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Steven Salzberg
Person information
- affiliation: Johns Hopkins University
- affiliation: University of Maryland, College Park, USA
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2020 – today
- 2023
- [j66]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): 700-708 (2023) - [j65]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) - 2022
- [j64]Christopher Pockrandt
, Martin Steinegger
, Steven L. Salzberg
:
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools. Bioinform. 38(5): 1440-1442 (2022) - [j63]Christopher Pockrandt, Aleksey V. Zimin, Steven L. Salzberg:
Metagenomic classification with KrakenUniq on low-memory computers. J. Open Source Softw. 7(80): 4908 (2022) - [j62]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) - 2021
- [j61]Alaina Shumate
, Steven L. Salzberg
:
Liftoff: accurate mapping of gene annotations. Bioinform. 37(12): 1639-1643 (2021) - [j60]Steven L. Salzberg, Derrick E. Wood:
Releasing the Kraken. Frontiers Bioinform. 1 (2021) - [j59]Markus J. Sommer, Steven L. Salzberg:
Balrog: A universal protein model for prokaryotic gene prediction. PLoS Comput. Biol. 17(2) (2021) - 2020
- [j58]Florian P. Breitwieser, Steven L. Salzberg:
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinform. 36(4): 1303-1304 (2020) - [j57]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) - [j56]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)
2010 – 2019
- 2019
- [j55]Florian P. Breitwieser
, Jennifer Lu, Steven L. Salzberg
:
A review of methods and databases for metagenomic classification and assembly. Briefings Bioinform. 20(4): 1125-1136 (2019) - [j54]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): 665-670 (2019) - 2018
- [j53]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) - [j52]Jennifer Lu
, Steven L. Salzberg
:
Removing contaminants from databases of draft genomes. PLoS Comput. Biol. 14(6) (2018) - 2017
- [j51]Jennifer Lu, Florian P. Breitwieser, Peter Thielen
, Steven L. Salzberg
:
Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3: e104 (2017) - [j50]Stefan Canzar
, Steven L. Salzberg
:
Short Read Mapping: An Algorithmic Tour. Proc. IEEE 105(3): 436-458 (2017) - 2015
- [j49]Mihai Pop
, Steven Salzberg
:
Use and mis-use of supplementary material in science publications. BMC Bioinform. 16: 237:1-237:4 (2015) - 2013
- [j48]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): 213-224 (2013) - [j47]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): 1718-1725 (2013) - [j46]Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg
, James A. Yorke:
The MaSuRCA genome assembler. Bioinform. 29(21): 2669-2677 (2013) - [j45]Liliana Florea, Steven L. Salzberg
:
Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing. IEEE ACM Trans. Comput. Biol. Bioinform. 10(5): 1234-1240 (2013) - [c21]Steven L. Salzberg:
Computational challenges in next-generation genomics. SSDBM 2013: 2:1 - [i2]Liliana Florea, Li Song, Steven L. Salzberg
:
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Research 2: 188 (2013) - 2011
- [j44]Samuel V. Angiuoli
, Steven L. Salzberg
:
Mugsy: fast multiple alignment of closely related whole genomes. Bioinform. 27(3): 334-342 (2011) - [j43]Tanja Magoc, Steven L. Salzberg
:
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinform. 27(21): 2957-2963 (2011) - [j42]Samuel V. Angiuoli
, Julie C. Dunning Hotopp
, Steven L. Salzberg
, Hervé Tettelin:
Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinform. 12: 272 (2011) - [j41]Mihaela Pertea
, Geo Pertea, Steven L. Salzberg
:
Detection of Lineage-Specific Evolutionary Changes among Primate Species. BMC Bioinform. 12: 274 (2011) - [j40]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): 11-14 (2011) - 2010
- [j39]David R. Kelley, Steven L. Salzberg
