publications posters press presentations


Publications

Preprints


P9. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
Nattestad, M, Goodwin, S, Ng, K, Baslan, T, Sedlazeck, FJ, Rescheneder, P, Garvin, T, Fang, H, Gurtowski, J, Hutton, E, Tseng, E, Chin, C, Beck, T, Sundaravadanam, Y, Kramer, M, Antoniou, E, McPherson, JD, Hicks, J, McCombie, WR, Schatz, MC (2017) bioRxiv doi: https://doi.org/10.1101/174938
P8. Accurate detection of complex structural variations using single molecule sequencing
Sedlazeck, FJ, Reschender, P, Smolka, M, Fang, H, Nattestad, M, von Haeseler, A, Schatz, MC (2017) bioRxiv https://doi.org/10.1101/169557
P7. Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution
Fang, H, Radhakrishnan, A, Siepel, A, Lyon, GJ, Schatz, MC (2017) bioRxiv https://doi.org/10.1101/156588
P6. Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library
Hulse-Kemp, AM, Maheshwari, S, Stoffel, K, Hill, TA, Jaffe, D, Williams, S, Weisenfeld, N, Ramakrishnan, S, Kumar, V, Shah, P, Schatz, MC, Church, DM, Van Deynze, A (2017) bioRxiv doi: https://doi.org/10.1101/152777
P5. LRSim: a Linked Reads Simulator generating insights for better genome partitioning
Luo, R, Sedlazeck, FJ, Darby, CA, Kelly, SM, Schatz, MC (2017) bioRxiv doi: https://doi.org/10.1101/103549
P4. SplitThreader: Exploration and analysis of rearrangements in cancer genomes
Nattestad, M, Alford, MC, Sedlazeck, FJ, Schatz, MC (2016) bioRxiv doi: https://doi.org/10.1101/087981
P3. Ribbon: Visualizing complex genome alignments and structural variation
Nattestad, M, Chin, CS, Schatz, MC (2016) bioRxiv doi: http://dx.doi.org/10.1101/082123
P2. The DOE Systems Biology Knowledgebase (KBase)
Arkin, AP, Steven, RL, Cottingham, RW, Maslov, S, Henry, CS, et al. (2016) bioRxiv doi: https://doi.org/10.1101/096354
P1. Third-generation sequencing and the future of genomics
Lee, H, Gurtowski, J, Yoo, S, Nattestad, M, Marcus, S, Goodwin, S, McCombie, WR Schatz, MC (2016) bioRxiv doi: http://dx.doi.org/10.1101/048603

2017


89. Hybrid assembly with long and short reads improves discovery of gene family expansions
Miller, JR, Zhou, P, Mudge, J, Gurtowski, J, Lee, H, Ramaraj, T, Walenz, BP, Liu, J, Stupar, RM, Denny, R, Song, L, Singh, N, Maron, LR, McCouch, SR, McCombie, WR, Schatz, MC, Tiffin, P, Young, KD, Silverstein, KAT (2017) BMC Genomics doi: 10.1186/s12864-017-3927-8. (Please cite this for ECTools hybrid error correction)
88. 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
Luo, R, Schatz, MC, Salzberg, SL (2017) GigaScience doi: https://doi.org/10.1093/gigascience/gix045
87. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
Feigin, ME, Garvin, T, Bailey, P, Waddell, N, Chang, DK, Kelley, DR, Shuai, S, Gallinger, S, McPherson, JD, Grimmond, SM, Khurana, E, Stein, LD, Biankin, AV, Schatz, MC, Tuveson, DA (2017) Nature Genetics doi:10.1038/ng.3861

86. GenomeScope: Fast reference-free genome profiling from short reads
Vurture, GW, Sedlazeck, FJ, Nattestad, M, Underwood, CJ, Fang, H, Gurtowski, J, Schatz, MC (2017) Bioinformatics doi: https://doi.org/10.1093/bioinformatics/btx153

85. Nanopore sequencing meets epigenetics
Schatz, MC (2017) Nature Methods 14, 347–348 (2017) doi:10.1038/nmeth.4240

84. Bioinformatics of DNA
Heath, LS, Bravo, HC, Caccamo, M, Schatz, MC (2017) Proceedings of the IEEE doi: 10.1109/JPROC.2017.2652958
See entire issue here

83. TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells
Pal, D, Pertot, A, Shirole, NH, Yao, Z, Anaparthy, N, Garvin, T, Cox, H, Chang, K, Rollins, F, Kendall, J, Edwards, L, Singh, VA, Stone, GC, Schatz, MC, Hicks, J, Hannon, G, Sordella, R (2017) eLife doi: http://dx.doi.org/10.7554/eLife.21615

