compbio.ucdenver.edu

Computational Bioscience at the School of Medicine, UC Colorado Denver

Welcome to the Computational Bioscience Program at the University of Colorado Anschutz Medical Campus! The Computational Bioscience Program brings a pioneering new approach to computation that advances human health and the molecular understanding of life. Founded and directed by Prof. Lawrence Hunter, the Program is globally recognized for its research and teaching of computational biology and bioinformatics at the University of Colorado’s Anschutz Medical Campus. The Program is designed to...Students wi...

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Computational Bioscience at the School of Medicine, UC Colorado Denver | compbio.ucdenver.edu Reviews

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Welcome to the Computational Bioscience Program at the University of Colorado Anschutz Medical Campus! The Computational Bioscience Program brings a pioneering new approach to computation that advances human health and the molecular understanding of life. Founded and directed by Prof. Lawrence Hunter, the Program is globally recognized for its research and teaching of computational biology and bioinformatics at the University of Colorado’s Anschutz Medical Campus. The Program is designed to...Students wi...

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Computational Bioscience at the School of Medicine, UC Colorado Denver | compbio.ucdenver.edu Reviews

https://compbio.ucdenver.edu

Welcome to the Computational Bioscience Program at the University of Colorado Anschutz Medical Campus! The Computational Bioscience Program brings a pioneering new approach to computation that advances human health and the molecular understanding of life. Founded and directed by Prof. Lawrence Hunter, the Program is globally recognized for its research and teaching of computational biology and bioinformatics at the University of Colorado’s Anschutz Medical Campus. The Program is designed to...Students wi...

INTERNAL PAGES

compbio.ucdenver.edu

1

Computational Bioscience Program, School of Medicine at the University of Colorado Denver: Our People

http://compbio.ucdenver.edu/pages/ourpeople.html

Our outstanding faculty, staff, trainees and alumni have come to Colorado from around the world. Before joining our program, they trained at Harvard, Yale, Stanford, Johns Hopkins and other top universities. Brief biographies, including research interests can be found on specific “Our People” pages:.

2

Computational Bioscience Program, School of Medicine at the University of Colorado Denver: News & Events

http://compbio.ucdenver.edu/pages/newsandevents.html

Training Faculty Katerina Kechris Awarded NIH R01. Predoctoral Student, Christopher Funk publishes first author paper in BMC Bioinformatics Journal. Link to the full article available here. Computational Bioscience Program Director, Dr. Larry Hunter in the news, many times over! Interviewed Dr. Hunter and others for their article, Biology, the big challenges of big data. Link to the full article available here. In an article in the. Link to the full article here. Lastly, Dr. Hunter was interviewed on.

3

Computational Bioscience Program, School of Medicine at the University of Colorado Denver: Graduate Studies

http://compbio.ucdenver.edu/pages/graduatestudies.html

Welcome to the University of Colorado Computational Bioscience Training Program! Applications for Fall 2015 are currently being accepted for the Ph.D. degree program in Computational Bioscience. More information about this opportunities, as well as funding through our National Library of Medicine Training Grant. Follows. Apply Online. Students once accepted must begin to become Colorado residents prior to the start of the second year of the program. Details of residency requirements can be found here.

4

CBP Calendar

http://compbio.ucdenver.edu/pages/CBPCalendar.html

5

Colorado Computational Pharmacology

http://compbio.ucdenver.edu/Hunter_lab

Colorado Computational Pharmacology (CCP). Creating novel algorithms and knowledge-based tools for the analysis and interpretation of high-throughput molecular biology data. Something I've been doing lately that I'm pretty excited about is assignment of broad semantic classes to biomedical text. I'm working on applying the lab's natural language processing to larger corpora (of documents) using, among others, the large Janus cluster in Boulder. https:/ www.rc.colorado.edu/page/janus. GeneRIFs annotated w...

