Steven Salzberg

According to our database, Steven Salzberg authored at least 85 papers between 1983 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.

Alina Guo, Steven L. Salzberg, Aleksey V. Zimin

PLoS Comput. Biol., March, 2023

Investigating open reading frames in known and novel transcripts using ORFanage.

Ales Varabyou, Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea

Nat. Comput. Sci., 2023

2022

Metagenomic classification with KrakenUniq on low-memory computers.

Christopher Pockrandt, Aleksey V. Zimin, Steven L. Salzberg

J. Open Source Softw., December, 2022

The SAMBA tool uses long reads to improve the contiguity of genome assemblies.

Aleksey V. Zimin, Steven L. Salzberg

PLoS Comput. Biol., 2022

PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools.

Christopher Pockrandt, Martin Steinegger, Steven L. Salzberg

Bioinform., 2022

2021

Balrog: A universal protein model for prokaryotic gene prediction.

Markus J. Sommer, Steven L. Salzberg

PLoS Comput. Biol., 2021

Releasing the Kraken.

Steven L. Salzberg, Derrick E. Wood

Frontiers Bioinform., 2021

Liftoff: accurate mapping of gene annotations.

Alaina Shumate, Steven L. Salzberg

Bioinform., 2021

2020

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.

Aleksey V. Zimin, Steven L. Salzberg

PLoS Comput. Biol., 2020

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes.

Jennifer Lu, Steven L. Salzberg

PLoS Comput. Biol., 2020

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.

Florian P. Breitwieser, Steven L. Salzberg

Bioinform., 2020

2019

The Terabase Search Engine: a large-scale relational database of short-read sequences.

Richard Wilton, Sarah J. Wheelan, Alexander S. Szalay, Steven L. Salzberg

Bioinform., 2019

A review of methods and databases for metagenomic classification and assembly.

Florian P. Breitwieser, Jennifer Lu, Steven L. Salzberg

Briefings Bioinform., 2019

2018

MUMmer4: A fast and versatile genome alignment system.

Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg, Aleksey V. Zimin

PLoS Comput. Biol., 2018

Removing contaminants from databases of draft genomes.

Jennifer Lu, Steven L. Salzberg

PLoS Comput. Biol., 2018

2017

Short Read Mapping: An Algorithmic Tour.

Stefan Canzar, Steven L. Salzberg

Proc. IEEE, 2017

Bracken: estimating species abundance in metagenomics data.

Jennifer Lu, Florian P. Breitwieser, Peter Thielen, Steven L. Salzberg

PeerJ Comput. Sci., 2017

2015

Use and mis-use of supplementary material in science publications.

Mihai Pop, Steven Salzberg

BMC Bioinform., 2015

2013

Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing.

Liliana Florea, Steven L. Salzberg

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.

Liliana Florea, Li Song, Steven L. Salzberg

F1000Research, 2013

The MaSuRCA genome assembler.

Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke

Bioinform., 2013

GAGE-B: an evaluation of genome assemblers for bacterial organisms.

Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg

Bioinform., 2013

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.

Michael C. Schatz, Adam M. Phillippy, Daniel D. Sommer, Arthur L. Delcher, Daniela Puiu, Giuseppe Narzisi, Steven L. Salzberg, Mihai Pop

Briefings Bioinform., 2013

Computational challenges in next-generation genomics.

Steven L. Salzberg

Proceedings of the Conference on Scientific and Statistical Database Management, 2013

2011

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.

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

Nucleic Acids Res., 2011

Detection of Lineage-Specific Evolutionary Changes among Primate Species.

Mihaela Pertea, Geo Pertea, Steven L. Salzberg

BMC Bioinform., 2011

Improving pan-genome annotation using whole genome multiple alignment.

Samuel V. Angiuoli, Julie C. Dunning Hotopp, Steven L. Salzberg, Hervé Tettelin

BMC Bioinform., 2011

FLASH: fast length adjustment of short reads to improve genome assemblies.

Tanja Magoc, Steven L. Salzberg

Bioinform., 2011

Mugsy: fast multiple alignment of closely related whole genomes.

Samuel V. Angiuoli, Steven L. Salzberg

Bioinform., 2011

2010

Clustering metagenomic sequences with interpolated Markov models.

David R. Kelley, Steven L. Salzberg

BMC Bioinform., 2010

2009

Insignia: a DNA signature search web server for diagnostic assay development.

Adam M. Phillippy, Kunmi Ayanbule, Nathan J. Edwards, Steven L. Salzberg

Nucleic Acids Res., 2009

OperonDB: a comprehensive database of predicted operons in microbial genomes.

Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff, Steven L. Salzberg

Nucleic Acids Res., 2009

Efficient oligonucleotide probe selection for pan-genomic tiling arrays.

Adam M. Phillippy, Xiangyu Deng, Wei Zhang, Steven L. Salzberg

BMC Bioinform., 2009

TopHat: discovering splice junctions with RNA-Seq.

Cole Trapnell, Lior Pachter, Steven L. Salzberg

Bioinform., 2009

2008

Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads.

Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee

PLoS Comput. Biol., 2008

2007

Comprehensive DNA Signature Discovery and Validation.

Adam M. Phillippy, Jacquline A. Mason, Kunmi Ayanbule, Daniel D. Sommer, Elisa Taviani, Anwar Huq, Rita R. Colwell, Ivor T. Knight, Steven L. Salzberg

PLoS Comput. Biol., 2007

Minimus: a fast, lightweight genome assembler.

Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop

BMC Bioinform., 2007

A computational survey of candidate exonic splicing enhancer motifs in the model plant <i>Arabidopsis thaliana</i>.

Mihaela Pertea, Stephen M. Mount, Steven L. Salzberg

BMC Bioinform., 2007

Identifying bacterial genes and endosymbiont DNA with Glimmer.

Arthur L. Delcher, Kirsten A. Bratke, Edwin C. Powers, Steven Salzberg

Bioinform., 2007

Using Protein Domains to Improve the Accuracy of <i>Ab Initio</i> Gene Finding.

Mihaela Pertea, Steven Salzberg

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Gemina: A Web-Based Epidemiology and Genomic Metadata System Designed to Identify Infectious Agents.

Lynn M. Schriml, Aaron Gussman, Kathy Phillippy, Samuel V. Angiuoli, Kumar Hari, Alan Goates, Ravi Jain, Tanja Davidsen, Anurhada Ganapathy, Elodie Ghedin, Steven Salzberg, Owen White, Neil Hall

Proceedings of the Intelligence and Security Informatics: Biosurveillance, 2007

2006

It is time to end the patenting of software.

John Quackenbush, Steven Salzberg

Bioinform., 2006

A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.

Jonathan E. Allen, Steven L. Salzberg

Algorithms Mol. Biol., 2006

2005

Efficient decoding algorithms for generalized hidden Markov model gene finders.

William H. Majoros, Mihaela Pertea, Arthur L. Delcher, Steven Salzberg

BMC Bioinform., 2005

Beware of mis-assembled genomes.

Steven Salzberg, James A. Yorke

Bioinform., 2005

JIGSAW: integration of multiple sources of evidence for gene prediction.

Jonathan E. Allen, Steven Salzberg

Bioinform., 2005

2004

An empirical analysis of training protocols for probabilistic gene finders.

William H. Majoros, Steven Salzberg

BMC Bioinform., 2004

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.

William H. Majoros, Mihaela Pertea, Steven Salzberg

Bioinform., 2004

DAGchainer: a tool for mining segmental genome duplications and synteny.

Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven Salzberg

Bioinform., 2004

Comparative genome assembly.

Mihai Pop, Adam M. Phillippy, Arthur L. Delcher, Steven Salzberg

Briefings Bioinform., 2004

2003

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders.

William H. Majoros, Mihaela Pertea, Corina Antonescu, Steven Salzberg

Nucleic Acids Res., 2003

Genome Paleontology: Discoveries from Complete Genomes.

Steven Salzberg

Proceedings of the 3nd ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2003), 2003

2002

Genome Sequence Assembly: Algorithms and Issues.

Mihai Pop, Steven Salzberg, Martin Shumway

Computer, 2002

A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding.

Mihaela Pertea, Steven Salzberg

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

2001

A probabilistic method for identifying start codons in bacterial genomes.

Baris E. Suzek, Maria D. Ermolaeva, Mark J. Schreiber, Steven Salzberg

Bioinform., 2001

1999

Gene discovery in DNA sequences.

Steven L. Salzberg

IEEE Intell. Syst., 1999

1998

A Decision Tree System for Finding Genes in DNA.

Steven Salzberg, Arthur L. Delcher, Kenneth H. Fasman, John C. Henderson

J. Comput. Biol., 1998

A Probabilistic Framework for Memory-Based Reasoning.

Simon Kasif, Steven Salzberg, David L. Waltz, John Rachlin, David W. Aha

Artif. Intell., 1998

1997

Finding Genes in DNA with a Hidden Markov Model.

John C. Henderson, Steven Salzberg, Kenneth H. Fasman

J. Comput. Biol., 1997

On Comparing Classifiers: Pitfalls to Avoid and a Recommended Approach.

Steven Salzberg

Data Min. Knowl. Discov., 1997

Testing Simple Polygons.

Esther M. Arkin, Patrice Belleville, Joseph S. B. Mitchell, David M. Mount, Kathleen Romanik, Steven Salzberg, Diane L. Souvaine

Comput. Geom., 1997

A method for identifying splice sites and translational start sites in eukaryotic mRNA.

Steven Salzberg

Comput. Appl. Biosci., 1997

A Teaching Strategy for Memory-Based Control.

John W. Sheppard, Steven Salzberg

Artif. Intell. Rev., 1997

1996

Learning nested concept classes with limited storage.

David G. Heath, Simon Kasif, S. Rao Kosaraju, Steven Salzberg, Gregory F. Sullivan

J. Exp. Theor. Artif. Intell., 1996

Local Induction of Decision Trees: Towards Interactive Data Mining.

Truxton Fulton, Simon Kasif, Steven Salzberg, David L. Waltz

Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96), 1996

Finding Genes in DNA Using Decision Trees and Dynamic Programming.

Steven Salzberg, Xin Chen, John C. Henderson, Kenneth H. Fasman

Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

1995

Best-Case Results for Nearest-Neighbor Learning.

Steven Salzberg, Arthur L. Delcher, David G. Heath, Simon Kasif

IEEE Trans. Pattern Anal. Mach. Intell., 1995

Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm.

Steven Salzberg

J. Comput. Biol., 1995

Testing Orthogonal Shapes.

Kathleen Romanik, Steven Salzberg

Comput. Geom., 1995

Decision Tree Induction: How Effective is the Greedy Heuristic?

Sreerama K. Murthy, Steven Salzberg

Proceedings of the First International Conference on Knowledge Discovery and Data Mining (KDD-95), 1995

Lookahead and Pathology in Decision Tree Induction.

Sreerama K. Murthy, Steven Salzberg

Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence, 1995

Efficient Algorithms for Finding Multi-way Splits for Decision Trees.

Truxton Fulton, Simon Kasif, Steven Salzberg

Proceedings of the Machine Learning, 1995

Combining Genetic Algorithms with Memory Based Reasoning.

John W. Sheppard, Steven Salzberg

Proceedings of the 6th International Conference on Genetic Algorithms, 1995

1994

Book Review: C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc., 1993.

Steven Salzberg

Mach. Learn., 1994

A System for Induction of Oblique Decision Trees.

Sreerama K. Murthy, Simon Kasif, Steven Salzberg

J. Artif. Intell. Res., 1994

Towards a Better Understanding of Memory-based Reasoning Systems.

John Rachlin, Simon Kasif, Steven Salzberg, David W. Aha

Proceedings of the Machine Learning, 1994

1993

A Weighted Nearest Neighbor Algorithm for Learning with Symbolic Features.

R. Scott Cost, Steven Salzberg

Mach. Learn., 1993

Induction of Oblique Decision Trees.

David G. Heath, Simon Kasif, Steven Salzberg

Proceedings of the 13th International Joint Conference on Artificial Intelligence. Chambéry, France, August 28, 1993

OC1: A Randomized Induction of Oblique Decision Trees.

Sreerama K. Murthy, Simon Kasif, Steven Salzberg, Richard Beigel

Proceedings of the 11th National Conference on Artificial Intelligence. Washington, 1993

1991

A Nearest Hyperrectangle Learning Method.

Steven Salzberg

Mach. Learn., 1991

Distance Metrics for Instance-Bsed Learning.

Steven Salzberg

Proceedings of the Methodologies for Intelligent Systems, 6th International Symposium, 1991

Learning with a Helpful Teacher.

Steven Salzberg, Arthur L. Delcher, David G. Heath, Simon Kasif

Proceedings of the 12th International Joint Conference on Artificial Intelligence. Sydney, 1991

1989

Nested Hyper-Rectangles for Exemplar-Based Learning.

Steven Salzberg

Proceedings of the Analogical and Inductive Inference, 1989

1985

Heuristics for Inductive Learning.

Steven Salzberg

Proceedings of the 9th International Joint Conference on Artificial Intelligence. Los Angeles, 1985

1983

Generating Hypotheses to Explain Prediction Failures.

Steven Salzberg

Proceedings of the National Conference on Artificial Intelligence, 1983