Generating Hypotheses to Explain Prediction Failures. - Steven Salzberg (AAAI, 1983)

Heuristics for Inductive Learning. - Steven Salzberg (IJCAI, 1985)

Nested Hyper-Rectangles for Exemplar-Based Learning. - Steven Salzberg (AII, 1989)

Learning with a Helpful Teacher. - Steven Salzberg; Arthur L. Delcher; David G. Heath; Simon Kasif (IJCAI, 1991)

Distance Metrics for Instance-Bsed Learning. - Steven Salzberg (ISMIS, 1991)

A Nearest Hyperrectangle Learning Method. - Steven Salzberg (Mach. Learn., 1991)

OC1: A Randomized Induction of Oblique Decision Trees. - Sreerama K. Murthy; Simon Kasif; Steven Salzberg; Richard Beigel (AAAI, 1993)

Induction of Oblique Decision Trees. - David G. Heath; Simon Kasif; Steven Salzberg (IJCAI, 1993)

A Weighted Nearest Neighbor Algorithm for Learning with Symbolic Features. - R. Scott Cost; Steven Salzberg (Mach. Learn., 1993)

Towards a Better Understanding of Memory-based Reasoning Systems. - John Rachlin; Simon Kasif; Steven Salzberg; David W. Aha (ICML, 1994)

A System for Induction of Oblique Decision Trees. - Sreerama K. Murthy; Simon Kasif; Steven Salzberg (J. Artif. Intell. Res., 1994)

Book Review: C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc., 1993. - Steven Salzberg (Mach. Learn., 1994)

Combining Genetic Algorithms with Memory Based Reasoning. - John W. Sheppard; Steven Salzberg (ICGA, 1995)

Efficient Algorithms for Finding Multi-way Splits for Decision Trees. - Truxton Fulton; Simon Kasif; Steven Salzberg (ICML, 1995)

Lookahead and Pathology in Decision Tree Induction. - Sreerama K. Murthy; Steven Salzberg (IJCAI, 1995)

Decision Tree Induction: How Effective is the Greedy Heuristic? - Sreerama K. Murthy; Steven Salzberg (KDD, 1995)

Testing Orthogonal Shapes. - Kathleen Romanik; Steven Salzberg (Comput. Geom., 1995)

Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm. - Steven Salzberg (J. Comput. Biol., 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)

Finding Genes in DNA Using Decision Trees and Dynamic Programming. - Steven Salzberg; Xin Chen; John C. Henderson; Kenneth H. Fasman (ISMB, 1996)

Local Induction of Decision Trees: Towards Interactive Data Mining. - Truxton Fulton; Simon Kasif; Steven Salzberg; David L. Waltz (KDD, 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)

A Teaching Strategy for Memory-Based Control. - John W. Sheppard; Steven Salzberg (Artif. Intell. Rev., 1997)

A method for identifying splice sites and translational start sites in eukaryotic mRNA. - Steven Salzberg (Comput. Appl. Biosci., 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)

On Comparing Classifiers: Pitfalls to Avoid and a Recommended Approach. - Steven Salzberg (Data Min. Knowl. Discov., 1997)

Finding Genes in DNA with a Hidden Markov Model. - John C. Henderson; Steven Salzberg; Kenneth H. Fasman (J. Comput. Biol., 1997)

A Probabilistic Framework for Memory-Based Reasoning. - Simon Kasif; Steven Salzberg; David L. Waltz; John Rachlin; David W. Aha (Artif. Intell., 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)

Gene discovery in DNA sequences. - Steven L. Salzberg (IEEE Intell. Syst., 1999)

A probabilistic method for identifying start codons in bacterial genomes. - Baris E. Suzek; Maria D. Ermolaeva; Mark J. Schreiber; Steven Salzberg (Bioinform., 2001)

A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding. - Mihaela Pertea; Steven Salzberg (WABI, 2002)

Genome Sequence Assembly: Algorithms and Issues. - Mihai Pop; Steven Salzberg; Martin Shumway (Computer, 2002)

Genome Paleontology: Discoveries from Complete Genomes. - Steven Salzberg (BIOKDD, 2003)

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. - William H. Majoros; Mihaela Pertea; Corina Antonescu; Steven Salzberg (Nucleic Acids Res., 2003)

Comparative genome assembly. - Mihai Pop; Adam M. Phillippy; Arthur L. Delcher; Steven Salzberg (Briefings 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)

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. - William H. Majoros; Mihaela Pertea; Steven Salzberg (Bioinform., 2004)

An empirical analysis of training protocols for probabilistic gene finders. - William H. Majoros; Steven Salzberg (BMC Bioinform., 2004)

JIGSAW: integration of multiple sources of evidence for gene prediction. - Jonathan E. Allen; Steven Salzberg (Bioinform., 2005)

Beware of mis-assembled genomes. - Steven Salzberg; James A. Yorke (Bioinform., 2005)

Efficient decoding algorithms for generalized hidden Markov model gene finders. - William H. Majoros; Mihaela Pertea; Arthur L. Delcher; Steven Salzberg (BMC Bioinform., 2005)

A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. - Jonathan E. Allen; Steven L. Salzberg (Algorithms Mol. Biol., 2006)

