Steve Chervitz (Trutane)

Steve Chervitz (Trutane)

Location
San Francisco Bay Area
Industry
Biotechnology

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Steve Chervitz (Trutane)'s Overview

Current
  • Founder at TeamHuman.org
  • Secretary, Webmaster, and Board member at FGED Society
  • Core developer at BioPerl Project
Past
  • Senior Computational Biologist at Omicia, Inc.
  • Bioinformatics Engineer, Informatics Dept. at Affymetrix
  • Core developer at Biodas Project
  • Bioinformatics Engineer, CIS Dept. at Affymetrix, Inc.
  • Software Engineer at Neomorphic
  • Postdoctoral Fellow, Botstein Lab at Stanford University

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Recommendations

1 person has recommended Steve

Connections

242 connections

Steve Chervitz (Trutane)'s Experience

Founder

TeamHuman.org

September 2009 – Present (2 years 9 months) Albany, CA

Secretary, Webmaster, and Board member

FGED Society

November 2002 – Present (9 years 7 months)

Core developer

BioPerl Project

August 1996 – Present (15 years 10 months)

Senior Computational Biologist

Omicia, Inc.

June 2010 – March 2012 (1 year 10 months)

Bioinformatics Engineer, Informatics Dept.

Affymetrix

January 2005 – June 2010 (5 years 6 months)

Core developer

Biodas Project

July 2004 – November 2008 (4 years 5 months)

Bioinformatics Engineer, CIS Dept.

Affymetrix, Inc.

November 2000 – December 2004 (4 years 2 months)

Software Engineer

Neomorphic

September 1998 – October 2000 (2 years 2 months)

Postdoctoral Fellow, Botstein Lab

Stanford University

1996 – 1998 (2 years)

Steve Chervitz (Trutane)'s Patents

  • METHOD, SYSTEM AND, COMPUTER SOFTWARE FOR EFFICIENT UPDATE OF PROBE ARRAY ANNOTATION DATA

    • United States Patent Application 20070134692
    • Filed 2007
    Inventors: Steve Chervitz (Trutane), Adam Tracy, Venu Valmeekam, Ron Shigeta, Ben Lai

    In one embodiment, a method of assigning transcripts to probe sets is described that comprises retrieving one or more data sets from one or more sources; generating one or more clusters using transcript data from the data sets; aligning one or more probe sequences to a representative sequence from one or more of the clusters; aligning the representative sequence to a genome sequence, wherein the genome sequence is annotated with probe location information; mapping the aligned probe sequences to the genome sequence using the alignment of the representative sequence and genome sequence; and computing a score using a number associated with the aligned probe sequences and a number associated with the probe location formation associated with a region of the genome sequence that corresponds to the aligned representative sequence.

  • Method, system, and computer software for providing a genomic web portal

    • United States Patent Application US2002/0183936
    • Filed May 2, 2002
    Inventors: Steve Chervitz (Trutane), David C. Kulp, Michael Siani-Rose, Shaw Sun, Ph.D., Ron Shigeta,

    A genomic portal system receives from a user a selection of one or more probe-set identifiers associated with one or more probe sets. The probe-set identifiers may be submitted in a batch file and may include one or more annotation terms. The system also correlates the user-selected probe-set identifiers with one or more biological sequences, and correlates the one or more biological sequences with a first set of probe sets. A network server identifies the first set of probe sets to the user. The genomic portal system may also receive from a user a selection of one or more probe-set identifiers associated with one or more probe sets, wherein the probe-set identifiers include one or more biological sequences. The system periodically update one or more local genomic databases, clusters the one or more biological sequences based on the local genomic databases, and provide the clustered data to a user.

Steve Chervitz (Trutane)'s Publications

  • The Genoviz Software Development Kit

    • BMC Bioinformatics
    • August 25, 2009
    Authors: Steve Chervitz (Trutane), Ed Erwin, , G.A. Helt, E. Blossom, S.G. Blanchard, C. Harmon, Ann Loraine

    The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities.

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