Steven Salzberg

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 in Bioinformatics 14(2): 213-224 (2013)

Samuel V. Angiuoli, Steven L. Salzberg: Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27(3): 334-342 (2011)

Tanja Magoc, Steven L. Salzberg: FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21): 2957-2963 (2011)

Samuel V. Angiuoli, Julie C. Dunning Hotopp, Steven L. Salzberg, Herve Tettelin: Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinformatics 12: 272 (2011)

Mihaela Pertea, Geo Pertea, Steven L. Salzberg: Detection of Lineage-Specific Evolutionary Changes among Primate Species. BMC Bioinformatics 12: 274 (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 Research 39(Database-Issue): 11-14 (2011)

David R. Kelley, Steven L. Salzberg: Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics 11: 544 (2010)

Cole Trapnell, Lior Pachter, Steven L. Salzberg: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9): 1105-1111 (2009)

Adam M. Phillippy, Xiangyu Deng, Wei Zhang, Steven L. Salzberg: Efficient oligonucleotide probe selection for pan-genomic tiling arrays. BMC Bioinformatics 10: 293 (2009)

Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff, Steven L. Salzberg: OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Research 37(Database-Issue): 479-482 (2009)

Adam M. Phillippy, Kunmi Ayanbule, Nathan J. Edwards, Steven L. Salzberg: Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Research 37(Web-Server-Issue): 229-234 (2009)

Steven Salzberg, Tandy Warnow (Eds.): Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings. Lecture Notes in Computer Science 5724, Springer 2009, isbn 978-3-642-04240-9

Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee: Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads. PLoS Computational Biology 4(9) (2008)

Arthur L. Delcher, Kirsten A. Bratke, Edwin C. Powers, Steven Salzberg: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6): 673-679 (2007)

Mihaela Pertea, Stephen M. Mount, Steven L. Salzberg: A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics 8 (2007)

Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop: Minimus: a fast, lightweight genome assembler. BMC Bioinformatics 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 Computational Biology 3(5) (2007)

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: Gemina: A Web-Based Epidemiology and Genomic Metadata System Designed to Identify Infectious Agents. BioSurveillance 2007: 228-229

Mihaela Pertea, Steven Salzberg: Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding. WABI 2007: 208-215

Jonathan E. Allen, Steven L. Salzberg: A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms for Molecular Biology 1 (2006)

John Quackenbush, Steven Salzberg: It is time to end the patenting of software. Bioinformatics 22(12): 1416-1417 (2006)

Jonathan E. Allen, Steven Salzberg: JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21(18): 3596-3603 (2005)

Steven Salzberg, James A. Yorke: Beware of mis-assembled genomes. Bioinformatics 21(24): 4320-4321 (2005)

William H. Majoros, Mihaela Pertea, Arthur L. Delcher, Steven Salzberg: Efficient decoding algorithms for generalized hidden Markov model gene finders. BMC Bioinformatics 6: 16 (2005)

William H. Majoros, Steven Salzberg: An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinformatics 6: 193 (2005)

Mihai Pop, Adam M. Phillippy, Arthur L. Delcher, Steven Salzberg: Comparative genome assembly. Briefings in Bioinformatics 5(3): 237-248 (2004)

William H. Majoros, Mihaela Pertea, Steven Salzberg: TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20(16): 2878-2879 (2004)

Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven Salzberg: DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20(18): 3643-3646 (2004)

William H. Majoros, Steven Salzberg: An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinformatics 5: 206 (2004)

William H. Majoros, Mihaela Pertea, Corina Antonescu, Steven Salzberg: GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Research 31(13): 3601-3604 (2003)

Steven Salzberg: Genome Paleontology: Discoveries from Complete Genomes. BIOKDD 2003: 1

Mihai Pop, Steven Salzberg, Martin Shumway: Genome Sequence Assembly: Algorithms and Issues. IEEE Computer 35(7): 47-54 (2002)

Mihaela Pertea, Steven Salzberg: A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding. WABI 2002: 210-219

Baris E. Suzek, Maria D. Ermolaeva, Mark J. Schreiber, Steven Salzberg: A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics 17(12): 1123-1130 (2001)

Simon Kasif, Steven Salzberg, David L. Waltz, John Rachlin, David W. Aha: A Probabilistic Framework for Memory-Based Reasoning. Artif. Intell. 104(1-2): 287-311 (1998)

Steven Salzberg, Arthur L. Delcher, Kenneth H. Fasman, John Henderson: A Decision Tree System for Finding Genes in DNA. Journal of Computational Biology 5(4): 667-680 (1998)

John W. Sheppard, Steven Salzberg: A Teaching Strategy for Memory-Based Control. Artif. Intell. Rev. 11(1-5): 343-370 (1997)

