Download Dr. Todd Richmond, Director of Research Informatics Brief Bio: Dr

Dr. Todd Richmond, Director of Research Informatics
Brief Bio: Dr. Richmond holds a PhD degree from the Department of Genetics at
the University of Wisconsin-Madison. He was a Postdoctoral Fellow at the
Carnegie Institution of Washington, Department of Plant Biology at Stanford
University, studying families of genes involved in cell wall biosynthesis, and
working with the Arabidopsis Functional Genomics Consortium on various
microarray projects. Todd joined Roche NimbleGen in 2001, where he currently
leads the Research Informatics group, responsible for providing bioinformatics and
statistical support to the development and innovation teams. He has been a key
contributor to Roche NimbleGen's innovative probe design methodologies for
DNA capture, for both human and non-human products, and to the recent products
for studying epigenetics and RNA expression.
Dr. Richmond’s background is in genetics and bioinformatics, and he has over 20
years of experience with nucleic acids, including microarrays, RNA-seq, and target
enrichment technologies. He was the lead bioinformatics developer for CGH
product development at NimbleGen Systems (later Roche NimbleGen) since
development began in 2003. In his role as Manager and Director of Research
Informatics at Roche NimbleGen, he developed, and supervised the development,
of multiple algorithms for microarray analysis, including several for copy number
variation (CNV) analysis. He has lead numerous analysis projects for industry and
academic collaborations, and has participated in the analysis of a cohort of over
5000 individuals. He has also co-developed the algorithms and software for Roche
NimbleGen’s SNP detection technology and Sequence Capture technology. As
Director of Research Informatics, he has extensive knowledge of the current state
of the art for both SNP discovery/detection, next generation sequencing products
and peptide arrays. As part of Roche NimbleGen’s contract research program, he
lead analysis efforts for various projects, including SNP and indel discovery and
validation in various organisms, and transgene characterization, using the 454,
Illumina, and Ion Torrent sequencing platforms. He has multiple years of
experience in next generation sequencing projects, including the development of
analysis pipelines for QC, mapping, and SNP calling. He has worked on RNA-seq
projects, DNA and cDNA sequence capture projects in multiple organisms, and
methylation analysis via next generation sequencing. He has also designed a
number of peptide arrays, including whole proteome arrays, and conducted peptide
microarray analysis, including serum profiling and epitope discovery. In his role as
Director of Research Informatics, he has visibility on many projects being
conducted by our customers/collaborators around the world, including many
projects related to human disease, especially in the areas of cancer and pathogen
detection.
Selected Publications
Forsström, B., et al. Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays. Mol Cell
Proteomics. 2014 Jun;13(6):1585-97.
Evans, J., et al. Nucleotide polymorphism and copy number variant detection using exome capture and nextgeneration sequencing in the polyploid grass Panicum virgatum. Plant J. 2014 Sep;79(6):993-1008.
Li, Q., et al. Genetic perturbation of the maize methylome. Plant Cell. 2014 Dec;26(12):4602-16.
Li, Q., et al. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic
Acids Res. 2015 Mar 26. pii: gkv244. [Epub ahead of print]
Allum, F., et al. Characterization of functional methylomes by next-generation capture sequencing identifies novel
disease-associated variants. Nat Commun. 2015 May 29;6:7211.
Cao, H., et al. An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human
MHC region using targeted high-throughput sequencing. PLoS One: e69388 (2013).
de Ligt, J., et al. Detection of clinically relevant copy number variants with whole-exome sequencing. Hum Mutat
34(10): 1439-48 (2013)
Liu, S., et al. Changes in Genome Content Generated via Segregation of Non-allelic Homologs. Plant J. 72(3): 390-9
(2012).
Hong, et al. Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissuespecific transcription in Drosophila melanogaster. G3 2(8): 873-82.
Winfield, M.O., et al. Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol J. 10(6), 733-42
(2012).
Liu, P., et al. Identification of somatic mutation in non-small lung carcinomas using whole-exome sequencing.
Carcinogenesis 33(7):1270-6.
Baille, J.K., et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479(7374), 5347 (2011)
Fairfield, H., et al. Mutation discovery in mice by whole exome sequence. Genome Biol. 12(9), R86 (2011).
