Tyler Alioto

Last updated June 1st 2011
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Tyler S. Alioto

Barcelona 08007 Spain


http://www.pcb.ub.es

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SUMMARY

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I have a combined background in molecular biology and genome bioinformatics, specializing in gene prediction algorithms and the computational analysis of splicing. I have consistently demonstrated my skills as a contributor to three gene annotation assessment projects as well as the ENCODE project.

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EDUCATION

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09/1992 - 06/1996

Stanford University

Stanford, CA

BS

  • Biological Sciences

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08/1998 - 05/2004

University of California at Berkeley

Berkeley, CA

PhD

  • Molecular and Cell Biology

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RESEARCH EXPERIENCE

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05/2010 - present
Group Leader Genome Annotation

Centro Nacional de Análisis Genómico (CNAG)

Barcelona, Spain
  • Gene structure annotation of newly sequenced genomes.
  • Functional annotation of gene models
  • Annotation of variation

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11/2004 - 05/2010
Senior Postdoctoral Researcher

Center for Genomic Regulation

Barcelona, Spain
  • Computational prediction of splicing, including U12-dependent splicing.
  • Evolution of splice sites and splice patterns.
  • Developed U12DB, a database of orthologous U12-type spliceosomal introns.
  • Development of GeneID 1.3 gene prediction software.
  • Implemented support for U12 intron prediction in conjunction with the ENCODE Gene Annotation Assessment Project (EGASP).
  • Implemented a gene prediction combiner (GenePC) based on GeneID code for the Nematode GASP (NGASP).
  • Implemented support for RNA-Seq data in conjunction with the RNA-Seq GASP (RGASP) workshop.
  • Analysis of next-generation sequencing data
  • Mapping (GEM,MAQ,etc.) and assembly (velvet) of RNA-seq/genomic reads from Illumina, Solid and Helicos platforms.
  • New gene/transcript isoform discovery and quantification.
  • Projects
  • INB (1/1/2009 -5/14/2010). "Desarrollo de métodos computacionales para el análisis de genomas eucariotes."

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08/1998 - 10/2004
Graduate Student/Postdoctoral Researcher

University of California

Berkeley, CA
Thesis Committee: John Ngai, Dan Rokhsar, Ehud Isacoff, Terry Speed
Dissertation Title: Molecular Diversity of Odorant Receptors in Zebrafish
Olfaction [Advisor: John Ngai]
  • Identified the complete repertoire of odorant receptors in zebrafish.
  • Verified receptor gene predictions through RT-PCR and in situ hybridizations in zebrafish.
  • Developed a suite of PERL scripts for the management of custom sequence databases, gene prediction automation, visualization of gene prediction results, and primer design.
Functional Genomics [Advisors: Josh Kaplan (Harvard University) and John Ngai]
  • Studied the extent and efficiency of trans-splicing in C. elegans and utilized this feature to amplify cell-type-specific mRNA for use with C. elegans DNA microarrays.
  • Organized and managed the production of whole genome DNA microarrays.
  • Employed functional genomic methods to identify genes required for the proper specification of interneuron-motorneuron synapses in C. elegans.
  • Led a team to design a Laboratory Information Management System (LIMS) in Oracle for DNA microarray production and experimental data storage and retrieval. Developed a JDBC compliant Java-based graphical user interface for the LIMS.

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09/1996 - 06/1998
Research Associate

Kyoto University, Institute for Chemical Research

Kyoto, Japan
[Advisors: Kunihiro Ueda, Seigo Tanaka]
  • Completed case control study (Alzheimer's Disease, Lewy Body Variant of AD, Parkinson's Disease, control) of microsatellite polymorphisms in the vicinity of the CYP2D locus on human Chromosome 22.
  • Identified candidate NACP/alpha-synuclein-interacting proteins.

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06/1996 - 09/1996
Research Associate

Kyoto Sangyo University, Faculty of Physics

Kyoto, Japan
[Advisor: Chikafusa Bessho]
  • Examined the long-term facilitation and habituation models of learning and memory in Aplysia californica.
  • Cloned and sequenced a putative adenylate cyclase-coupled serotonin receptor gene from Aplysia californica.

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04/1995 - 04/1996
Independent Research / Undergraduate Honors Thesis

Stanford University, Department of Biochemistry

Stanford, CA
[Advisor: Mark Krasnow]
  • Cloned and sequenced the Drosophila gene misguided, identifying it as a nuclear lamin.
  • Determined that mutations in misguided disrupt cell polarity and the morphology of terminal tracheal branches.

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06/1994 - 04/1996
Technician

Stanford University, Protein and Nucleic Acid Analysis Facility

Stanford, CA
[Supervisor: Alan Smith]
  • Synthesized peptides (Fmoc chemistry).
  • Microsequenced N-terminal peptides (Edman degradation). Assembled microsequences and performed homology searches.

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PUBLICATIONS

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Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigo R, Hubbard T, Harrow J. The origins, evolution and functional potential of alternative splicing in vertebrates.
Mol Biol Evol 2011, doi:10.1093/molbev/msr127

The International Aphid Genomics Consortium (incuding Alioto T). Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol 2010, 8(2): e1000313. doi:10.1371/
journal.pbio.1000313

Bovine Genome Sequencing and Analysis Consortium, Elsik CG et al. (incuding Alioto T). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324:522-8

Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R. Identifying protein-coding genes in genomic sequences. Genome Biology 2009, 10:201.

Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D; nGASP Consortium (including Alioto T), Stein LD. nGASP--the nematode genome annotation assessment project. BMC Bioinformatics 2008, 9:549.

Alioto T, Guigó R. "State of the art in eukaryotic gene prediction." Modern Genome Annotation. The Biosapiens Network, Ed. Frishman D, Valencia A. Springer: 2008, 7-40

Alioto TS, Guigó R, Picardi E, Pesole G. GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts. APBC 2008, 363-372

The ENCODE Project Consortium (incuding Alioto T). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007, 17:746-759.

Alioto TS, Ngai J. "Genomics of Odor Receptors in Zebrafish." The Senses - A Comprehensive Reference, Six-Volume Set. Ed. Basbaum, Bushnell, Smith, Beauchamp, Firestein, Dallos, Oertel, Masland, Albright, Kaas, Gardner. Elsevier Science & Technology: 2007.

Alioto TS, Ngai J. The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids. BMC Genomics 2006, 7:309.

Alioto, TS. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Res. 2006 Nov 1

Alioto TS, Ngai J. The odorant receptor repertoire of teleost fish. BMC Genomics 2005, 6:173.

Takehashi M, Alioto T, Stedeford T, Persad AS, Banasik M, Masliah E, Tanaka S, Ueda K. Septin 3 gene polymorphism in Alzheimer's disease. Gene Expr 2004, 11:263-70.

Guillemin K, Williams T, Krasnow MA. A nuclear lamin is required for cytoplasmic organization and egg polarity in Drosophila. Nat Cell Biol 2001, 3:848-51.

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PRESENTATIONS

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01/14/2008 - 01/17/2008
Talk: "GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts"

Asia Pacific Bioinformatics Conference (APBC)

Kyoto, Japan

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07/21/2007 - 07/25/2007
Poster: "GeneID as an Integrator of Evidence"

ISMB/ECCB

Vienna, Austria

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05/11/2005 - 05/15/2005
Poster: "Prediction of Genes with U12-Dependent Introns in the Human Genome"

The Biology of Genomes

Cold Spring Harbor Labs, NY

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10/05/2003 - 10/08/2003
Talk: "Zebrafish family C odorant receptors: from sequence to expression to function"

Helen Wills Neuroscience Institute Conference

Lake Tahoe, CA

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09/27/2003 - 09/30/2003
Poster: "Identification and Characterization of GPCR Family C Odorant Receptors in Zebrafish"

European Conference on Computational Biology (ECCB)

Paris, France

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11/2000
Poster: "Cell type specific gene expression profiles in C. elegans using splice leader mRNA tagging"

UC Berkeley Cell and Developmental Biology Retreat

Lake Tahoe, CA

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TEACHING EXPERIENCE

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03/09/2001
Instructor

University of Barcelona, Master of Traslational Medicine

Barcelona, Spain
  • Gave lecture on genome annotation

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03/11/2010
Plenary Lecture

I Workshop Massive Parallel Sequencing using 454

Barcelona, Spain
  • Computational annotation of functional regions in genome sequences.

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07/01/2008
Instructor

University of Málaga, Advanced Use of Bioinformatics Tools

Málaga, Spain
  • Taught tutorial on gene prediction

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12/19/2007
Instructor

University of Navarra, INB Roadshow

Pamplona, Spain
  • Taught tutorial on gene prediction

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11/26/2007 - 11/28/2007
Instructor

INB/IRB/EBI, Bioinformatics Resource Days

Barcelona, Spain
  • Taught tutorial on gene prediction and gene prediction workflows using web services

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10/22/2007
Instructor

Cold Spring Harbor Labs, Programming for Biologists

Cold Spring Harbor, NY
  • Taught module on the topic of gene prediction, including a tutorial on calculating log-likelihood scores for splice sites and coding potential.

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11/2005
Instructor

Universitat Pompeu Fabra, MSc. on Bioinformatics for Health Sciences

Barcelona, Spain
  • Developed and taught a module covering the topic of orthology.

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03/2005 - 04/2005
Supervisor

Universitat Pompeu Fabra, Bioinformatics (Health and Life Sciences program)

Barcelona, Spain
  • Supervised an undergraduate bioinformatics research project designed to teach basic PERL scripting and presentation of search results.

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08/2001 - 05/2002
Graduate Student Instructor

UC Berkeley, Department of Molecular and Cell Biology

Berkeley, CA
Brain, Mind and Behavior [Professor: David Presti]
Neurons and Networks [Professor: Frank Werblin]
  • Lectured on the olfactory system

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SKILLS

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Technologies: PERL, C, Java, SQL, PHP, HTML, AJAX

Languages:
  • English (native)
  • Spanish (Intermediate level speaking, reading and writing)
  • Catalan (Elementary level speaking, reading and writing: UPF Level 1A)
  • Japanese (Certificate of Japanese Proficiency Test 3rd Level)

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