Chad Nusbaum

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. ncbi request reprint DNA sequence and analysis of human chromosome 8
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, Massachusetts 02141, USA
    Nature 439:331-5. 2006
  2. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
  3. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
  4. pmc Short-term genome evolution of Listeria monocytogenes in a non-controlled environment
    Renato H Orsi
    Department of Food Science, Cornell University, Ithaca, NY, USA
    BMC Genomics 9:539. 2008
  5. ncbi request reprint DNA sequence and analysis of human chromosome 18
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 437:551-5. 2005
  6. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael C Zody
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 440:671-5. 2006
  7. pmc Integrative analysis of the melanoma transcriptome
    Michael F Berger
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 20:413-27. 2010
  8. pmc Finished bacterial genomes from shotgun sequence data
    Filipe J Ribeiro
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Genome Res 22:2270-7. 2012
  9. pmc Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
  10. pmc Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell Guttman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:503-10. 2010

Detail Information

Publications56

  1. ncbi request reprint DNA sequence and analysis of human chromosome 8
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, Massachusetts 02141, USA
    Nature 439:331-5. 2006
    ..The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution...
  2. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
    ..More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine...
  3. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
    ..MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available...
  4. pmc Short-term genome evolution of Listeria monocytogenes in a non-controlled environment
    Renato H Orsi
    Department of Food Science, Cornell University, Ithaca, NY, USA
    BMC Genomics 9:539. 2008
    ..While a genome sequence for the 1988 food isolate has been reported, we sequenced the genomes of the 1988 human isolate as well as a human and a food isolate from the 2000 outbreak to allow for comparative genome analyses...
  5. ncbi request reprint DNA sequence and analysis of human chromosome 18
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 437:551-5. 2005
    ..This has important implications for the nature and roles of non-protein-coding sequence elements...
  6. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael C Zody
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 440:671-5. 2006
    ..Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome...
  7. pmc Integrative analysis of the melanoma transcriptome
    Michael F Berger
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 20:413-27. 2010
    ..Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types...
  8. pmc Finished bacterial genomes from shotgun sequence data
    Filipe J Ribeiro
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Genome Res 22:2270-7. 2012
    ..Cost and time requirements are thus dramatically reduced...
  9. pmc Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
    ..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
  10. pmc Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell Guttman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:503-10. 2010
    ..Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes...
  11. pmc Comprehensive comparative analysis of strand-specific RNA sequencing methods
    Joshua Z Levin
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 7:709-15. 2010
    ..Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms...
  12. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  13. pmc Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
    Moran Yassour
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 11:R87. 2010
    ..However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directional transcription in a dense genome...
  14. pmc High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    Sante Gnerre
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 108:1513-8. 2011
    ..The ALLPATHS-LG program is available at http://www.broadinstitute.org/science/programs/genome-biology/crd...
  15. pmc Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
    Michal Rabani
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:436-42. 2011
    ..Certain transcripts, including those encoding cytokines and transcription factors, mature faster. Our study provides a quantitative approach to study the integrative process of RNA regulation...
  16. pmc DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
    Michael C Zody
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Massachusetts 02142, USA
    Nature 440:1045-9. 2006
    ..Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome...
  17. pmc A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
    Manuel Garber
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:810-22. 2012
    ....
  18. pmc Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    Daniel Aird
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 12:R18. 2011
    ..Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate...
  19. pmc Quality scores and SNP detection in sequencing-by-synthesis systems
    William Brockman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 18:763-70. 2008
    ..We demonstrate good specificity in single reads, and excellent specificity (no false positives in 215 kb of genome) in high-coverage data...
  20. pmc How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
    Brian J Haas
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:734. 2012
    ..A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance...
  21. pmc Paired-end sequencing of Fosmid libraries by Illumina
    Louise J S Williams
    Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Res 22:2241-9. 2012
    ..Our Fosill-powered assembly of the mouse genome has an N50 scaffold length of 17.0 Mb, rivaling the connectivity (16.9 Mb) of the Sanger-sequencing based draft assembly...
  22. pmc Hybrid selection for sequencing pathogen genomes from clinical samples
    Alexandre Melnikov
    Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA
    Genome Biol 12:R73. 2011
    ..This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla...
  23. pmc A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
    Sheila Fisher
    Genome Sequencing Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Biol 12:R1. 2011
    ..Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol...
  24. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 478:476-82. 2011
    ..Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease...
  25. pmc Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
    Joshua Z Levin
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 10:R115. 2009
    ..Thus, targeted RNA-Seq produces an enhanced view of the molecular state of a set of "high interest" genes...
  26. doi request reprint Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
    Brian J Haas
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 461:393-8. 2009
    ..infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential...
  27. pmc Closing gaps in the human genome using sequencing by synthesis
    Manuel Garber
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 10:R60. 2009
    ..We present an approach for closing these gaps using 454 sequencing. As a proof of principle, we closed all three remaining non-structural gaps in chromosome 15...