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evolutionarygenomics.com

Todd Castoe

http://www.evolutionarygenomics.com/Denizens/Castoe.html

Adaptation and evolution of protein structure and function - Molecular evolutionary dynamics and adaptation in vertebrate mitochondria - Squamate genomics and evolution - Phylogenetic methodology.

evolutionarygenomics.com

Pollock Laboratory: PClouds

http://www.evolutionarygenomics.com/ProgramsData/PClouds/PClouds.html

Package is designed to identify repeat structure in large eukaryotic genomes using oligonucleotide counts. It works efficiently on a single desktop computer with 1 Gb memory. The basic program is described in Gu et al. (2008), below, with more details, analysis of human genome, and description of element-specific P-clouds in de Koning et al. (2011). An even newer version that includes a full pipeline for running vertebrate genomes is in preparation. Is included in the zip file. Sample files include input.

evolutionarygenomics.com

Pollock Laboratory: projects

http://www.evolutionarygenomics.com/projects.html

Protein sequence, structure, and functional evolution. Adaptive coevolution and ancestral reconstruction. Evolution of mitochondrial genomes. Testing evolutionary predictions through mutagenesis and directed evolution. Further information on projects to be put up shortly.

evolutionarygenomics.com

codeml ancestral

http://www.evolutionarygenomics.com/ProgramsData/codeml_ancestral/ancestral.html

Code is available to calculate divergence and convergence. Of the codeml program from Ziheng Yang. Package. This software calculates posterior convergent and divergent substitution probabilities and their expected counts using posterior integration and amino acid substitution models: codeml-ancestral. Please see readme. File for more information. Code credits to Jason de Koning. Evidence for an ancient adaptive episode of convergent molecular evolution.

evolutionarygenomics.com

Advanced Scientific Programming

http://www.evolutionarygenomics.com/PresentationsCourses/7785/7785.html

CPBS 7785: Advanced Scientific Programming. The course is designed and directed by Prof. Pollock. In collaboration with various lab members. The course is 1 unit, and will be held in a time and place to be determined by Prof. Pollock and those who are in the class. For further enrollment information contact Elizabeth.Wethington@UCDenver.edu. The course starts soon. Scientific Programming Flyer (pdf). A Primer of Population Genetics. Hartl), if you have not already read it.

evolutionarygenomics.com

Pollock Laboratory: PLEX

http://www.evolutionarygenomics.com/ProgramsData/PLEX/PLEX.html

Phylogenetics, Likelihood, Evolution, and CompleXity. Package is designed to perform rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. The basic program is described in references listed below. PLEX is under continued development. The current version 0.95 zip file. Can be downloaded here. The distribution contains code, manual files, example data files with respective control files, and mac and unix compiled versions. File, a quick start guide. A P J de Koni...

evolutionarygenomics.com

Pollock Laboratory Programs

http://www.evolutionarygenomics.com/ProgramsData/Programs.html

Ancestral TE: A program to infer relationships among replicating ancestral TE sequences in a TE family. Phylogenetics, Likelihood, Evolution, and CompleXity: A program for rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Identify repeat structure in large eukaryotic genomes using oligonucleotide counts. It works efficiently on a single desktop computer with 1 Gb memory. Three programs used to analyze coevolution of transcription factor binding sites.

evolutionarygenomics.com

Pollock Laboratory: PLEX

http://www.evolutionarygenomics.com/ProgramsData/SULDEX/SULDEX.html

Simultaneous Ultra high throughput Ligand Dissociation EXperiment. The SULDEX packages is designed to u se high throughput sequencing to simultaneously analyze binding dissociation constants for large repertoires of sequences. The basic program is described in. David D. Pollock, A. P. Jason de Koning, Hyunmin Kim, Todd A. Castoe, Mair E. A. Churchill, and Katerina J. Kechris , PloS ONE. Code is under continued development, with alpha versions available as a tarball. Current version is 0.01.

evolutionarygenomics.com

Pollock Laboratory: TFCoEvolve

http://www.evolutionarygenomics.com/ProgramsData/TFCoevolve/TFCoEvolve.html

Transcription Factor CoEvolution Analysis. The TFCoeEvolve packages is designed to analyze evolution of transcription factors. The basic set of program is described in Ken Daigoro Yokoyama and David D. Pollock,. Code and data sets are available as a compressed file. Original concept by Ken Yokoyama and DD Pollock. All programming by Ken Yokoyama. Ken Daigoro Yokoyama and David D. Pollock,.

evolutionarygenomics.com

Genomics

http://www.evolutionarygenomics.com/PresentationsCourses/7620/7620.html

HMGP, STBB, and CPBS 7620: Genomics. HMGP CPBS and STBB 7620 (Human Medical Genetics and Genomics, Structural Biology and Biochemistry, and Computational Bioscience), Spring 2014, will introduce graduate students (and interested postdocs, PRAs, and faculty) to the field of genomics. The lecture course is designed and directed by Profs. Pollock. Johnston, and Sikela, with guest lectures by Martin, Shaikh, and Spritz. Professors and students are encouraged to take a break and stretch midway). Griffiths, Ge...

