Steven L. Salzberg

Publication Activity (10 Years)

Years Active: 1999-2023
Publications (10 Years): 17

Top Topics

Terms Of Classification Accuracy

Escherichia Coli

Top Venues

PLoS Comput. Biol.

Briefings Bioinform.

Publications

Alina Guo, Steven L. Salzberg, Aleksey V. Zimin
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies. PLoS Comput. Biol. 19 (3) (2023)
Ales Varabyou, Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea
Investigating open reading frames in known and novel transcripts using ORFanage. Nat. Comput. Sci. 3 (8) (2023)
Aleksey V. Zimin, Steven L. Salzberg
The SAMBA tool uses long reads to improve the contiguity of genome assemblies. PLoS Comput. Biol. 18 (2) (2022)
Christopher Pockrandt, Aleksey V. Zimin, Steven L. Salzberg
Metagenomic classification with KrakenUniq on low-memory computers. J. Open Source Softw. 7 (80) (2022)
Christopher Pockrandt, Martin Steinegger, Steven L. Salzberg
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools. Bioinform. 38 (5) (2022)
Alaina Shumate, Steven L. Salzberg
Liftoff: accurate mapping of gene annotations. Bioinform. 37 (12) (2021)
Markus J. Sommer, Steven L. Salzberg
Balrog: A universal protein model for prokaryotic gene prediction. PLoS Comput. Biol. 17 (2) (2021)
Steven L. Salzberg, Derrick E. Wood
Releasing the Kraken. Frontiers Bioinform. 1 (2021)
Jennifer Lu, Steven L. Salzberg
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes. PLoS Comput. Biol. 16 (12) (2020)
Aleksey V. Zimin, Steven L. Salzberg
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS Comput. Biol. 16 (6) (2020)
Florian P. Breitwieser, Steven L. Salzberg
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinform. 36 (4) (2020)
Florian P. Breitwieser, Jennifer Lu, Steven L. Salzberg
A review of methods and databases for metagenomic classification and assembly. Briefings Bioinform. 20 (4) (2019)
Richard Wilton, Sarah J. Wheelan, Alexander S. Szalay, Steven L. Salzberg
The Terabase Search Engine: a large-scale relational database of short-read sequences. Bioinform. 35 (4) (2019)
Jennifer Lu, Steven L. Salzberg
Removing contaminants from databases of draft genomes. PLoS Comput. Biol. 14 (6) (2018)
Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg, Aleksey V. Zimin
MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol. 14 (1) (2018)
Stefan Canzar, Steven L. Salzberg
Short Read Mapping: An Algorithmic Tour. Proc. IEEE 105 (3) (2017)
Jennifer Lu, Florian P. Breitwieser, Peter Thielen, Steven L. Salzberg
Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3 (2017)
Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg
GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinform. 29 (14) (2013)
Liliana Florea, Li Song, Steven L. Salzberg
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Research 2 (2013)
Steven L. Salzberg
Computational challenges in next-generation genomics. SSDBM (2013)
Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke
The MaSuRCA genome assembler. Bioinform. 29 (21) (2013)
Michael C. Schatz, Adam M. Phillippy, Daniel D. Sommer, Arthur L. Delcher, Daniela Puiu, Giuseppe Narzisi, Steven L. Salzberg, Mihai Pop
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings Bioinform. 14 (2) (2013)
Liliana Florea, Steven L. Salzberg
Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (5) (2013)
Samuel V. Angiuoli, Steven L. Salzberg
Mugsy: fast multiple alignment of closely related whole genomes. Bioinform. 27 (3) (2011)
Tanja Magoc, Steven L. Salzberg
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinform. 27 (21) (2011)
Samuel V. Angiuoli, Julie C. Dunning Hotopp, Steven L. Salzberg, Herve Tettelin
Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinform. 12 (2011)
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
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res. 39 (Database-Issue) (2011)
Mihaela Pertea, Geo Pertea, Steven L. Salzberg
Detection of Lineage-Specific Evolutionary Changes among Primate Species. BMC Bioinform. 12 (2011)
David R. Kelley, Steven L. Salzberg
Clustering metagenomic sequences with interpolated Markov models. BMC Bioinform. 11 (2010)
Adam M. Phillippy, Kunmi Ayanbule, Nathan J. Edwards, Steven L. Salzberg
Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Cole Trapnell, Lior Pachter, Steven L. Salzberg
TopHat: discovering splice junctions with RNA-Seq. Bioinform. 25 (9) (2009)
Adam M. Phillippy, Xiangyu Deng, Wei Zhang, Steven L. Salzberg
Efficient oligonucleotide probe selection for pan-genomic tiling arrays. BMC Bioinform. 10 (2009)
Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff, Steven L. Salzberg
OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res. 37 (Database-Issue) (2009)
Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee
Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads. PLoS Comput. Biol. 4 (9) (2008)
Mihaela Pertea, Stephen M. Mount, Steven L. Salzberg
. BMC Bioinform. 8 (2007)
Adam M. Phillippy, Jacquline A. Mason, Kunmi Ayanbule, Daniel D. Sommer, Elisa Taviani, Anwar Huq, Rita R. Colwell, Ivor T. Knight, Steven L. Salzberg
Comprehensive DNA Signature Discovery and Validation. PLoS Comput. Biol. 3 (5) (2007)
Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop
Minimus: a fast, lightweight genome assembler. BMC Bioinform. 8 (2007)
Jonathan E. Allen, Steven L. Salzberg
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms Mol. Biol. 1 (2006)
Steven L. Salzberg
Gene discovery in DNA sequences. IEEE Intell. Syst. 14 (6) (1999)