Bioinformatics & Computational Biology Bioinformatics & Computational Biology

BCB Laboratory Rotations
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The Purpose of Rotations

An important aspect of the BCB training program is participation in Research Exploration Rotations. Participation in four research exploration rotations is required for all first year BCB students. The rotations serve several purposes:

  • They are designed to help students choose their future major professors and to help professors choose graduate students;
  • They provide students an opportunity to actively participate in research projects of BCB faculty laboratories; and
  • They promote interaction and exchange of information among BCB research groups.

Selecting a Lab for Rotation

The selection of labs for rotations should be guided by the following:

  • At least one rotation must be a "wet" laboratory experience (usually in a biological science laboratory using molecular biological, biophysical or biochemical techniques).
  • At least one rotation must involve a strong computational component (usually in a research group in computer science, mathematics, physics, statistics or engineering).
  • Students are strongly encouraged to participate in rotations in at least two different departments.

Faculty interested in having students rotate through their labs this Fall and in Spring, 2010, are below. Faculty who had rotations in the past are also listed. Links to their home pages are provided so you can become familiar with their on-going research projects. Some also have brief descriptions of potential rotation projects you might be involved with if you rotate in their labs.

Information on the research interests and links to all BCB faculty member's webpages can be found on our website at: http://www.bcb.iastate.edu/faculty.html.

Rotation Expectations

Because rotations are necessarily brief, students are not usually able to "complete" a project, in either a biological or computational research group. Instead, during the research exploration rotation period, students should:

  • get to know the professor and the students and postdocs working in the research group;
  • learn as much as possible about the professor's research projects;
  • obtain "hands on" experience in one of the group's research projects;
  • attend research group meetings and journal club meetings; and
  • read reprints, reviews, and grant proposals related to the group's research.

It is appropriate for a rotating student to ask the rotation advisor whether the advisor would consider accepting him/her as a graduate student, but the final decision should not be made until all rotations have been completed.

Dates for Fall 2009/Spring 2010 Rotation Program

Please submit Rotation Planning Form
to the BCB Office by:

September 14

 

Dates for Rotations

Rotation #1 - September 16 through November 11

Rotation #2 - November 16 through January 11

Rotation #3 - January 13 through March 10
Please notify BCB Office of your
lab selection by:

April 6

Please file your Home Department
form by:

May 7

Forms to submit Rotation choices, evaluate your Rotations, and establish your Home Department

 

EXAMPLES OF POSSIBLE ROTATION PROJECTS

(A 2009 date appears after rotations which will be offered Fall 2009 and Spring 2010.)

Adam Bogdanove, Plant Pathology

Rotation projects available center on 1) Reprogramming of host gene expression by bacterial pathogens of rice and 2) Comparative genomics of host and tissue-specificity in bacterial interactions with plants. Contact him to talk. (8/18/08)

Volker Brendel  Genetics, Development and Cell Biology

  • Dr. Brendel's research - Algorithms for gene identification in genomic sequences; sequence alignment methods; transcriptional regulation; molecular phylogeny. He is accepting rotation students and invites interested students to visit his lab website for information about his research. (8/18/08)

Anne Bronikowski  Ecology, Evolution and Organismal Biology

  • Dr. Bronikowski's research - Our research focuses on the evolution of life history variation with an emphasis on the evolution of senescence (the functional decline in biochemical and physiological processes with age). We address fundamental questions in life history evolution using field studies, laboratory experiments (physiological and molecular), and mathematical modeling. Current research focuses on the evolution and ecology of senescence in 1) natural reptile populations; 2) laboratory populations of mice and 3) semi-natural populations of baboons
  • A rotation opportunity exists for Fall 2009 and Spring 2010 in the Bronikowski lab on either of two projects: The first project involves computational research on combining 454 (pyro) sequencing with Illumina (RNA-seq) sequencing to construct an enhanced transcriptome for snakes and assist in identifying up- and down- regulated genes in stress pathways.  The second project involves mathematical modeling of reproductive and mortality senescence in primates. (7/19/09)

    Dr. Bronikowski is accepting rotation students. Visit her lab website for information about her research and contact her for more details on the rotation opportunities in her lab.. (7/19/09)

Steven Cannon Agronomy and USDA ARS

Research in his lab includes:

  • Genome assembly and analysis in soybean and the model biological species Medicago truncatula. What are the parameters and mechanisms of genome change? This work is in collaboration several international groups and with the local USDA-ARS group that develops http://soybase.org .
  • Analysis of an early-diverging legume species, Chamaecrista fasciculata, to determine how a novel biological organ -- the structure that contains nitrogen-fixing bacteria -- that has evolved in the legume plant family. This project involves high-throughput phylogenetic analysis of gene families from several legume and non-legume species, and analysis of gene expression patterns in plant organs.
  • Development of software tools for translational genomics in the legumes (the bean and pea family). There are three sequenced genomes in the legumes, and dozens of domesticated or semi-domesticated legume species. The goals of the Legume Information System (LIS) are to integrate genetic and molecular data from multiple legume species and enables cross-species genomic, transcript and map comparisons. The software tools will help researchers and plant breeders leverage data-rich model plants to fill knowledge gaps across crop plant species and navigate diverse genomic and genetic data. Project site: http://www.comparative-legumes.org/ . This project is a collaboration with the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico. (8/27/09)

Hui-Hsien Chou  Genetics, Development and Cell Biology and Computer Science

  • Dr. Chou's research - Bioinformatics, Computational Biology and Artificial Life.

Project title: Microarray assisted genome assembly.
I am seeking rotation student(s) to help me conduct the preliminary study of a novel microarray assisted genome assembly method. When coupled with next generation sequencing machines, this new method could lead to genome assembly paradigm shift if successful. Ideal rotation students should have experience both with actual microarray experiment (i.e., comfortable with pipetters and centrifuges) and its data analysis. Send me email if you wish to learn more about this project.(7/19/09)

Project Title: Thermodynamic re-evaluation of existing microarrays may improve statistical discovery results.
Many microarrays are in use today, but some of them might include probes that are not well-designed. When data points reported by these inferior probes were included in the statistical data analysis, they actually degraded the resolution of the microarray and may lead false or weak discoveries. I am seeking rotation student(s) to help me test the novel idea that by thermodynamically reanalyze the probes on a microarray and cherry-pick only data points reported by reliable probes, we may improve the statistical discovery of microarrays without having to repeat the experiments. Ideal rotation students should have some experience with microarray data analysis and computer programming. (7/19/09)

 

Drena Dobbs  Genetics, Development and Cell Biology

Four BCB Rotation Projects - Fall 2008 - she also has some available for F09/S2010...

  • #1- Tools for cracking the protein-RNA recognition code: RNABindR & PRIDB

    Protein-RNA interactions play critical roles in many essential biological processes. We are developing tools to investigate the molecular recognition code that mediates protein-RNA interactions.

    Dobbs lab projects involve collaborations with Honavar & Jernigan groups, and include:

    1) design, implementation and evaluation of improved machine learning algorithms to predict RNA binding sites in proteins (& protein binding sites in RNAs); implement in our web-based server, RNABindR

    2) design and implementation of a new database, Protein-RNA Interface Database(PRIDB), a comprehensive resource for analysis, characterization and visualization of structurally-characterized RNA-protein complexes (database will be modeled after PPIDB, see URL below):

    Web Resources: RNABindR: http://bindr.gdcb.iastate.edu/RNABindR/

    PPIDB: http://ppidb.cs.iastate.edu/

    References: Terribilini M, Sander JD, Lee JH, Zaback P, Jernigan RL, Honavar V, Dobbs D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 2007 May 5; [Epub ahead of print]

    http://nar.oxfordjournals.org/cgi/content/full/gkm294v1

    Preferred skills: Some computer programming ability & basic biology

  • #2- Using structural information to re-engineer Zinc Finger DNA binding domains

    We are using both computational and wet-lab experiments to design DNA binding proteins that specifically recognize unique sequences in genomic DNA. Our server, Zinc Finger Targeter (ZiFiT), is designed to facilitate the modular design of ZFPs as well as the discovery of "rules" that govern protein-DNA interactions.

    Dobbs lab projects involve collaborations with Voytas, Miller and Honavar groups, and include:

    1) develop improved algorithms for site-specific ZFP design, e.g., by evaluating the use of structural information, in addition to sequence information

    2) analyze and develop algorithms for distinguishing ZFPs that bind DNA vs RNA vs protein

    3) develop high throughput DNA binding assays (e.g., SPR or microarray-based) to evaluate affinity & specificity of designed ZFPs

    Web Resources: http://bindr.gdcb.iastate.edu/ZiFiT

    http://www.zincfingers.org/

    Reference: Sander JD, Zaback P, Keith Joung J, Voytas DF, Dobbs D. Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res. 2007 May 25;

    http://nar.oxfordjournals.org/cgi/content/full/gkm349v1

    Preferred skills: Some computer programming ability & basic biology

  • #3- Predicting structure and functional sites in the human telomerase RNP complex

    Telomerase is a ribonucleoprotein (RNP) enzyme that adds telomeric DNA repeat sequences to the ends of linear chromosomes. The enzyme plays pivotal roles in cellular senescence and aging, and because it provides a telomere maintenance mechanism for ~90% of human cancers, it is a promising target for cancer therapy. Despite its importance, a high-resolution structure of the telomerase enzyme has been elusive.

    Dobbs lab projects involve collaborations with Ho, Honavar and Jernigan groups, and include:

    1) using threading and homology modeling to predict the structure of the telomerase reverse transcriptase enzyme, including its protein components (hTERT & dyskerin) and its RNA component (hTERC).

    2) using machine learning algorithms to predict which residues in the hTERT protein interact with DNA, RNA and other proteins.

     Web Resources: http://www.genlink.wustl.edu/teldb/tel.html

    http://www4.utsouthwestern.edu/cellbio/shay-wright/intro/sw_intro.html

    Reference: Blackburn, EH, Greider, CW, and Szostak, JW Telomeres and telomerase: the path from maize, Tetrahymena and yeast to human cancer & aging Nature Medicine 12, 1133 - 1138 (2006).

    http://www.nature.com/doifinder/10.1038/nm1006-1133

    Preferred skills: Some computer programming ability & basic biology

  • #4- Deciphering SNARE complex interactions in Arabidopsis (Bassham/Dobbs Rotation)

    Membrane fusion reactions within cells are catalyzed by members of the SNARE protein family and regulated by SM proteins. Expansion of the SNARE family in plants makes Arabidopsis a particularly attractive system for studying the specificity and functional specialization of SNARE family members. We are beginning to use computational modeling approaches, in conjunction with genetic and biochemical analyses, to investigate the mechanism and regulation of SNARE function and complex formation. Our overall goal is to understand how structural features of the SNARE proteins lead to specificity in membrane fusion pathways in vivo.

    This Bassham/Dobbs rotation project also involves collaborations with Honavar, Jernigan, and Ho groups. Specific projects include:

    1) computational structure prediction: homology modeling of helical bundle interactions required for SNARE-catalyzed membrane fusion and analysis/prediction of both structural and phenotypic effects of mutations on helix association and SNARE functional specificity

    2) machine learning: analysis and prediction of interactions between SM proteins and SNAREs in Arabidopsis; tools originally developed for prediction of MHC epitopes will be modified to investigate specific sequence and structural motifs that mediate specific SM-SNARE interactions

    Web Resources: PepMIL: http://ailab.cs.iastate.edu/PepMIL

    References: Chen Y, Y-K Shin and DC Bassham. 2005. YKT6 is a core constituent of membrane fusion machineries at the Arabidopsis trans-Golgi network. J Mol Biol 350:92-101.

    Preferred skills: Some computer programming ability & basic biology (8/15/08)

Karin Dorman  Statistics

Rohan Fernando Animal Science

  • Contact him to see if there is a rotation opportunity available. (8/15/08)

Xun Gu  Genetics, Development and Cell Biology and Computer Science

  • Contact him to ask about rotation opportunities. (8/4/09)

Mark Hargrove Biochemistry, Biophysics and Molecular Biology

  • May have a Rotation opportunity. Please contact him. (8/15/08)

Vasant Honavar  Computer Science

Richard Honzatko Biochemistry, Biophysics and Molecular Biology

  • May have a Rotation opportunity. Contact him. (8/15/08)

Fred Janzen Ecology, Evolution and Organismal Biology

  • May have a rotation opportunity. Contact him. (8/15/08)

Robert Jernigan Biochemistry, Biophysics and Molecular Biology

  • May have a Rotation opportunity. Contact him. (8/4/09)

Dennis Lavrov Ecology, Evolution and Organismal Biology

  • We are interested in understanding the early evolution of animals from both phylogenetic and functional perspectives.  Several rotation opportunities are available in our group:

    1) Phylogenetic reconstruction of animal relationships based on mitochondrial and cDNA data;
    2) Software development for the analysis of gene order data;
    3) Sponge cDNA exploration and annotation

    If you are interested in any of these projects or if you have some other ideas, send me an email (dlavrov@iastate.edu) and come to chat. (7/19/08)

Allen Miller, Plant Pathology

  • Bioinformatical opportunities in my lab involve RNA structure and function:  from structure of eukaryotic mRNAs in protein synthesis, to plant viral phylogenetic analysis.
  • RNA is a good macromolecule to do bioinformatics with because its structure is a lot easier to predict than protein, thanks to Watson-Crick base pairing. But thanks to non-Watson-Crick tertiary interactions, it's unpredictable enough to make it challenging (and a lot more fun than DNA). Also RNA can be an enzyme and the genetic material at the same time. How cool is that?

1.  We have discovered a novel structure in which the 5' and 3' untranslated regions (UTRs) of a plant virus mRNA must base pair (by forming "kissing stem-loops") to facilitate translation initiation.   Similar interactions may exist in some human viruses.   I'd like a bioinformatics student to search mRNA databases to seek host and viral mRNAs (from plants to humans) that may have similar long-distance base pairing interactions.   If successful, and backed up by experimental evidence, this could lead to a very significant publication.

2.  Another project involves building and curating a database of plant viral sequences and mining them for interesting stuff.   Papers guaranteed from this project (but not necessarily from the rotation alone).

3.  Also, work with a structural biology student to predict RNA 3D structure, based on phylogenetic conservation and known structural data. In my lab, enthusiasm, curiosity and drive are most important. (7/23/07)

Basil Nikolau  Biochemistry, Biophysics and Molecular Biology

  • Nikolau's research is focused on the functional genomics of metabolism; the discovery and charcaterization of new gene functions using system based approaches; integrating genomics, transcript profiling, proteomics and metabolomics. The lab has recently been funded by the National Science Foundation and plays a major role in CBiRC (www.cbirc.iastate.edu/) in developing biorenewable resources.  Several opportunities are available in the group, particularly in the development of bioinformatics tools for metabolomics research. If you are interested, drop me an email and come to chat. (7/15/09)

Krishna Rajan  Materials Science Engineering

* Machine learning for functional biomaterials: The work > requires the linking of molecular descriptors of polymeric systems to their functionality in terms of their interaction with biological molecules. The rotation will involve the student to aggressively test/develop a wide range of advanced data mining strategies to develop both classification and predictive models for materials design.

* Informatics for databases: This project involves setting up a web based system and associated GUI , using systems like "google pipes" to link data bases to data mining tools.

* Informatics for spectral and imaging data: Using data mining > methods to analyze spectroscopy and 3D imaging data.

All these projects will be well suited for a student who is willing to > look beyond their present interests adapt their interests in > computational biology and bioinformatics and their skills in machine > learning to biomaterials, physics, chemistry and engineering problems > in general. (7/15/09)

James Reecy Animal Science

  • Contact him to set up a rotation opportunity. He will provide projects for publication on this page, soon. Watch for them. (8/22/08)

Guang Song Computer Science

Our research goals are to understand the mechanism of biological systems and functions, especially the dynamic processes of how they take place. We are interested in studying: how proteins fold; ligand migration pathways; how proteins change conformations upon ligand binding, to name a few. We design computational models and simulation programs to study, simulate, and understand biological processes. Here are some possible projects:

  • Protein Dynamics In this project, you will have a chance to study the
    effects of crystal packing on protein dynamics using elastic network models.
    This will be an extension of work I did on vGNM model (Journal of Molecular
    Biology. Vol. 369, pp. 880-93, 2007). Specifically, you will investigate how
    crystal packing may suppress some internal vibrations of a protein molecule
    and influence its external rigid body motion within the crystal environment.
  • Allostery communication - How proteins make conformation changes upon ligand
    binding? In this project, the student will use several possible models to
    study the conformation changes in proteins, and how the conformation change at
    one site is communicated to a distant site.
  • Molecular Dynamics simulations one interesting project would be to use MD
    simulation to study protein transition pathways. This is an important topic
    since much can be learned about a proteins functional mechanism if we know
    its transition pathways. (8/4/09)

