Assignment 4

Assignment 4

take a look
a) a the website of our guest lecturer Debra S. Goldberg

b) explore the web and articulate one question for the guest lecturer

Lee Becker - I noticed that the Center for Computational Pharmacology has lots of natural language processing research relating to information extraction and knowledge bases for medical literature. Aside from being domain specific, how does this differ from the natural language processing research done in the Center for Spoken Language Research? Do these two departments ever collaborate?

David Gnabasik - Massive amounts of bioinformatic data, particularly 2-D gel electrophoresis and mass spectrometry data, are collected under experimental conditions that are very difficult to replicate. Under what kind of statistics can sound statistical inferences be made under this type of confounding experimental condition?

KyuHan Koh - On your web site, I found that you have worked on genomic networks and protein interactions. I've heard proteomics is the most promising field in bio-informatics and needs a cutting edge technology. How could computer science be utilized for that field?

Michael Otte - The sequencing of the human genome captivated the interest of the general public and opened the door to many new areas of research that have the potential to improve the lives of ordinary people. What are the current research topics in the field of bioinformatics that promise similar benefits to humankind in general?

Paul Marshall - Is there any bioinformatics research being done at CU which involves the use of high performance computing? If so, what? If not, why not?

Saroch Panichsakul - As far as I know, the research has been conducted in Harvard or CU-Denver. Is there any communication problem for us? What about labs, materials and the like?

Jinho Choi - In Natural Language Processing, we parse sentences mainly into two kinds of trees: one representing their syntactic structures, and the other representing their semantic structures. In Bioinformatics, I assume you perform about the same operations to analyze the data. If you do, what are the equivalences for sentences, syntactic structures, and semantic structures?

Dan Knights - There are tools in Linear Programming that can be very effective for solving certain graph problems, such as flow problems and TSPs. Are there any applications for Linear Programming in Computational Biology?

Guy Cobb - Is a protein built up "all at once", or does it happen that it is built incrementally? If so, how much is this a complicating factor in determining the final shape of the protein?

John Michalakes - The Computational Bioscience Program web site includes material on using computation to study structure and function of genes and proteins. Is there research at CU into genes and proteins as computers? What are your thoughts about so-called Molecular or "DNA" Computing? (

Yuli Liang - When you said "predicting the protein function ", do you need to know the protein structure in advance or just know the amino acid sequence is enough? How well is your method (or the other bio-informatics method in general) to have a successful prediction? Does computational bio-informatics comprehensively used in the pharmaceutical industry?

Yifei Jiang - You adopted machine learning methods in your research work in the field of computational biology. How did the machine learning methods work for your research?

Shumin Wu - I have heard of research in computational (spherical) geometry applied to modeling protein unfolding. What makes protein unfolding modeling such a difficult problem?

Ashok Basawapatna- You say something very interesting in your Research Statement: "Mathematicians (computer scientists) and biologists often think about problems in different ways. While some may find this an impediment to collaboration, I find that they complement one another, and I embrace diverse styles of attacking a problem." I love this interdisciplinary approach to research and would like to hear more about your experience with it in general. Here's a question if you need a prompt: Can you give examples of small specific problems you encountered that were Mathematical in nature and yet more conducive to a Biologist's thought process or vice versa, and in your point of view what characteristics of Biology or mathematics make these two disciplines complimentary?

Mohammad Al-Mutawa - How helpful was your strong background in biology in doing your research? and would it be possible for someone to be involved in the area of computational biology without any background in biology?

Keith Maull - When did it become apparent that the tools and techniques of computer science were necessary or could be applied to solving this set of problems in biology? How did such a relationship evolve and what's the history of such interdisciplinary interaction?

Nwanua Elumeze - What's with the tiger cub? No really; I've seen this picture on your site for almost two years now and I still feel like I'm missing something that might be glaringly obvious. For instance, is the milk a sythesized product? If it isn't, are there any evolutionary reasons why (cow) milk appears to be such a good cross-mammalian source of nutrition (i.e. why don't cats get indigestion from it)?

Jane Meyers - What are the similarities/relationships between a field such as health informatics and computational biology? In terms of interdisciplinary projects, what types of collaboration do you see present/developing between these areas?

Jeffrey LaMarche - Has your silence tactic ever failed? Have you developed any other tactics to engage a class more effectively?

Joel Pfeiffer - You state that it would be helpful to create classes in Computer Science that focus on concepts important to bioinformaticians. Would it also be helpful to teach classes in Biology that come from a more Computer Science point of view, to help interdisciplinary communication? I was curious because on your research page you point out that mathematicians and biologists think about problems differently, and perhaps that could help bridge the gap.

Holger Dick - While working with Bio-Scientists, do you get the feeling that they think of Bio-Informatics as an own discipline that they collaborate with? Or Bio-Informatics (and computer science in general) only "tools" that they need to do the stuff that is of interest to them?

Soumya Ghosh - How much of a biology background do you need to successfully work in bio-informatics. I get the feeling that to make a contribution of any significance at all, one needs to be pretty much a biologist.

Dola Saha - High Performance Scientific Computing has changed the scientific research domain. Do you use any of the techniques of parallel computing in your research?