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Publications

38. Current challenges in de novo plant genome sequencing and assembly
Schatz, MC, Witkowski, J, McCombie, WR (2012) Genome Biology. 12:243
37. De novo gene disruptions in children on the autism spectrum
Iossifov, I. et al. (2012) Neuron. 74:2 285-299
36. Rate of meristem maturation determines inflorescence architecture in tomato
Park, SJ, Jiang, K, Schatz, MC, Lippman, ZB (2011) PNAS. doi: 10.1073/pnas.1114963109
35. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
Schatz, MC, et al. (2011) Briefings in Bioinformatics. doi: 10.1093/bib/bbr074
34. GAGE: A critical evaluation of genome assemblies and assembly algorithms
Salzberg, SL, et al. (2011) Genome Research. doi: 10.1101/gr.131383.111
33. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis.
Donia, MS, et al. (2011) PNAS. doi: 10.1073/pnas.1111712108
32. Assemblathon 1: A competitive assessment of de novo short read assembly methods.
Earl, DA, et al. (2011) Genome Research. doi: 10.1101/gr.126599.111
31. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.
Bogdanove, AJ, et al. (2011) Journal of Bacteriology. doi:10.1128/JB.05262-11
30. Rapid Parallel Genome Indexing with MapReduce.
Menon, RK, Bhat, GP, Schatz, MC (2011) Proceedings of the 2nd International Workshop on MapReduce and its applications. HPDC'11, San Jose, CA. [preprint]
29. Quake: quality-aware detection and correction of sequencing reads.
Kelley, DR, Schatz, MC, Salzberg, SL (2010) Genome Biology. 11:R116
28. Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera.
Cornman, SR, Schatz, MC, et al. (2010) BMC Genomics. 11:602
27. Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis.
Dalloul, RA, et al. (2010) PLoS Biology. 8(9): e1000475.
26. The missing graphical user interface for genomics.
Schatz, MC. (2010) Genome Biology. 11:128
25. Design patterns for efficient graph algorithms in MapReduce.
Lin, J., Schatz, MC. (2010) Proceedings of the Eighth Workshop on Mining and Learning with Graphs Workshop (MLG-2010) .
24. Cloud Computing and the DNA Data Race.
Schatz, MC, Landmead, B, Salzberg, SL. (2010) Nature Biotechnology. 28:691-693
23. Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray.
Schatz, MC, Phillippy, AM, Gajer, P, DeSantis, TZ, Anderson, GL, Ravel, J. (2010) Applied and Environmental Microbiology.
22. Assembly of large genomes using second-generation sequencing.
Schatz, MC, Delcher, AL, Salzberg, SL. (2010) Genome Research, 20: 1165-1173.
21. Assembly complexity of prokaryotic genomes using short reads.
Kingsford, C, Schatz, MC, Pop, M (2010) BMC Bioinformatics 11:21.
20. Searching for SNPs with cloud computing.
Langmead, B, Schatz, MC, Lin, J, Pop, M, Salzberg, SL (2009) Genome Biology 10:R134.
19. Optimizing data intensive GPGPU computations for DNA sequence alignment.
Trapnell, C, Schatz, MC (2009) Parallel Computing 35(8-9):429-440.
18. Genomic Analyses of the Microsporidian Nosema ceranae, an Emergent Pathogen of Honey Bees.
Cornman, RS, Chen, YP, Schatz, MC, et al. (2009) PLoS Pathogens 5(6):e1000466.
17. A whole-genome assembly of the domestic cow, Bos taurus.
Zimin, AV, Delcher, AL, Florea, L, Kelley, DR, Schatz, MC, et al. (2009) Genome Biology 10:R42.
16. CloudBurst: Highly Sensitive Read Mapping with MapReduce.
Schatz, MC (2009) Bioinformatics 25:1363-1369.
15. Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps.
Desjardins, CA, et al. (2009) Genome Biology 9:R183.
14. Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop.
Suzuki, JY, et al. (2008) Tropical Plant Biology 1:293-309.
13. Revealing Biological Modules via Graph Summarization.
Navlakha, S, Schatz, M, Kingsford, C. (2008) Journal of Computational Biology 16(2): 253-264.
12. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
Salzberg, SL, Sommer DS, Schatz, MC, et al. (2008) BMC Genomics 9:204.
11. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
Ming, R, et al. (2008) Nature 452, 991-996.
10. Genome Assembly forensics: finding the elusive mis-assembly.
Phillippy, AM, Schatz, MC, Pop, M. (2008) Genome Biology 9:R55.
9. High-throughput sequence alignment using Graphics Processing Units.
Schatz, MC, Trapnell, C, Delcher, AL, Varshney, A. (2007) BMC Bioinformatics 8:474.
8. Evolution of genes and genomes on the Drosophila phylogeny.
Drosophila 12 Genomes Consortium. (2007) Nature Nov 8;450(7167):203-18.
7. Draft Genome of the Filarial Nematode Parasite Brugia malayi.
Ghedin, E, et al. (2007) Science 317(5845):1756-1760.
6. Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus.
Desjardins, CA, et al. (2007) BMC Microbiology 7:61
5. Genome Sequence of Aedes aegypti, a Major Arbovirus Vector.
Nene, V et al. (2007) Science 316(5832), 1718-1723.
4. Hawkeye: a visual analytics tool for genome assemblies.
Schatz, MC, Phillippy, AM, Shneiderman, B, Salzberg, SL. (2007) Genome Biology 8:R34.
3. Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis.
Carlton, JM, Hirt, RP, Silva, JC, Delcher, AL, Schatz, M, et al. (2007) Science 315 (5809), 207-212.
2. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.
Fouts, DE et al. (2005) PLoS Biology 3 (1):e15.
1. Automated correction of genome sequence errors.
Gajer, P, Schatz, M, Salzberg, SL. (2004) Nucleic Acids Research 32 (2):562-569.

Thesis

2. Scoring-and-Unfolding Trimmed Tree Assembler: Algorithms for Assembling Genome Sequences Accurately and Efficiently.
Narzisi, G. (2011) Ph.D. Disseration, Department of Computer Science, New York University
1. High Performance Computing for DNA Sequence Alignment and Assembly.
Schatz, M.C. (2010) Ph.D. Disseration, Department of Computer Science, University of Maryland


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Last Updated: Apr 27 2012 04:52:22 PM