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with Dept. of Biological
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Graduate Handbook 2012/2013
Health Science Campus
Health Education Building & Center for Creative Education Building
BPG Computer Classroom: HEB 1st Floor, Room #127
Genomic Core Lab: HEB 2nd Floor, Room #200
BPG Office: CCE 3rd Floor, Lobby
BPG STUDENT RECEIVES PRESTIGIOUS FELLOWSHIP AWARD
Arnab Saha Mandal, M.S., who defended his thesis in June 2013, and received his degree, has received a CIHR (Canadian Institutes of Health Research) Training Program Fellowship award of $20,000, for research expenses during the first year of his PhD studies at the University of Calgary, in Alberta, Canada. Mr. Saha Mandal has been accepted into the Dept. of Biochemistry and Molecular Biology, and will pursue his doctorate degree in Bioinformatics at the University of Calgary. We congratulate Mr. Saha Mandal on this achievement, which is comparable to receiving an NIH grant here in the U.S.
"UT COMPLETE" RE-ADMIT CAMPAIGN FOR FALL 2013
The University of Toledo has announced a new program for undergraduate and graduate students who started a degree at UT, but have not completed that degree. Students who are readmitted for Fall 2013, who have been out for two or more semesters, will be eligible for a tuition discount of 25%. For complete details, please click here to be directed to the UTComplete web page
The University of Toledo Announces Graduate School Tuition Waiver for Employees
Dependents and spouses of full-time UT faculty members who have been employed for at leaast one year will be eligible to receive a 50% tuition waiver for most UT graduate programs beginning in the Fall of 2013. The BPG Program courses are included in this benefit. To read the entire article, click the following link:
DISTINGUISHED UNIVERSITY PROFESSOR
Our BPG Program proudly congratulates Dr. Robert Blumenthal, BPG Program director, for being one of five UT faculty members who have been recommended to receive the rank of Distinguished University Professor, after approval by the UT Board of Trustees on November 19, 2012. Dr. Blumenthal, professor of medical microbiology and immunology, has been at UT for 31 years. His reputation is known internationally for work in the field of global gene regulation in bacteria. He received the UT Outstanding Research Award this year, the Dean's Award for Teaching Excellence in 2008, and the Dean's Award for Graduate Student Mentoring in 2005. In addition, in 2008, Dr. Blumenthal presented at a Distinguished Scientist Seminar in the National Institutes of Health Rocky Mountain Lab.
COLLEGE OF BUSINESS & INNOVATION COURSES ADDED TO BPG ELECTIVES
Two courses have been added to the list of electives for the BPG Program:
1) HURM6730 Performance Management
2) MGMT6160 Leading with Power and Influence.
To view new course descriptions, please click the following link, and scroll down
to "Suggested Course Options":
WHY IS THERE A MAJOR AND GROWING NEED FOR BIOINFORMATICS?
To read the entire article titled, "Whole Genome Sequencing Is the Future of Genetics, BUT the ‘$1000 Genome’ is a Bait
and Switch", featured in The DNA Exchange, please click on the following link:
NEW! PROFESSIONAL SCIENCE MASTERS DEGREE UTILIZES BPG PROGRAM COURSES
BIOMARKERS AND DIAGNOSTICS Professional Science Master's Degree Program
A PSM degree in Biomarkers and Diagnostics is now available at the University of Toledo. This new and exciting graduate degree provides advanced training in science and business skills in approximately 18 months, without an MBA or PhD. Students are exposed to current, cutting edge topics, such as, genetics, molecular biology, protein structure, along with business skills and leadership development.
Click here for a pdf version of complete details. Click here for HTML version.
A list of required courses can be found at the following link: (pdf fully-formatted version).
The Professional Science Master's National website can be found here.
"Defence Global" article features BRIM
An article titled, "The University of Toledo: Improving Human Performance through Biomarker Discovery", was featured in the August 2012 publication of Defence Global. Biomarkers were explained, as well as the new School of BRIM vision, and its relationship with the US Air Force at Wright Patteson Air Foce Base.
Please click on this link to view the entire article (in pdf format)
Above editorial by Dr. Alexei Fedorov, Vice Director of the BPG Program and Director of the Bioinformatics computer lab, and key collaborators, Shuhao Qiu and Arnab Saha Mandal, has been published in the May 2012 issue of International Innovation. Click here for full article (in pdf format).