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compbio.soihub.org

Computational Systems Biology

Please login to view:. If you would like to login and you do not already have an account please contact csb@soihub.org. Acknowledgements: This work was supported by NSF Grant DBI 0835677 and by the Center for Science of Information.

compbio.sookmyung.ac.kr

NetCSSP.

Neural networks for calculating Contact-dependent Secondary Structure Propensity. Applications in predicting non-native secondary structures and amyloid fibril formation. 1 Select a method for CSSP calculation. Single network provides helical and beta propensity in a single profile while dual mode calculates the helical and. Beta propensities in two separate neural networks. Three ways to submit a query sequence. 2-1 Paste your protein sequence. PDB ID (4 letters) :. Type sequence (Single letter) :.

compbio.stanford.edu

Computational Biology Group - Stanford Computer Science Dept

Apply for the Computer Science Ph.D. program. Deadline: Winter 2014. Because of the colleagues, opportunities, facilities, and the true interdisciplinary and entrepreneurial spirit on campus (as well as unmatched weather and Bay Area setting). US News ranks Stanford University as the #1 Best Graduate School in both computer science, biological sciences, and in genetics, genomics and bioinformatics. Stanford Computer Science Department. Related Graduate Programs and Departments.

compbio.tel

Share this .tel.

compbio.triiprograms.org

Computational Biology & Medicine

Computational Biology and Medicine. Student Life & Housing. FAQs for Prospective Students. Faculty & Research. Students & Alumni. Weill Cornell Medical College. Memorial Sloan-Kettering Cancer Center. Student Life & Housing. FAQs for Prospective Students. Faculty & Research. Students & Alumni. CBM’s personalized program uses computational methods, often in conjunction with experimental approaches, to solve problems across a broad spectrum of biomedical disciplines. About 6 months ago. Via Mobile Web (M5).

compbio.ucdenver.edu

Computational Bioscience at the School of Medicine, UC Colorado Denver

Welcome to the Computational Bioscience Program at the University of Colorado Anschutz Medical Campus! The Computational Bioscience Program brings a pioneering new approach to computation that advances human health and the molecular understanding of life. Founded and directed by Prof. Lawrence Hunter, the Program is globally recognized for its research and teaching of computational biology and bioinformatics at the University of Colorado’s Anschutz Medical Campus. The Program is designed to...Students wi...

compbio.uchicago.edu

Doctoral Training in Computational Genomics | The University of Chicago

Skip to main navigation. Skip to main content. The University of Chicago. Doctoral Training in Computational Genomics. Doctoral Training in Computational Genomics. A look at some of the computational resources available to students and Faculty Computational Resources. A list of the courses that make up the Computational Biology training program Curriculum. Genomics, Genetics, and Systems Biology Committee PhD Program. Human Genetics Departmental PhD Program. Statistics Departmental PhD Program.

compbio.ucmerced.edu

Computational Biology at UC Merced

compbio.ufl.edu

Computational Biology and Bioinformatics » UF Health Cancer Center » University of Florida

Training on UF campus. Bioinformatics and computational biology courses @ UF. Text-only version of this website. UF Health at Gainesville. UF Health Shands Hospital. UF Health Shands Cancer Hospital. Shands Emergency & Trauma. UF Health Shands Children's Hospital. UF Health Shands Rehab Hospital. UF Health Shands Psychiatric Hospital. Archer Family Health Care. Student Health Care Center. UF Health at Jacksonville. UF Health Proton Therapy Institute. College of Public Health and Health Professions.

compbio.umbc.edu

Erill Lab

Welcome to the Erill Lab. By ErillLab on April 10, 2013. As Robert Robbins* put it, the DNA sequence of an organism is the result of literally millions of maintenance revisions performed by the worst possible set of kludge using. Opportunistic hackers (i.e. evolution) who delight in clever tricks like writing self modifying code. And relying upon undocumented system quirks . As a result, deciphering molecular biology is the ultimate dream of a computer scientist. What’s cookin’?

compbio.unl.edu

Computational Biology Research Lab, Home Page

Istvan (Steve) Ladunga, Ph.D. Professor of Computational Biology, E145 Beadle Center. At the University of Nebraska-Lincoln. Our Laboratory conducts research in the computational aspects of:. Reconstructing transcriptional regulatory networks in algae and S. cerevisiae. Carbon dioxide concentration mechanisms in algae. Transcriptional Competency of Nucleosomes. In these works, we utilize existing methods and develop new ones in:. Transcription factor binding site predictions,. Machine learning, and.