2016


82. NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads
Amin, M.R., Skiena, S, Schatz, MC (2016) Proceedings of the Computational Advances in Bio and Medical Sciences (ICCABS) Conference. doi: 10.1109/ICCABS.2016.7802776
81. Indel variant analysis of short-read sequencing data with Scalpel
Fang, H, Grabowska, EA, Arora, K, Vacic, V, Zody, MC, Iossifov, I, ORawe, JA, Wu, Y, Jimenez-Barron, LT, Rosenbaum, J, Ronemus, M, Lee, Y, Wang, Z, Lyon, GJ, Wigler, M, Schatz, MC , Narzisi G (2015) Nature Protocols doi:10.1038/nprot.2016.150
80. The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation
Lemmon, ZH, Park, SJ, Jiang, K, Van Eck, J, Schatz, MC, Lippman ZB (2016) Genome Research doi: 10.1101/gr.207837.116
79. Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
Chin, CS, Peluso, P, Sedlazeck, FJ, Nattestad, M, Concepcion, GT, Clum, A, Dunn, C, O'Malley, R, Figueroa-Balderas, R, Morales-Cruz, A, Cramer, GR, Delledonne, M, Luo, C, Ecker, JR, Cantu, D, Rank, DR., Schatz, MC (2016) Nature Methods doi:10.1038/nmeth.4035
78. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing
Vembar, SS, Seetin, M, Lambert, C, Nattestad, M, Schatz, MC, Baybayan, P, Scherf, A, Smith, ML. (2016) DNA Research doi: 10.1093/dnares/dsw022
77. Assemblytics: a web analytics tool for the detection of variants from an assembly
Nattestad, M, Schatz, MC (2016) Bioinformatics doi: 10.1093/bioinformatics/btw369
76. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
Bombarely, A et al. (2016) Nature Plants doi:10.1038/nplants.2016.74
75. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
Vij, S et al. (2016) PLOS Genetics http://dx.doi.org/10.1371/journal.pgen.1005954
74. Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius
Rosenfeld, JA et al. (2016) Nature Communication doi:10.1038/ncomms10164

2015


73. The pineapple genome and the evolution of CAM photosynthesis
Ming, R, VanBuren, R, Man Wai, C, Tang, H, Schatz MC, et al. (2015) Nature Genetics doi:10.1038/ng.3435
72. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
Smolka M, Rescheneder P, Schatz MC, Haeseler AV, Sedlazeck FJ. (2015) Genome Biology 16:235 doi:10.1186/s13059-015-0803-1
71. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
Goodwin, S, Gurtowski, J, Ethe-Sayers, S, Deshpande, P, Schatz MC*, McCombie, WR* (2015) Genome Research doi: 10.1101/gr.191395.115
70. Biological data sciences in genome research
Schatz MC (2015) Genome Research 25: 1417-1422. doi: 10.1101/gr.191684.115
69. Metassembler: merging and optimizing de novo genome assemblies
Wences, AH Schatz MC (2015) Genome Biology 16:207. doi:10.1186/s13059-015-0764-4
68. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano
Wasik, KA, Gurtowski J, Zhou, X, Mendivil Ramos O, Delás MJ, Battistoni, G, El Demerdash, O, Faciatori, I, Vizoso, DV, Ladurner, P, Schärer, L, McCombie, WR, Hannon, GJ*, Schatz MC* (2015) PNAS doi: 10.1073/pnas.1516718112
67. Interactive analysis and assessment of single-cell copy-number variations.
Garvin, T, Aboukhalil, R, Kendall, J, Baslan, T, Atwal, GS, Hicks, J, Wigler, M, Schatz MC (2015) Nature Methods doi:10.1038/nmeth.3578
66. Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano
Zhou X, Battistoni G, Demerdash OE, Gurtowski J, Wunderer J, Falciatori I, Ladurner P, Schatz MC, Hannon GJ, Wasik KA (2015) RNA doi: 10.1261/rna.052456.115
65. Big Data: Astronomical or Genomical?
Stephens, Z, et al. (2015) PLOS Biology DOI: 10.1371/journal.pbio.1002195
64. Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis
MacColl E, et al. (2015) Molecular Phylogenetics and Evolution 86:1-7. doi:10.1016/j.ympev.2015.02.017
63. Extending reference assembly models
Church, DM, et al. (2015) Genome Biology 16:13 doi:10.1186/s13059-015-0587-3
62. The challenge of small-scale repeats for indel discovery
Narzisi, G, Schatz MC (2015) Frontiers in Bioengineering and Biotechnology 3:8. doi: 10.3389/fbioe.2015.00008

