Contact info

• Name: Larry Helseth, Ph.D.
• Email: helseth_at_uic.edu
• School: University of Illinois - Chicago
• Office: Proteomic and Informatic Services
  835 S. Wolcott Ave.
  MSB Room E-125
  Chicago, IL 60612
  
• Web site: http://proteomics.rrc.uic.edu/
• Comment: I was a postdoctoral research fellow developing proteomics software applications at DePaul from May 2006 until July 2007 when I joined the CBC Proteomics Core Facility at UIC as a Staff Informatician.

My Background

ACADEMIC BACKGROUND:

• B.S. in Chemistry with emphasis in Biochemistry from Texas Christian University (graduated with Honors in Chemistry)
• Ph.D. in Biochemistry from Northwestern University, 1981
• Thesis title: "Role of the telopeptides of collagen in directing in vitro self-assembly.".
• Publications: To find my earlier publications search PubMed using "helseth dl" (a key paper was published in Biopolymers, which was not indexed in Medline/PubMed at the time). In addition, I have authored numerous abstracts and several conference papers. Please contact me for a full list or reprints.
• Teaching Experience: I was an Assistant Professor at Northwestern University Dental School from 1984-1989, working in a basic science department (Oral Biology). I participated in teaching Dental School students basic histology and cellular/developmental biology of the oral cavity. I also taught graduate courses in inherited diseases, gene therapy and other topics. I also ran our department's graduate training program.
• Grant experience: I was awarded an F32 Postdoctoral Research Fellowship for my postdoctoral training experience. I was awarded an R01 research grant as a new faculty member. In addition, I served as both an ad hoc reviewer and as a regular member (3 year appointment) of the NIH/NIDR Special Grant Review Committee. I also contributed to several departmental grant submissions and participated as a committee member conducting site visits to review requests for center funding.
• Summary of ("Wet lab") Research & Laboratory Experience: I was engaged in protein biochemistry research for 13 years, receiving my Ph. D. in biochemistry for physical biochemical studies on the structural protein collagen. My thesis research involved studies of collagen fibril formation, and included preparation of large quantities of collagen peptide fragments, physical interaction studies, and modeling and calculations of specific molecular interactions. My postgraduate research involved the isolation and characterization of procollagen biosynthetic enzymes, cathepsins, collagenase and other neutral metalloproteinases.
• Laboratory Experience:
  • Tissue culture, including organ culture and primary isolates from human tissue, in vitro biocompatibility testing, effects of cytokines on enzyme production.
  • SDS polyacrylamide gel electrophoresis, Western Blotting, Isoelectric focusing and 2D electrophoresis
  • Various detection techniques, including fluorography, silver staining and antibody (Western Blot). Native gel separation of active enzymes followed by in situ detection by substrate proteolysis (Zymograms).
  • Ion exchange and gel filtration chromatography.
  • Affinity chromatography, including immunoaffinity, biospecific ligand affinity and dye matrix affinity chromatography.
  • HPLC (isocratic gel filtration) of macromolecules.
  • Antibody production (polyclonal), screening with ELISA, and preparation of monospecific antisera using affinity chromatography.
  • Enzyme purification from tissue homogenates and tissue culture media.
  • Enzyme assays, including spectrophotometric, radioisotopic, and "Zymogram" technique; inhibitor studies.
  • Selective chemical, radiochemical, and enzymatic modification of proteins.
  • Peptide isolation and characterization by chromatographic fractionation and amino acid analysis, biological activity testing in in vitro assays.
  • Physical characterization of proteins, including analytical ultracentrifugation, circular dichroism, difference spectroscopy, computerized structural analysis, conformation prediction and model building.
  • Subcellular fractionation.
  • Electron microscopy, thin section and negative stain, of biological tissues, subcellular fractions, and macromolecules.