Steven Salzberg: A method for identifying splice sites and translational start sites in eukaryotic mRNA. Computer Applications in the Biosciences 13(4): 365-376 (1997)

Esther M. Arkin, Patrice Belleville, Joseph S. B. Mitchell, David M. Mount, Kathleen Romanik, Steven Salzberg, Diane L. Souvaine: Testing Simple Polygons. Comput. Geom. 8: 97-114 (1997)

Steven Salzberg: On Comparing Classifiers: Pitfalls to Avoid and a Recommended Approach. Data Min. Knowl. Discov. 1(3): 317-328 (1997)

John Henderson, Steven Salzberg, Kenneth H. Fasman: Finding Genes in DNA with a Hidden Markov Model. Journal of Computational Biology 4(2): 127-141 (1997)

David G. Heath, Simon Kasif, S. Rao Kosaraju, Steven Salzberg, Gregory F. Sullivan: Learning nested concept classes with limited storage. J. Exp. Theor. Artif. Intell. 8(2): 129-147 (1996)

Steven Salzberg, Xin Chen, John Henderson, Kenneth H. Fasman: Finding Genes in DNA Using Decision Trees and Dynamic Programming. ISMB 1996: 201-210

Truxton Fulton, Simon Kasif, Steven Salzberg, David L. Waltz: Local Induction of Decision Trees: Towards Interactive Data Mining. KDD 1996: 14-19

Kathleen Romanik, Steven Salzberg: Testing Orthogonal Shapes. Comput. Geom. 5: 33-49 (1995)

Steven Salzberg: Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm. Journal of Computational Biology 2(3): 473-485 (1995)

Steven Salzberg, Arthur L. Delcher, David G. Heath, Simon Kasif: Best-Case Results for Nearest-Neighbor Learning. IEEE Trans. Pattern Anal. Mach. Intell. 17(6): 599-608 (1995)

John W. Sheppard, Steven Salzberg: Combining Genetic Algorithms with Memory Based Reasoning. ICGA 1995: 452-459

Truxton Fulton, Simon Kasif, Steven Salzberg: Efficient Algorithms for Finding Multi-way Splits for Decision Trees. ICML 1995: 244-251

Sreerama K. Murthy, Steven Salzberg: Lookahead and Pathology in Decision Tree Induction. IJCAI 1995: 1025-1033

Sreerama K. Murthy, Steven Salzberg: Decision Tree Induction: How Effective is the Greedy Heuristic? KDD 1995: 222-227

Sreerama K. Murthy, Simon Kasif, Steven Salzberg: A System for Induction of Oblique Decision Trees. J. Artif. Intell. Res. (JAIR) 2: 1-32 (1994)

Steven Salzberg: Book Review: C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc., 1993. Machine Learning 16(3): 235-240 (1994)

John Rachlin, Simon Kasif, Steven Salzberg, David W. Aha: Towards a Better Understanding of Memory-based Reasoning Systems. ICML 1994: 242-250

R. Scott Cost, Steven Salzberg: A Weighted Nearest Neighbor Algorithm for Learning with Symbolic Features. Machine Learning 10: 57-78 (1993)

Sreerama K. Murthy, Simon Kasif, Steven Salzberg, Richard Beigel: OC1: A Randomized Induction of Oblique Decision Trees. AAAI 1993: 322-327

Esther M. Arkin, Patrice Belleville, Joseph S. B. Mitchell, David M. Mount, Kathleen Romanik, Steven Salzberg, Diane L. Souvaine: Testing Simple Polygons. CCCG 1993: 387-392

David G. Heath, Simon Kasif, Steven Salzberg: Induction of Oblique Decision Trees. IJCAI 1993: 1002-1007

Steven Salzberg: A Nearest Hyperrectangle Learning Method. Machine Learning 6: 251-276 (1991)

Steven Salzberg, Arthur L. Delcher, David G. Heath, Simon Kasif: Learning with a Helpful Teacher. IJCAI 1991: 705-711

David G. Heath, Simon Kasif, S. Rao Kosaraju, Steven Salzberg, Gregory F. Sullivan: Learning Nested Concept Classes with Limited Storage. IJCAI 1991: 777-782

Steven Salzberg: Distance Metrics for Instance-Bsed Learning. ISMIS 1991: 399-408

Steven Salzberg: Nested Hyper-Rectangles for Exemplar-Based Learning. AII 1989: 184-201

Steven Salzberg: Heuristics for Inductive Learning. IJCAI 1985: 603-609

Steven Salzberg: Generating Hypotheses to Explain Prediction Failures. AAAI 1983: 352-355