BUSINESS ANALYSIS PREDICTS RAPID GROWTH IN BIOINFORMATICS OVER COMING YEARS
For complete article, please click following link:
BIOINFORMATIC STUDENTS DEVELOP SOFTWARE
The students of Dr. Alexei Fedorov, Vice Director of the BPG Program, and director of the Bioinformatics lab, have their own software, which they developed themselves. Please click on the link below to view their photo and accomplishments:
PUBLICATIONS AND PRESENTATIONS BY STUDENTS IN THE BPG PROGRAM (click on link to read complete article)
Editorial: Fedorov A. Reexamining introns. International Innovation, May 2012, p. 60-63. (Key Collaborators: Qiu, Shuhao, Saha Mandal, Arnab).
Shepard S, McSweeny A, Serpen G, Fedorov A. Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models Nucleic Acids Research doi: 10.1093/nar/gks154, 2012.
Nabiyouni M, Prakash A., Fedorov A. Peculiarities in vertebrate codon bias suggest a highly GC-rich ancestral genome. Submitted, December 2011.
He J, Shepard S.S., Fedorov A., Leisner S. Identification of candidate genes regulated through argonaute4-dependent RNA-dependent DNA methylation in Arabidopsis. Under revision for Gene.
Shepard S, McSweeny A, Serpen G, Fedorov A. Binary-absrtacted Markov models and their application to sequence classification. Under minor review in Nucleic Acids Research, 2011.
Yu B, Fey P, Kestin-Pilcher KE, Fedorov A, Prakash A, Chisholm RL, Wu JY. Spliceosomal genes in the D. discoideum genome: a comparison with those in. sapiens, D. melanogaster, A. thaliana and S. cerevisiae. Protein Cell. May;2(5):395-409, 2011.
Prakash A, Bechtel J, Fedorov A. Genomic MRI – a public resource for studying sequence patterns within genomic DNA. J Vis Exp. 9;(51). pii: 2663, 2011
Rearick D, Prakash A, McSweeny A, Shepard S, Fedorova L, Fedorov A, Critical association of ncRNA with introns. Nucleic Acids Research, Nov. 2011, Vol. 39, No. 6, p. 2357-2366.
Presentation: Andrew McSweeny: "Biniary-abstraction Markov models and their application to sequence classification". Ohio Collaborative Conference in Bioinformatics (OCCBIO), June 15-17, 2010, The Ohio State University, Columbus, Ohio.
Bazeley P, Shepelev V, Talebizadeh Z, Butler M, Fedorova L, Filatov V, Fedorov A. snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene, 2008, 408:172-179.
Bechtel J, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, Shepard S, Fedorov A. Genomic mid-range inhomogeneity immpacts RNA secondary structures. Genome Biology 2007 (submitted, MS ID 2023183612167122)
Shepard S., McCreary M., Fedorov A. “The peculiarities of large intron splicing in animals”, PLoS ONE, 2009, 4(11):e7853.
Prakash A., Shepard S., Mileyeva-Biebesheimer O., He J., Hart B., Chen M., Amarachiniha S., Bechtel J., Fedorov A. “Molecular forces shaping human genomic sequence at mid-range scales”, BMC Genomics 2009, 10:513.
Bechtel J. M., Rajesh P., Ilikchyan I., Deng Y., Mishra P.K., Wang G., Wu X., Afonin
K., Grose W., Wang Y., Khuder S., and Fedorov A. Calculation of Splicing Potential from the Alternative Splicing Mutation Database Research Notes 2008, 1:4.
24. Bechtel J. M., Rajesh P., Ilikchyan I., Deng Y., Mishra P.K., Wang G., Wu X., Afonin K., Grose W., Wang Y., Khuder S., and Fedorov A. The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence. Research Notes 2008, 1:3.
Havlioglu N., Wang J., Fushimi K., Vibranovski M.D., Kan Z., Gish W., Fedorov A., Long M., Wu J.Y. An intronic signal for alternative splicing in the human genome. PloS ONE 2007, 11:e1246.
Shepelev V., Fedorov A. Advances in the Exon-Intron Database. Briefings in Bioinformatics 2006, 7: 178-185.
19. Shao X., Shepelev V., Fedorov A. Bioinformatc analysis of exon repetition, exon scrambling and trans-splicing in humans. Bioinformatics 2006, 22:692-698.