffolding With Bambus (2008)
Mihai Pop, Daniel S. Kosack, Steven L. Salzberg
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is...
Arthur L. Delcher, Steven L. Salzberg, Mihai Pop
research interests include genome assembly and comparative genomics.
Genome assembly forensics: finding the elusive mis-assembly (2008)
Phillippy, Adam M, Schatz, Michael C, Pop, Mihai
Abstract We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their...
Figaro: a novel statistical method for vector sequence removal (2008)
White, James Robert, Roberts, Michael, Yorke, James A., Pop, Mihai
Motivation: Sequences produced by automated Sanger sequencing machines frequently contain fragments of the cloning vector on their ends. Software tools currently available for identifying and...
Scaffolding and validation of bacterial genome assemblies using optical restriction maps (2008)
Nagarajan, Niranjan, Read, Timothy D., Pop, Mihai
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of...
Minimus: a fast, lightweight genome assembler (2007)
Sommer, Daniel D, Delcher, Arthur L, Salzberg, Steven L, Pop, Mihai
Abstract Background Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most...
Minimus: a fast, lightweight genome assembler (2007)
Sommer, Daniel D., Delcher, Arthur L., Salzberg, Steven L., Pop, Mihai
Background: Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses...
Bmc Bioinformatics, Daniel D Sommer, Arthur L Delcher, Steven L Salzberg, Biomed Central, Daniel D Sommer, ...
Software Minimus: a fast, lightweight genome assembler
Initial role assignments (2006)
Mihai Pop, Michael Schatz, Assembly Algorithms, Base Calling, Genome Scaffold, Gene Finding, ...
sequence editing
Correction: Serendipitous discovery of Wolbachiagenomes in multiple Drosophilaspecies (2005)
Salzberg, Steven L, Dunning Hotopp, Julie, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
No abstract available.
Serendipitous discovery of Wolbachiagenomes in multiple Drosophilaspecies (2005)
Salzberg, Steven L, Hotopp, Julie, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
Abstract Background The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005)
Salzberg, Steven L., Dunning Hotopp, Julie C., Delcher, Arthur L., Pop, Mihai, Smith, Douglas R, Eisen, Michael B., ...
Background: The Trace Archive is a repository for the raw, unanalyzed data generated by largescale genome sequencing projects. The existence of this data offers scientists the possibility of...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005)
Salzberg, Steven L., Dunning Hotopp, Julie C., Delcher, Arthur L., Pop, Mihai, Smith, Douglas R, Eisen, Michael B., ...
Background: The Trace Archive is a repository for the raw, unanalyzed data generated by largescale genome sequencing projects. The existence of this data offers scientists the possibility of...
Hierarchical Scaffolding With Bambus (2004)
Pop, Mihai, Kosack, Daniel S., Salzberg, Steven L.
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is...
Comparative genome assembly (2004)
Pop, Mihai, Phillippy, Adam, Delcher, Arthur L., Salzberg, Steven L.
One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a...
Efficient perspective-accurate silhouette computation and applications (2001)
Mihai Pop, Christian A. Duncan, Gill Barequet, Michael T. Goodrich, Wenjing Huang
� � � � � �Æ � � � � � � � � � � � ��Æ � � � � � � � � �Æ � � � � � � � �Æ � � � � � � � � � � � �...
Drawing of Two-Dimensional Irregular Meshes (1998)
Aggarwal, Alok, Kosaraju, Rao, Pop, Mihai
We present a method for transforming two-dimensional irregular meshes into square meshes with only a constant blow up in area. We also explore context invariant transformations of irregular meshes...
Drawing of Two-Dimensional Irregular Meshes (1998)
Aggarwal, Alok, Kosaraju, Rao, Pop, Mihai
We present a method for transforming two-dimensional irregular meshes into square meshes with only a constant blow up in area. We also explore context invariant transformations of irregular meshes...
Drawing of Two-Dimensional Irregular Meshes (1998)
Aggarwal, Alok, Kosaraju, Rao, Pop, Mihai
We present a method for transforming two-dimensional irregular meshes into square meshes with only a constant blow up in area. We also explore context invariant transformations of irregular meshes...
Efficient Data Structures for use in Geographic Information Systems (1997)
Introduction Geographic Information Systems (GIS) is a broad term to describe systems designed to manipulate spatial and geographic data. They are, in essence, databases of geographic information....
Unsupervised Part-of-speech Tagging (1996)
Different approaches have been taken in order to solve the part-of-speech tagging problem. Several methods for unsupervised tagging have obtained good accuracies in practice. The approach taken by...
Protein Folding: Computational Challenges (1996)
We review several results related to the protein folding problem. We start by analyzing the nature of the interactions among protein atoms and their influence on folding. We then examine several...
Comparative Study of Electronic Mail Systems (1994)
this paper. As part of the practical work I will create configuration files that can be used at all levels of the hierarchy, making the conversion to this solution as well as the inclusion of new...
Hierarchical Scaffolding With Bambus
Pop, Mihai, Kosack, Daniel S., Salzberg, Steven L.
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Hotopp, Julie C Dunning, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly:...
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Dunning Hotopp, Julie C, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology...
Hierarchical Scaffolding With Bambus
Pop, Mihai, Kosack, Daniel S., Salzberg, Steven L.
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Hotopp, Julie C Dunning, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly:...
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Dunning Hotopp, Julie C, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology...
Minimus: a fast, lightweight genome assembler
Sommer, Daniel D, Delcher, Arthur L, Salzberg, Steven L, Pop, Mihai
Genome assembly forensics: finding the elusive mis-assembly
Phillippy, Adam M, Schatz, Michael C, Pop, Mihai
A collection of software tools is combined for the first time in an automated pipeline for detecting large-scale genome assembly errors and for validating genome assemblies.
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
Nagarajan, Niranjan, Read, Timothy D., Pop, Mihai
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of...
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
White, James Robert, Nagarajan, Niranjan, Pop, Mihai
Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more...
ARDB—Antibiotic Resistance Genes Database
The treatment of infections is increasingly compromised by the ability of bacteria to develop resistance to antibiotics through mutations or through the acquisition of resistance genes. Antibiotic...
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Langmead, Ben, Trapnell, Cole, Pop, Mihai, Salzberg, Steven L
Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.