Close
  • Latest News
  • Cybersecurity
  • Big Data and Analytics
  • Cloud
  • Mobile
  • Networking
  • Storage
  • Applications
  • IT Management
  • Small Business
  • Development
  • Database
  • Servers
  • Android
  • Apple
  • Innovation
  • Blogs
  • PC Hardware
  • Reviews
  • Search Engines
  • Virtualization
Read Down
Sign in
Close
Welcome!Log into your account
Forgot your password?
Read Down
Password recovery
Recover your password
Close
Search
Menu
Search
  • Latest News
  • Cybersecurity
  • Big Data and Analytics
  • Cloud
  • Mobile
  • Networking
  • Storage
  • Applications
  • IT Management
  • Small Business
  • Development
  • Database
  • Servers
  • Android
  • Apple
  • Innovation
  • Blogs
  • PC Hardware
  • Reviews
  • Search Engines
  • Virtualization
More
    Home Latest News

      Diverse Sciences Propel Bioinformatics

      By
      Jessica Tenenbaum
      -
      August 20, 2004
      Share
      Facebook
      Twitter
      Linkedin

        At conferences in computational biology, speakers generally start with questions: “How many people in the room are biologists? Computer scientists? Other?” It can be hard to predict what kinds of experts will show up in the audience. This years Computational Systems Bioinformatics Conference, the third of its kind, was no exception.

        The CSB 2002 Web site described the conferences goal as bringing together “biology and computer science” experts. This year, the conference organizers hope to “promote a systems biology approach that links biology, computer science, mathematics, chemistry, physics, medicine and engineering.” Thats five new disciplines in two years. Even so, weve left out statistics.

        And contributing disciplines seem poised to become more nuanced, not less. The obvious methods for understanding precisely how molecular machinery yields breathing, thinking beings have already been tried, UC Berkeley Professor Eugene Myers said in a keynote speech. Cross-disciplinary conferences, and scientists, are needed for future discovery. Myers disputed the common notion that the completion of the human genome project has supplied the “parts list” needed to understand the mechanisms underlying human disease.

        The former vice president of Celera Genomics, who helped lead the companys human genome assembly effort, said Celeras and the public consortiums “completion” of the human genome project was a huge accomplishment. But he insisted that the parts list is still far from complete, reminding attendees that we are in fact still a long way from identifying the location of every gene, let alone identifying their functions.

        One is struck both by how far the field has come in a relatively short period of time, and also by how far it has yet to go. In the past 10 years, the numbers of sequences stored in public databases such as GenBank, SwissProt and even the Protein Data Bank all have increased exponentially. But as scientists understand all too well, data does not equal knowledge. Also, as experiments get faster, there is more room for error.

        Perhaps the most sobering presentation came from Patrik Dhaeseleer, a member of George Churchs lab at Harvard Medical School, who compared three high-throughput data sets of protein-protein interactions in yeast with disturbingly low overlap between sets and estimated false-positive rates as high as 90 percent. Such findings are discouraging: What scientist wants to risk pursuing an intriguing hypothesis only to find, perhaps years later, that the initial “evidence” was no more than a statistical fluke or an artifact of an experimental protocol?

        Help may come from unexpected quarters. The conference agenda itself highlighted how interdisciplinary this field is. Talks included a keynote speech by Benoit Mandelbrot, the founder of the division of mathematics known as fractal geometry. Other presentations included methods from high-throughput microscopy, text processing, data mining, artificial intelligence and more.

        Fusions of fields are not just expected but required. Stephen Wong of Harvard University explained how to use robotic automation and digital microscopy to screen thousands of cells simultaneously for, among other tasks, high-throughput drug screening.

        /zimages/5/28571.gifClick here to read about a committees efforts to develop bioinformatics standards.

        An example from Eran Segal of Stanford University showed what can happen when combining computer science, expression profiling, statistics and protein signaling. The projects start in a field of mathematics known as graph theory. Genes and proteins are modeled as nodes in a graph; edges between the nodes represent interactions in a biological system. Such systems may represent how cells in healthy and diabetic patients process glucose in the presence of insulin, or how cancerous and healthy cells respond to signals to stop dividing.

        Researchers plug in results from DNA microarray experiments as a data set for a form of probabilistic reasoning known as Bayesian networks. The experimental data let the researchers computationally refine the hypothetical interactions in an effort to figure out how genes and proteins regulate one another. And the results can be supported with additional microarray experiments.

        Science famously builds on the work that precedes it, and some researchers make sure that others work has as much leverage as possible. They focus on the body of literature that exists in free text form in public databases, such as MEDLINE. They use natural language processing and machine learning to ease efficient use of other scientists research. The tools may sort out ambiguous gene and protein names in article abstracts or enable more accurate literature searches.

        As experts from these diverse and previously unrelated fields continue to work together on new approaches and technologies, they will make discoveries never before possible. Despite all of the progress that has been made, or perhaps because of it, the potential to use ones own expertise to shape a scientific discipline has never been greater.

        Jessica D. Tenenbaum is a graduate student in biomedical informatics at Stanford University.

        /zimages/5/28571.gifCheck out eWEEK.coms Health Care Center at http://healthcare.eweek.com for the latest news, views and analysis of technologys impact on health care.

        Avatar
        Jessica Tenenbaum

        MOST POPULAR ARTICLES

        Android

        Samsung Galaxy XCover Pro: Durability for Tough...

        Chris Preimesberger - December 5, 2020 0
        Have you ever dropped your phone, winced and felt the pain as it hit the sidewalk? Either the screen splintered like a windshield being...
        Read more
        Cloud

        Why Data Security Will Face Even Harsher...

        Chris Preimesberger - December 1, 2020 0
        Who would know more about details of the hacking process than an actual former career hacker? And who wants to understand all they can...
        Read more
        Cybersecurity

        How Veritas Is Shining a Light Into...

        eWEEK EDITORS - September 25, 2020 0
        Protecting data has always been one of the most important tasks in all of IT, yet as more companies become data companies at the...
        Read more
        Big Data and Analytics

        How NVIDIA A100 Station Brings Data Center...

        Zeus Kerravala - November 18, 2020 0
        There’s little debate that graphics processor unit manufacturer NVIDIA is the de facto standard when it comes to providing silicon to power machine learning...
        Read more
        Apple

        Why iPhone 12 Pro Makes Sense for...

        Wayne Rash - November 26, 2020 0
        If you’ve been watching the Apple commercials for the past three weeks, you already know what the company thinks will happen if you buy...
        Read more
        eWeek


        Contact Us | About | Sitemap

        Facebook
        Linkedin
        RSS
        Twitter
        Youtube

        Property of TechnologyAdvice.
        Terms of Service | Privacy Notice | Advertise | California - Do Not Sell My Information

        © 2021 TechnologyAdvice. All Rights Reserved

        Advertiser Disclosure: Some of the products that appear on this site are from companies from which TechnologyAdvice receives compensation. This compensation may impact how and where products appear on this site including, for example, the order in which they appear. TechnologyAdvice does not include all companies or all types of products available in the marketplace.

        ×