:
Clustering metagenomic sequences with interpolated Markov models. BMC Bioinform. 11: 544 (2010)
2000 – 2009
- 2009
- [j38]Cole Trapnell, Lior Pachter
, Steven L. Salzberg
:
TopHat: discovering splice junctions with RNA-Seq. Bioinform. 25(9): 1105-1111 (2009) - [j37]Adam M. Phillippy
, Xiangyu Deng, Wei Zhang, Steven L. Salzberg
:
Efficient oligonucleotide probe selection for pan-genomic tiling arrays. BMC Bioinform. 10: 293 (2009) - [j36]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): 479-482 (2009) - [j35]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): 229-234 (2009) - [e1]Steven Salzberg, Tandy J. Warnow:
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 [contents] - 2008
- [j34]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) - 2007
- [j33]Arthur L. Delcher, Kirsten A. Bratke, Edwin C. Powers, Steven Salzberg
:
Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinform. 23(6): 673-679 (2007) - [j32]Mihaela Pertea
, Stephen M. Mount, Steven L. Salzberg
:
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinform. 8 (2007) - [j31]Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg
, Mihai Pop
:
Minimus: a fast, lightweight genome assembler. BMC Bioinform. 8 (2007) - [j30]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) - [c20]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 - [c19]Mihaela Pertea
, Steven Salzberg:
Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding. WABI 2007: 208-215 - 2006
- [j29]Jonathan E. Allen
, Steven L. Salzberg
:
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms Mol. Biol. 1 (2006) - [j28]John Quackenbush
, Steven Salzberg
:
It is time to end the patenting of software. Bioinform. 22(12): 1416-1417 (2006) - 2005
- [j27]Jonathan E. Allen
, Steven Salzberg
:
JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinform. 21(18): 3596-3603 (2005) - [j26]Steven Salzberg
, James A. Yorke:
Beware of mis-assembled genomes. Bioinform. 21(24): 4320-4321 (2005) - [j25]William H. Majoros, Mihaela Pertea, Arthur L. Delcher, Steven Salzberg
:
Efficient decoding algorithms for generalized hidden Markov model gene finders. BMC Bioinform. 6: 16 (2005) - [j24]William H. Majoros, Steven Salzberg
:
An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinform. 6: 193 (2005) - 2004
- [j23]Mihai Pop
, Adam M. Phillippy
, Arthur L. Delcher, Steven Salzberg
:
Comparative genome assembly. Briefings Bioinform. 5(3): 237-248 (2004) - [j22]William H. Majoros, Mihaela Pertea
, Steven Salzberg
:
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinform. 20(16): 2878-2879 (2004) - [j21]Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman
, Steven Salzberg
:
DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinform. 20(18): 3643-3646 (2004) - [j20]William H. Majoros, Steven Salzberg
:
An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinform. 5: 206 (2004) - 2003
- [j19]William H. Majoros, Mihaela Pertea, Corina Antonescu, Steven Salzberg
:
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res. 31(13): 3601-3604 (2003) - [c18]Steven Salzberg:
Genome Paleontology: Discoveries from Complete Genomes. BIOKDD 2003: 1 - 2002
- [j18]Mihai Pop
, Steven Salzberg
, Martin Shumway:
Genome Sequence Assembly: Algorithms and Issues. Computer 35(7): 47-54 (2002) - [c17]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 - 2001
- [j17]Baris E. Suzek
, Maria D. Ermolaeva, Mark J. Schreiber, Steven Salzberg
:
A probabilistic method for identifying start codons in bacterial genomes. Bioinform. 17(12): 1123-1130 (2001)
1990 – 1999
- 1999
- [j16]Steven L. Salzberg
:
Gene discovery in DNA sequences. IEEE Intell. Syst. 14(6): 44-48 (1999) - 1998
- [j15]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) - [j14]Steven Salzberg
, Arthur L. Delcher, Kenneth H. Fasman, John C. Henderson:
A Decision Tree System for Finding Genes in DNA. J. Comput. Biol. 5(4): 667-680 (1998) - 1997
- [j13]John W. Sheppard, Steven Salzberg
:
A Teaching Strategy for Memory-Based Control. Artif. Intell. Rev. 11(1-5): 343-370 (1997) - [j12]Steven Salzberg:
A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci. 13(4): 365-376 (1997) - [j11]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) - [j10]Steven Salzberg
:
On Comparing Classifiers: Pitfalls to Avoid and a Recommended Approach. Data Min. Knowl. Discov. 1(3): 317-328 (1997) - [j9]John C. Henderson
, Steven Salzberg
, Kenneth H. Fasman:
Finding Genes in DNA with a Hidden Markov Model. J. Comput. Biol. 4(2): 127-141 (1997) - 1996
- [j8]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) - [c16]Steven Salzberg, Xin Chen, John C. Henderson, Kenneth H. Fasman:
Finding Genes in DNA Using Decision Trees and Dynamic Programming. ISMB 1996: 201-210 - [c15]Truxton Fulton, Simon Kasif, Steven Salzberg, David L. Waltz:
Local Induction of Decision Trees: Towards Interactive Data Mining. KDD 1996: 14-19 - 1995
- [j7]Kathleen Romanik, Steven Salzberg
:
Testing Orthogonal Shapes. Comput. Geom. 5: 33-49 (1995) - [j6]Steven Salzberg
:
Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm. J. Comput. Biol. 2(3): 473-485 (1995) - [j5]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) - [c14]John W. Sheppard, Steven Salzberg:
Combining Genetic Algorithms with Memory Based Reasoning. ICGA 1995: 452-459 - [c13]Truxton Fulton, Simon Kasif, Steven Salzberg:
Efficient Algorithms for Finding Multi-way Splits for Decision Trees. ICML 1995: 244-251 - [c12]Sreerama K. Murthy, Steven Salzberg:
Lookahead and Pathology in Decision Tree Induction. IJCAI 1995: 1025-1033 - [c11]Sreerama K. Murthy, Steven Salzberg:
Decision Tree Induction: How Effective is the Greedy Heuristic? KDD 1995: 222-227 - 1994
- [j4]Sreerama K. Murthy, Simon Kasif, Steven Salzberg:
A System for Induction of Oblique Decision Trees. J. Artif. Intell. Res. 2: 1-32 (1994) - [j3]Steven Salzberg:
Book Review: C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc., 1993. Mach. Learn. 16(3): 235-240 (1994) - [c10]John Rachlin, Simon Kasif, Steven Salzberg, David W. Aha:
Towards a Better Understanding of Memory-based Reasoning Systems. ICML 1994: 242-250 - [i1]Sreerama K. Murthy, Simon Kasif, Steven Salzberg:
A System for Induction of Oblique Decision Trees. CoRR abs/cs/9408103 (1994) - 1993
- [j2]R. Scott Cost, Steven Salzberg
:
A Weighted Nearest Neighbor Algorithm for Learning with Symbolic Features. Mach. Learn. 10: 57-78 (1993) - [c9]Sreerama K. Murthy, Simon Kasif, Steven Salzberg, Richard Beigel:
OC1: A Randomized Induction of Oblique Decision Trees. AAAI 1993: 322-327 - [c8]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 - [c7]David G. Heath, Simon Kasif, Steven Salzberg:
Induction of Oblique Decision Trees. IJCAI 1993: 1002-1007 - 1991
- [j1]Steven Salzberg
:
A Nearest Hyperrectangle Learning Method. Mach. Learn. 6: 251-276 (1991) - [c6]Steven Salzberg, Arthur L. Delcher, David G. Heath, Simon Kasif:
Learning with a Helpful Teacher. IJCAI 1991: 705-711 - [c5]David G. Heath, Simon Kasif, S. Rao Kosaraju, Steven Salzberg, Gregory F. Sullivan:
Learning Nested Concept Classes with Limited Storage. IJCAI 1991: 777-782 - [c4]Steven Salzberg
:
Distance Metrics for Instance-Bsed Learning. ISMIS 1991: 399-408
1980 – 1989
- 1989
- [c3]Steven Salzberg
:
Nested Hyper-Rectangles for Exemplar-Based Learning. AII 1989: 184-201 - 1985
- [c2]Steven Salzberg:
Heuristics for Inductive Learning. IJCAI 1985: 603-609 - 1983
- [c1]Steven Salzberg:
Generating Hypotheses to Explain Prediction Failures. AAAI 1983: 352-355
Coauthor Index
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