INDUSTRY EXPERIENCE:

• I left Northwestern in 1989 to work at Baxter Healthcare. I held several positions over the 14 years I worked at Baxter. Initially I worked in their corporate library, searching on-line databases to support Baxter's R&D community, but that quickly morphed into an Internet development position. I was Baxter's first web author, helped launch & maintain Baxter's first external web site, published the annual report on-line for five years, and was Baxter's web master for half a year. I also developed enterprise software applications for collaboration, dynamic publishing of our main intranet site and developed numerous web applications for technical and business groups. I introduced JavaServer pages (JSP) for dynamic publishing at Baxter, developed a course and helped train over 75 Baxter web authors to use that platform for dynamic publishing. I also led a team that installed and configured an enterprise Java web server farm using commercial software, developed guidelines for migrating existing content from Tomcat to the commercial software platform, and helped implement many migrations before transitioning this role to Baxter's support staff. I also led a team that implemented an enterprise search solution using that new commercial Java web server farm. I left Baxter when I became tired of the "selling widgets on the web" approach and began looking for a way to merge my IT background with my biochemistry background and discovered ... bioinformatics!

Bioinformatics training:

• I enrolled in the University of Illinois' BiTmaP Bioinformatics training program starting in January 2006. My curriculum includes:
  • Introduction to Bioinformatics - Completed June 2006
  • Computational Genomics (Microarray data analysis) - Completed June 2006
  • Molecular Modeling for Bioinformatics - pending
  • Course details
  • Listen to an interview about the BiTmaP Bioinformatics Training Program on Genetic Engineering News' podcast. They discuss how much biology a computer scientist needs for bioinformatics and salaries (among other topics).
  • The program leads to 12 semester credits and a certificate in Bioinformatics from UIC.

Research Interests

• Proteomics
  • Developing software applications to extend work done at CTI by Kevin Drew and others
    • Quantitating Phosphorylation ratios
  • Analyzing FT MS data from SELDI experiments at the University of Chicago studying yeast cell cycle regulation by phosphorylation
  • Developing the next cool way to analyze MS data!
• Protein folding & macromolecular self-assembly
  • Prions & amyloidogenic proteins (implicated in mad cow disease, Huntington disease and Alzheimer's disease)
  • Collagen
• TBD

Recent Publications and Abstracts

• Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth, Jr., David S. Angulo, Timothy McMurry, David Jabon, Stephen B. H. Kent and Stephen J. Kron "Quantitation of phosphorylation using MALDI-TOF mass spectrometry" (submitted for publication, March 2007)

• Donald L. Helseth Jr, Don Wolfgeher, Kolbrun Kristjánsdóttir, Stephen Kron and David Sigfredo Angulo, "Computational Analysis of Mass Spectrometry Isotopic Data", DePaul CTI Research Symposium. Chicago, IL, May 5, 2007. (Abstract, Poster).

• Mariellen Dwyer, Victoria Huang, Donald L. Helseth Jr and David Sigfredo Angulo, "Using Screencasts to Demonstrate the IBG Desktop", DePaul CTI Research Symposium. Chicago, IL, May 5, 2007. (Abstract, Poster).

• Kolbrun Kristjiansdottir, Donald Wolfgeher, Donald L. Helseth Jr., Nick Lucius, David Sigfredo Angulo and Stephen J. Kron, "Phosphoprotein profiling: Cell cycle regulated phosphoproteins and complexes in yeast. American Association for Cancer Research Special Conference: Advances in Proteomics in Cancer Research, Amelia Island, Florida, February 27 - March 2, 2007 (Poster) (Nick was a graduate student I supervised whose independent research project led to a software tool that allowed our collaborator, Kolla, to analyze her data completely in 15 minutes compared with three days to manually analyze less than half the data.)

• Donald L. Helseth, Jr., Laurie Parker, Kolbrun Kristjánsdóttir, Kevin Drew, Don Wolfgeher, Alex Schilling and David Sigfredo Angulo, Developing Post-Translational Modification MS Tools, BioMedical Informatics Workshop. Chicago, IL. October 13, 2006. (Abstract, Poster)

• Gil D. Kwak, Donald L. Helseth, Jr., Alex Schilling and David Sigfredo Angulo, Hypothetical Sequence Analyzer, BioMedical Informatics Workshop. Chicago, IL. October 13, 2006. (Abstract, Poster)

• Donald L. Helseth, Jr., Laurie Parker, Kolbrun Kristjánsdóttir, Kevin Drew, Don Wolfgeher, Alex Schilling and David Sigfredo Angulo, Developing Post-Translational Modification MS Tools, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract, Poster)

