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ORCIDSteven Salzberg
Steven L. Salzberg
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- 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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