Xueyu Song  Chemistry

  • I anticipate I can take one rotational student with chemistry background. I also have the grant money to support the student if s/he would like to work on our project on the theory of protein crystallization. (8/15/08)

Alex Travesset  Physics

  • I have an opening for a graduate student and/or a rotation student on computational studies of different families of GTPases proteins with phospholipids (more concretely, phosphoinositides) in cell membranes. The study will also include a characterization of the dynamics of the signalling pathways that result from such interactions. Interested students should not hesitate to contact me at: trvsst@ameslab.gov (8/15/09)

Christopher Tuggle  Animal Science

  • Dr. Tuggle's research - Genomic and molecular genetic approaches to understanding the control of gene expression; bioinformatics analysis of microarray data to find the transcriptional response to infection, in developmental processes, and in appetite control. He is accepting BCB students for rotations, to work on one of the following rotation projects that are part of collaborative group (Tuggle, Honavar, Dekkers, Nettleton, Anderson) efforts in functional genomics that includes a full-time programmer and several graduate students:

    1) We are developing a database and associated tools to store and analyze data from approximately 150 current and 200 additional future Affymetrix Genechip experiments. We need help to develop the PHP/Java scripting for visualization and querying the database to pull out biologically relevant answers.

    2) We are also developing a web interface between the above database and on-campus and off-campus users of our Affymetrix data. We need someone to contribute to improvements in the PHP/Java to database interface, especially in streamlining and improving the useability of the interface for users.

    Please email him at cktuggle@iastate.edu or phone 515-294-4252 for further information. (8/8/07)

Nicole Valenzuela, Ecology, Environment, and Organismal Biology

  • My research program focuses on the integrative study of the ecological (proximate) and evolutionary (ultimate) processes that explain the origin and persistence of sex determining mechanisms in vertebrates. This integrative approach requires investigating the development of the sexual phenotype from several perspectives spanning classical ecology to modern evolutionary and ecological genomics, and at several levels of biological organization. See my website for more information on our research areas ( http://www.public.iastate.edu/~nvalenzu/). At the moment, rotation opportunities in my lab include the bioinformatic analysis of multiple genes related to sex differentiation across turtles and other taxa. Interested students with computational skills can contact me for further details. (8/15/08)

Steve Whitham  Plant Pathology

My research program involves the functional genomics analysis of plant-microbe interactions. The projects that we have integrate genomic sequence information, novel high throughput functional genomics tools for soybean, extensive mRNA expression profiling data sets, and massively parallel sequencing to identify the regulatory networks that control responses of soybean plants to environmental stresses.

We have several goals including:

  • Identification of promoter elements that regulate defense gene networks
  • Characterization and functional analysis of transcription factor families associated with defense gene networks
  • Assembly and annotation of 454 sequence from plant pathogens or infected plant tissues
  • Identification of pathogen proteins that modify the functions of plant proteins
  • Integrating information on sequence, gene expression, and function (based on experimentation) into a database

Students are encouraged to contact me by email or phone to discuss possible rotation projects. (8/15/08)

Roger Wise  Plant Pathology

  • Research in the Wise laboratory is focused on the functional analysis of important agronomic genes in cereal crops. We are actively involved in high-throughput GeneChip studies to analyze the interactions among plants and plant pathogens. Visit his website and these: http://wiselab.org/, http://barleybase.org/, and http://plexdb.org/ to learn more about his research. (8/4/09)

Eve Wurtele  Genetics, Development and Cell Biology
  • Dr. Wurtele's Research - Metabolic networking; evolution of biotin-containing enzymes; methods for analysis and visualization of high throughput data; development of the Meta!Blast cell videogame. She is accepting rotation students, and invites interested students to visit her lab website for information about her research.

    Two opportunities are available in her group:

    Regulatory and metabolic networks
    Biological aim- identify genes that control composition and metabolic flux in yeast and E. coli
    Informatics goal    - Develop approaches to combine multiple types of high-throughput data within the MetNet database graph model of a biological network.

    Funding- National Science Foundation


    Development of novel capabilities for Meta!Blast, an open-Sg-based video game focused on cell structure and metabolic biology
    Biological aim- Work with a team of biologists, teachers, artists, and computer scientists to create a state of the art biology video game targeted at high school and university students.
    Informatics goal- Develop and program approaches to visualize changes in cellular structures and support player-game environment interactions.

    Funding- National Institute of Health (8/4/09)

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