  28. pmc High-resolution mapping of copy-number alterations with massively parallel sequencing
    Derek Y Chiang
    Broad Institute, Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
    Nat Methods 6:99-103. 2009
    ....
  29. pmc A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
    Niall J Lennon
    Genome Sequencing Platform, Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, MA 02141, USA
    Genome Biol 11:R15. 2010
    ..Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method...
  30. pmc ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
    Iain MacCallum
    Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
    Genome Biol 10:R103. 2009
    ..Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR)...
  31. pmc Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing
    Chad Nusbaum
    Broad Institute of Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA
    Nat Methods 6:67-9. 2009
    ..VAAL also pinpointed a single mutation between Vibrio cholerae genomes, identifying an antibiotic's site of action by identifying sequence differences between drug-sensitive strains and drug-resistant derivatives...
  32. doi request reprint Semiconductor-based DNA sequencing of histone modification states
    Christine S Cheng
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Commun 4:2672. 2013
    ..We leverage this method for epigenetic profiling of tumour tissues. ..
  33. pmc Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica
    Rays H Y Jiang
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Genet 9:e1003272. 2013
    ..parasitica...
  34. doi request reprint Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
    Andrew Kirby
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Genet 45:299-303. 2013
    ..These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing...
  35. pmc Pacific biosciences sequencing technology for genotyping and variation discovery in human data
    Mauricio O Carneiro
    Broad Institute of MIT and Harvard, Medical and Population Genetics Program, Cambridge, MA 02141, USA
    BMC Genomics 13:375. 2012
    ..With these potential advantages in mind, we here evaluate the utility of the Pacific Biosciences RS platform for human medical amplicon resequencing projects...
  36. pmc Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
    Georgia Giannoukos
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Biol 13:R23. 2012
    ..The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA...
  37. pmc ALLPATHS: de novo assembly of whole-genome shotgun microreads
    Jonathan Butler
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 18:810-20. 2008
    ..We describe a general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads...
  38. pmc Mammalian microRNAs: experimental evaluation of novel and previously annotated genes
    H Rosaria Chiang
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 24:992-1009. 2010
    ....
  39. ncbi request reprint The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003
    ..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
  40. doi request reprint Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach
    D Lee Taylor
    Institute of Arctic Biology, 311 Irving I Building, University of Alaska, Fairbanks, AK 99775, USA, Broad Institute, Massachusetts Institute of Technology, 320 Charles Street, Cambridge, MA 02141, USA
    Mol Ecol Resour 8:742-52. 2008
    ..Similar results were obtained using UniFrac phylogenetic comparisons. Together, these results suggest that the pig-tagged primers can be used to increase ecological inference in high throughput sequencing projects on fungi...
  41. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations...
  42. pmc Assembly of polymorphic genomes: algorithms and application to Ciona savignyi
    Jade P Vinson
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141 2023, USA
    Genome Res 15:1127-35. 2005
    ..Our method represented loci in a single copy more reliably and achieved greater contiguity than a conventional whole-genome assembly method...
  43. ncbi request reprint Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    J Graham Ruby
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 127:1193-207. 2006
    ..The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs)...
  44. pmc The complete genome and proteome of Mycoplasma mobile
    Jacob D Jaffe
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 14:1447-61. 2004
    ..The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage...
  45. pmc The genome of M. acetivorans reveals extensive metabolic and physiological diversity
    James E Galagan
    Whitehead Institute Center for Genome Research, Cambridge, Massachusetts 02141, USA
    Genome Res 12:532-42. 2002
    ..acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]..
  46. pmc Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
    ..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...
  47. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  48. ncbi request reprint Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
    Jörg Kämper
    Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, D 35043 Marburg, Germany
    Nature 444:97-101. 2006
    ..Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens...
  49. ncbi request reprint The genome sequence of the rice blast fungus Magnaporthe grisea
    Ralph A Dean
    Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nature 434:980-6. 2005
    ..The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation...
  50. pmc Uneven chromosome contraction and expansion in the maize genome
    Remy Bruggmann
    Munich Information Center for Protein Sequences MIPS, Institute for Bioinformatics, GSF Research Center for Environment and Health, D 85764 Neuherberg, Germany
    Genome Res 16:1241-51. 2006
    ..In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species...
  51. ncbi request reprint Human chromosome 11 DNA sequence and analysis including novel gene identification
    Todd D Taylor
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nature 440:497-500. 2006
    ..5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena...
  52. ncbi request reprint Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    Olivier Jaillon
    UMR 8030 Genoscope, CNRS and Université d Evry, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    Nature 431:946-57. 2004
    ....
  53. pmc Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements
    Josee Dostie
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 0103, USA
    Genome Res 16:1299-309. 2006
    ..5C should be widely applicable for large-scale mapping of cis- and trans- interaction networks of genomic elements and for the study of higher-order chromosome structure...
  54. pmc Mapping of Myxococcus xanthus social motility dsp mutations to the dif genes
    Hope Lancero
    Molecular Biology Institute and School of Dentistry, University of California Los Angeles, Los Angeles, CA 90095 1668, USA
    J Bacteriol 184:1462-5. 2002
    ..Another dsp allele contains a mutation in the sglK gene. About 36.6 kb around the dsp-dif locus was sequenced and annotated, and 50% of the genes are novel...
  55. pmc The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats
    Aikaterini Barbouti
    Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
    Am J Hum Genet 74:1-10. 2004
    ....
  56. pmc Structure and architecture of the maize genome
    Georg Haberer
    Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft für Strahlenforschung Research Center for Environment and Health, D 85764 Neuherberg, Germany
    Plant Physiol 139:1612-24. 2005
    ..Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes...