Steven L. Salzberg

39 papers B 1Journal 38
YearRankTypeTitle / Venue / Authors
2023 J jnl
Investigating open reading frames in known and novel transcripts using ORFanage.
Nat. Comput. Sci.
Ales Varabyou, Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea
2023 J jnl
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.
PLoS Comput. Biol.
Alina Guo, Steven L. Salzberg, Aleksey V. Zimin
2022 J jnl
Metagenomic classification with KrakenUniq on low-memory computers.
J. Open Source Softw.
Christopher Pockrandt, Aleksey V. Zimin, Steven L. Salzberg
2022 J jnl
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools.
Bioinform.
Christopher Pockrandt, Martin Steinegger, Steven L. Salzberg
2022 J jnl
The SAMBA tool uses long reads to improve the contiguity of genome assemblies.
PLoS Comput. Biol.
Aleksey V. Zimin, Steven L. Salzberg
2021 J jnl
Balrog: A universal protein model for prokaryotic gene prediction.
PLoS Comput. Biol.
Markus J. Sommer, Steven L. Salzberg
2021 J jnl
Liftoff: accurate mapping of gene annotations.
Bioinform.
Alaina Shumate, Steven L. Salzberg
2021 J jnl
Releasing the Kraken.
Frontiers Bioinform.
Steven L. Salzberg, Derrick E. Wood
2020 J jnl
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.
Bioinform.
Florian P. Breitwieser, Steven L. Salzberg
2020 J jnl
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes.
PLoS Comput. Biol.
Jennifer Lu, Steven L. Salzberg
2020 J jnl
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
PLoS Comput. Biol.
Aleksey V. Zimin, Steven L. Salzberg
2019 J jnl
A review of methods and databases for metagenomic classification and assembly.
Briefings Bioinform.
Florian P. Breitwieser, Jennifer Lu, Steven L. Salzberg
2019 J jnl
The Terabase Search Engine: a large-scale relational database of short-read sequences.
Bioinform.
Richard Wilton, Sarah J. Wheelan, Alexander S. Szalay, Steven L. Salzberg
2018 J jnl
MUMmer4: A fast and versatile genome alignment system.
PLoS Comput. Biol.
Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg, Aleksey V. Zimin
2018 J jnl
Removing contaminants from databases of draft genomes.
PLoS Comput. Biol.
Jennifer Lu, Steven L. Salzberg
2017 J jnl
Bracken: estimating species abundance in metagenomics data.
PeerJ Comput. Sci.
Jennifer Lu, Florian P. Breitwieser, Peter Thielen, Steven L. Salzberg
2017 J jnl
Short Read Mapping: An Algorithmic Tour.
Proc. IEEE
Stefan Canzar, Steven L. Salzberg
2013 B conf
Computational challenges in next-generation genomics.
SSDBM
Steven L. Salzberg
2013 J jnl
GAGE-B: an evaluation of genome assemblers for bacterial organisms.
Bioinform.
Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg
2013 J jnl
Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing.
IEEE ACM Trans. Comput. Biol. Bioinform.
Liliana Florea, Steven L. Salzberg
2013 J jnl
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.
Briefings Bioinform.
Michael C. Schatz, Adam M. Phillippy, Daniel D. Sommer, Arthur L. Delcher, Daniela Puiu, Giuseppe Narzisi, Steven L. Salzberg, Mihai Pop
2013 J jnl
The MaSuRCA genome assembler.
Bioinform.
Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke
2013 J jnl
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.
F1000Research
Liliana Florea, Li Song, Steven L. Salzberg
2011 J jnl
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.
Nucleic Acids Res.
Richard J. Roberts, Yi-Chien Chang, Zhenjun Hu, John Rachlin, Brian P. Anton, Revonda M. Pokrzywa, Han-Pil Choi, Lina L. Faller, Jyotsna Guleria, Genevieve Housman, Niels Klitgord, Varun Mazumdar, Mark G. McGettrick, Lais Osmani, Rajeswari Swaminathan, Kevin R. Tao, Stanley Letovsky, Dennis Vitkup, Daniel Segrè, Steven L. Salzberg, Charles DeLisi, Martin Steffen, Simon Kasif
2011 J jnl
Detection of Lineage-Specific Evolutionary Changes among Primate Species.
BMC Bioinform.
Mihaela Pertea, Geo Pertea, Steven L. Salzberg
2011 J jnl
FLASH: fast length adjustment of short reads to improve genome assemblies.
Bioinform.
Tanja Magoc, Steven L. Salzberg
2011 J jnl
Improving pan-genome annotation using whole genome multiple alignment.
BMC Bioinform.
Samuel V. Angiuoli, Julie C. Dunning Hotopp, Steven L. Salzberg, Hervé Tettelin
2011 J jnl
Mugsy: fast multiple alignment of closely related whole genomes.
Bioinform.
Samuel V. Angiuoli, Steven L. Salzberg
2010 J jnl
Clustering metagenomic sequences with interpolated Markov models.
BMC Bioinform.
David R. Kelley, Steven L. Salzberg
2009 J jnl
Efficient oligonucleotide probe selection for pan-genomic tiling arrays.
BMC Bioinform.
Adam M. Phillippy, Xiangyu Deng, Wei Zhang, Steven L. Salzberg
2009 J jnl
Insignia: a DNA signature search web server for diagnostic assay development.
Nucleic Acids Res.
Adam M. Phillippy, Kunmi Ayanbule, Nathan J. Edwards, Steven L. Salzberg
2009 J jnl
OperonDB: a comprehensive database of predicted operons in microbial genomes.
Nucleic Acids Res.
Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff, Steven L. Salzberg
2009 J jnl
TopHat: discovering splice junctions with RNA-Seq.
Bioinform.
Cole Trapnell, Lior Pachter, Steven L. Salzberg
2008 J jnl
Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads.
PLoS Comput. Biol.
Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee
2007 J jnl
A computational survey of candidate exonic splicing enhancer motifs in the model plant
BMC Bioinform.
Mihaela Pertea, Stephen M. Mount, Steven L. Salzberg
2007 J jnl
Comprehensive DNA Signature Discovery and Validation.
PLoS Comput. Biol.
Adam M. Phillippy, Jacquline A. Mason, Kunmi Ayanbule, Daniel D. Sommer, Elisa Taviani, Anwar Huq, Rita R. Colwell, Ivor T. Knight, Steven L. Salzberg
2007 J jnl
Minimus: a fast, lightweight genome assembler.
BMC Bioinform.
Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop
2006 J jnl
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.
Algorithms Mol. Biol.
Jonathan E. Allen, Steven L. Salzberg
1999 J jnl
Gene discovery in DNA sequences.
IEEE Intell. Syst.
Steven L. Salzberg