Haun, W.J., et al. The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference
Cultivar Williams 82. Plant Physiol. 155(2), 645-55 (2011).
Fu, Y., et al. High-resolution genotyping via whole genome hybridizations to microarrays containing long
oligonucleotide probes. PLoS One. 5(12), e14178 (2010).
Fu, Y., et al. Repeat subtraction-mediated sequence capture from a complex genome. Plant J. 62(5), 898-909 (2010).
Bainbridge, M.N., et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 11(6), R62 (2010).
Springer, N.M., et al. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence
variation (PAV) in genome content. PLoS Genet. 5(11), e1000734 (2009).
Walter, M.J., et al. Acquired copy number alterations in adult acute myeloid leukemia genomes. Proc Natl Acad Sci
U S A. 106(31), 12950-5 (2009).
Oda, M., et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number
analysis and optimization for limited cell numbers. Nucleic Acids Res. 37(12), 3829-39 (2009).
D'Ascenzo, M., et al. Mutation discovery in the mouse using genetically guided array capture and resequencing.
Mamm Genome. 20(7), 424-36 (2009).
Thompson, R. F., et al. An analytical pipeline for genomic representations used for cytosine methylation studies.
Bioinformatics 24, 1161–1167 (2008).
Cahan, P., et al. WUHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide
microarray data. Nucleic Acids Res 36, e41 (2008).
McCormick, M. R., Selzer, R. R. & Richmond, T. A. Methods in high-resolution, array-based comparative genomic
hybridization. Methods Mol Biol 381, 189–211 (2007).
Maydan, J. S., et al. Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative
genomic hybridization. Genome Res 17, 337–347 (2007).
Graubert, T. A., et al. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS
Genet 3, e3 (2007).
Gribble, S. M., et al. Ultra-high resolution array painting facilitates breakpoint sequencing. J Med Genet 44, 51–58
(2007).
Albert, T. J., et al. Direct selection of human genomic loci by microarray hybridization. Nat Methods 4, 903–905
(2007).
Birney, E., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE
pilot project. Nature 447, 799–816 (2007).
Dostie, J., et al. Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping
interactions between genomic elements. Genome Res 16, 1299–1309 (2006).
Sharp, A. J., et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the
human genome. Nat Genet 38, 1038–1042 (2006).
Rice, G. M., et al. Microdissection-based high-resolution genomic array analysis of two patients with
cytogenetically identical interstitial deletions of chromosome 1q but distinct clinical phenotypes. Am J Med
Genet A 140, 1637–1643 (2006).
Khulan, B., et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 16,
1046–1055 (2006).
Sabo, P. J., et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods
3, 511–518 (2006).
Strefford, J. C., et al. Complex genomic alterations and gene expression in acute lymphoblastic leukemia with
intrachromosomal amplification of chromosome 21. Proc Natl Acad Sci U S A 103, 8167–8172 (2006).
Urban, A. E., et al. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density
tiling oligonucleotide arrays. Proc Natl Acad Sci U S A 103, 4534–4539 (2006).
Selzer, R. R., et al. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using finetiling oligonucleotide array CGH. Genes Chromosomes Cancer 44, 305–319 (2005).
Kim, T. H., et al. A high-resolution map of active promoters in the human genome. Nature 436, 876–880 (2005).
Molla, M., Shavlik, J., Richmond, T. & Smith, S. A self-tuning method for one-chip snp identification. Proc IEEE
Comput Syst Bioinform Conf 69–79 (2004).
Wong, C. W., et al. Tracking the evolution of the SARS coronavirus using high-throughput, high-density
resequencing arrays. Genome Res 14, 398–405 (2004).
Nuwaysir, E., et al. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography.
Genome Research 12: 1749-55 (2002).
Richmond, T. A. & Somerville, C. R. Integrative approaches to determining CSL function. Plant Mol Biol 47, 131–
143 (2001).
Richmond, T.A. and Somerville, S. Chasing the dream: plant EST microarrays. Curr Opin. Plant Bio 3,108-116
(2000).
Richmond, TA. Higher plant cellulose synthases. Genome Biology 1(4): reviews3001.1-3001.6 (2000).
Schenk, P.M., et al. Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc Natl
Acad Sci USA 97(21):11655-60 (2000).