• Gil D. Kwak, Donald L. Helseth, Jr., Alex Schilling and David Sigfredo Angulo, Hypothetical Sequence Analyzer, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract, Poster)

• Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth, Jr., David Sigfredo Angulo, Alex Schilling and Stephen J. Kron, Quantifying peptide phosphorylation using MALDI-TOF mass spectrometry, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract, Poster)

Editorial Review Service

• Reviewer for Connective Tissue Research and ACM Crossroads

Recommended Bioinformatics Reading

• In The Beginning Was The Worm: Finding the Secrets of Life in a Tiny Hermaphrodite, by Andrew Brown, Columbia University Press, 2003, ISBN: 0231131461 (hardcover); 2004, ISBN: 0743415981 (paperback).
  • Don't be put off by the title; this book describes research into the flatworm C. elegans that layed the groundwork in DNA sequencing and bioinformatics tools which helped launch the Human Genome Project. The main scientists who's work is discussed received the Nobel Prize in Physiology or Medicine in 2002. As one reviewer put it, "The human genome project was possible due to the 30-year struggle to decode the complete DNA of a nematode worm. This title tells of the remarkable characters whose struggle changed our approach to modern science, including: Sydney Bremmer, John Sulston, Bob Orvitz and Fred Sanger."
• The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World, by James Shreeve, 2004, ISBN: 0345433742 (paperback edition).
  • This book tells the other side of the Human Genome Project, the commercial side driven by Dr. Craig Venter of Celera (now a part of Applied Biosystems). It also discusses how his work with ESTs (expressed sequence tags) changed the way molecular biologists approached a genome. The book also discusses the bioinformatic challenges (developing shotgun techniques and algorithms to sequence the genome, storage issues, etc.) in the genome project. It's also a lively portrayal of the principal characters (with emphasis on the word "character") involved in this exciting phase of basic scientific research where bioinformatics emerged as a separate discipline.
• The O'Reilly Bioinformatics series
  • Developing Bioinformatics Computer Skills, by Per Jambeck & Cynthia Gibas, April 2001, ISBN: 1-56592-664-1
  • Beginning Perl for Bioinformatics, James Tisdall, October 2001, ISBN: 0-596-00080-4
  • Mastering Perl for Bioinformatics, James Tisdall, September 2003, ISBN: 0-596-00307-2
• Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, by Andreas D. Baxevanis & B. F. Francis Ouellette, 2004, ISBN: 0471478784
  • This book includes a great chapter by Lincoln Stein, M.D., Ph.D., who developed many of the basic Perl modules used in bioinformatics and Perl on the web. They also have several excellent chapters on proteomics, protein modeling, tools to study protein-protein interactions for systems biology and other topics.
• Introduction to BioInformatics, by Arthur M. Lesk, Oxford University Press, 2002. ISBN: 0199251967 (paperback).
• Introduction to Protein Architecture, by Arthur M. Lesk, Oxford University Press, 2001. ISBN: 0198504748 (paperback). An exceptionally well illustrated companion to the above book that emphasizes 3D displays of protein structure.
• Introduction to Genomics, by Arthur M. Lesk, Oxford University Press, 2007. ISBN: 978-0-19-929695-8 (paperback).

My Links (every site has to have some links, right?)

• Bioinformatics.org is a great resource and gateway to the Bioinformatics community at large. Their jobs list is a great way to find opportunities in the field and to find out what other groups are studying.
• BiTmaP is a great Midwest Bioinformatics training resource and one that helped introduce me to the field and to the breadth of projects underway at DePaul.
• Ph.D. Comics is a fun look at the life of a graduate student through the eyes of a graduate student (and his professor).

-- LarryHelseth - 11 Jul 2007
-- LarryHelseth - 06 May 2007
-- LarryHelseth - 27 Feb 2007
-- LarryHelseth - 09 Feb 2007
-- LarryHelseth - 29 Oct 2006
-- LarryHelseth - 04 Oct 2006
-- LarryHelseth - 05 Sep 2006
-- LarryHelseth - 29 Aug 2006