It is time to end the patenting of software. - John Quackenbush; Steven Salzberg (Bioinform., 2006)

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; et al. (BioSurveillance, 2007)

Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding. - Mihaela Pertea; Steven Salzberg (WABI, 2007)

Identifying bacterial genes and endosymbiont DNA with Glimmer. - Arthur L. Delcher; Kirsten A. Bratke; Edwin C. Powers; Steven Salzberg (Bioinform., 2007)

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. - Mihaela Pertea; Stephen M. Mount; Steven L. Salzberg (BMC Bioinform., 2007)

Minimus: a fast, lightweight genome assembler. - Daniel D. Sommer; Arthur L. Delcher; Steven L. Salzberg; Mihai Pop (BMC Bioinform., 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)

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)

TopHat: discovering splice junctions with RNA-Seq. - Cole Trapnell; Lior Pachter; Steven L. Salzberg (Bioinform., 2009)

Efficient oligonucleotide probe selection for pan-genomic tiling arrays. - Adam M. Phillippy; Xiangyu Deng; Wei Zhang 039; Steven L. Salzberg (BMC Bioinform., 2009)

OperonDB: a comprehensive database of predicted operons in microbial genomes. - Mihaela Pertea; Kunmi Ayanbule; Megan Smedinghoff; Steven L. Salzberg (Nucleic Acids Res., 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)

Clustering metagenomic sequences with interpolated Markov models. - David R. Kelley; Steven L. Salzberg (BMC Bioinform., 2010)

Mugsy: fast multiple alignment of closely related whole genomes. - Samuel V. Angiuoli; Steven L. Salzberg (Bioinform., 2011)

FLASH: fast length adjustment of short reads to improve genome assemblies. - Tanja Magoc; Steven L. Salzberg (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)

Detection of Lineage-Specific Evolutionary Changes among Primate Species. - Mihaela Pertea; Geo Pertea; Steven L. Salzberg (BMC Bioinform., 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; et al. (Nucleic Acids Res., 2011)

Computational challenges in next-generation genomics. - Steven L. Salzberg (SSDBM, 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)

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)

The MaSuRCA genome assembler. - Aleksey V. Zimin; Guillaume Marçais; Daniela Puiu; Michael Roberts; Steven L. Salzberg; James A. Yorke (Bioinform., 2013)

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. - Liliana Florea; Li Song; Steven L. Salzberg (F1000Research, 2013)

Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing. - Liliana Florea; Steven L. Salzberg (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Use and mis-use of supplementary material in science publications. - Mihai Pop; Steven Salzberg (BMC Bioinform., 2015)

Bracken: estimating species abundance in metagenomics data. - Jennifer Lu; Florian P. Breitwieser; Peter Thielen; Steven L. Salzberg (PeerJ Comput. Sci., 2017)

Short Read Mapping: An Algorithmic Tour. - Stefan Canzar; Steven L. Salzberg (Proc. IEEE, 2017)

Removing contaminants from databases of draft genomes. - Jennifer Lu; Steven L. Salzberg (PLoS Comput. Biol., 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)

A review of methods and databases for metagenomic classification and assembly. - Florian P. Breitwieser; Jennifer Lu; Steven L. Salzberg (Briefings Bioinform., 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)

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. - Florian P. Breitwieser; Steven L. Salzberg (Bioinform., 2020)

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes. - Jennifer Lu; Steven L. Salzberg (PLoS Comput. Biol., 2020)

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. - Aleksey V. Zimin; Steven L. Salzberg (PLoS Comput. Biol., 2020)

Liftoff: accurate mapping of gene annotations. - Alaina Shumate; Steven L. Salzberg (Bioinform., 2021)

Releasing the Kraken. - Steven L. Salzberg; Derrick E. Wood (Frontiers Bioinform., 2021)

Balrog: A universal protein model for prokaryotic gene prediction. - Markus J. Sommer; Steven L. Salzberg (PLoS Comput. Biol., 2021)

PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools. - Christopher Pockrandt; Martin Steinegger; Steven L. Salzberg (Bioinform., 2022)

The SAMBA tool uses long reads to improve the contiguity of genome assemblies. - Aleksey V. Zimin; Steven L. Salzberg (PLoS Comput. Biol., 2022)

Metagenomic classification with KrakenUniq on low-memory computers. - Christopher Pockrandt; Aleksey V. Zimin; Steven L. Salzberg (J. Open Source Softw., 2022)

Investigating open reading frames in known and novel transcripts using ORFanage. - Ales Varabyou; Beril Erdogdu; Steven L. Salzberg; Mihaela Pertea (Nat. Comput. Sci., 2023)

JASPER: A fast genome polishing tool that improves accuracy of genome assemblies. - Alina Guo; Steven L. Salzberg; Aleksey V. Zimin (PLoS Comput. Biol., 2023)

A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies. - Xihao Li; Han Chen; Margaret Sunitha Selvaraj; Eric Van Buren; Hufeng Zhou; Yuxuan Wang 008; Ryan Sun; Zachary R. McCaw; Zhi Yu; Min-Zhi Jiang; Daniel DiCorpo; Sheila M. Gaynor; et al. (Nat. Comput. Sci., 2025)