2014


61. Whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica
Schatz MC, Maron, LG, Stein, JC, Wences, AH, Gurtowski, J, Biggers, E, Lee, H, Kramer, M, Antoniou, E, Ghiban, E, Wright, MH, Chia, JM, Ware, D, McCouch, S, McCombie, WR (2014) Genome Biology 15:506 doi:10.1186/s13059-014-0506-z
60. SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips
Marcus, S, Lee, H, Schatz MC (2014) Bioinformatics doi: 10.1093/bioinformatics/btu756
59. The contribution of de novo coding mutations to autism spectrum disorder
Iossifov, I et al. (2014) Nature doi:10.1038/nature13908
58. Reducing INDEL calling errors in whole-genome and exome sequencing data
Fang, H, Narzisi, G, O'Rawe, J, Wu, Y, Rosenbaum, J, Ronemus, M, Iossifov, I, Schatz MC, Lyon, GJ (2014) Genome Medicine 6:89. doi:10.1186/s13073-014-0089-z
57. Accurate de novo and transmitted indel detection in exome-capture data using microassembly.
Narzisi, G, O'Rawe, JA, Iossifov, I, Fang, H, Lee, YH, Wang, Z, Wu, Y, Lyon, G, Wigler, M, Schatz MC (2014) Nature Methods doi:10.1038/nmeth.3069
56. High-coverage sequencing and annotated assemblies of the budgerigar genome
Ganapathy, G et al. (2014) GigaScience 3:11 doi:10.1186/2047-217X-3-11
55. Large-scale sequencing and assembly of cereal genomes using Blacklight
Blood, P, Marcus, S, Schatz MC (2014) XSEDE14 Atlanta GA, July 13-18. 2014 [preprint]
54. On Algorithmic Complexity of Biomolecular Sequence Assembly Problem
Narzisi, G, Mishra, B, Schatz MC (2014) Algorithms for Computational Biology Lecture Notes in Computer Science, Vol. 8542 [preprint]

2013


53. Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i
Saw JHW, Schatz M, Brown MV, Kunkel DD, Foster JS, et al. (2013) PLoS One 8(10): e76376. doi:10.1371/journal.pone.0076376
52. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Bradnam, KR. et al (2013) GigaScience 2:10 doi:10.1186/2047-217X-2-10
51. The advantages of SMRT sequencing
Roberts, RJ, Carneiro, MO, and Schatz, MC (2013) Genome Biology 14:405 doi:10.1186/gb-2013-14-6-405
50. The DNA60IFX Contest
Schatz, MC, Taylor, J and Schelhorn, S (2013) Genome Biology 14:124 doi:10.1186/gb-2013-14-6-124
49. The DNA Data Deluge
Schatz, MC and Langmead, B (2013) IEEE Spectrum July, 2013
48. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
Ming, R et al. (2013) Genome Biology 14:R41
47. Sixty years of genome biology
Doolittle, WF et al. (2013) Genome Biology 14:113
46. Aluminum tolerance in maize is associated with higher MATE1 gene copy number
Maron, LG et al. (2013) PNAS doi: 10.1073/pnas.1220766110

2012


45. Computational thinking in the era of big data biology
Schatz, MC (2012) Genome Biology 13:177
44. Answering the demands of digital genomics
Titmus, MA, Gurtowski, J, Schatz, MC (2012) Concurrency and Computation: Practice and Experience DOI: 10.1002/cpe.2925
43. De novo identification of 'heterotigs' towards accurate and in-phase assembly of complex plant genomes
Price J, et al. (2012) Proceedings of BIOCOMP'12 Las Vegas, NV. [preprint]
42. Genotyping in the Cloud with Crossbow
Gurtowski, J, Schatz, MC, Langmead, B (2012) Current Protocols in Bioinformatics 39:15.3.1-15.3.15
41. The rise of a digital immune system
Schatz, MC, Phillippy, AM (2012) GigaScience 1:4
40. Hybrid error correction and de novo assembly of single-molecule sequencing reads
Koren, S, Schatz, MC, Walenz, BP, Martin, J, Howard, JT, Ganapathy, G, Wang, Z, Rasko, DA, McCombie, WR, Jarvis, ED, Phillippy, AM (2012) Nature Biotechnology. doi:10.1038/nbt.2280
39. Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score
Lee, H, Schatz, MC (2012) Bioinformatics. 10.1093/bioinformatics/bts330
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

2011


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]

2010


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.

2009


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.

2008


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.

2007


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.

2006 & earlier


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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