Alexei Fedorov, Ph'D'

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Alexei Fedorov, Ph.D. Associate ProfessorHead
of Bioinformatics LabDepartment of
Medicine Program in Bioinformatics and
Genomics/Proteomics Tel [phone]Email
alexei.fedorov_at_utoledo.edu http//hsc.utoledo.edu
/depts/bioinfo/fedorov.html
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Program in Bioinformatics and Genomics/Proteomics
(BPG)

• http//hsc.utoledo.edu/depts/bioinfo/
• BPG offers a Certificate in association with the
  degrees of Doctor of Philosophy (Ph.D.) or Doctor
  of Medicine (M.D.). BPG also offers a Master of
  Science in Biomedical Sciences (MSBS).

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Two courses in Spring semester

• Application of Bioinformatics, Proteomics, and
  Genomics (BIPG 640) or Advanced Bioinformatics
  (should be taken after Fundamental
  Bioinformatics of Dr. Trumbly)
• Introduction to Bioinformatic Computation (BIPG
  610) The main goal of this course is to provide
  basic programming skills to biological and
  medical students who may lack a background in
  computer sciences. Programming will be
  specifically taught using important biological
  examples, focusing in particular on the PERL
  language.
• http//hsc.utoledo.edu/depts/bioinfo/courses.html

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• In the Introduction to Bioinformatic
  Computation course, rather than doing cookbook
  lab exercises, students participate in
  real-world, challenging problems whose resolution
  advances the field of genome biology. In addition
  to learning programming and other bioinformatic
  skills the students of this course acquire
  knowledge in how to present the final product of
  bioinformatic research and how to write a
  scientific paper on the subject.

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In 2005 the class developed a program to identify
novel genes for non-coding RNAs in humans and
other mammals

• SNO.pl program
• http//hsc.utoledo.edu/depts/bioinfo/database.html
  
• Fedorov A, Stombaugh J, Harr MW, Yu S, Nasalean
  L, Shepelev V
• Computer identification of snoRNA genes using a
  Mammalian Orthologous Intron Database
• Nucleic Acids Res 2005, 334578-4583

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In 2006 course students created a novel public
database and also a novel computational resource
Splicing Potential.

• Alternative Splicing Mutation Database
• http//mco321125.meduohio.edu/jbechtel/asmd/1.1/
• Bechtel JM, Rajesh P, Ilikchyan I, Deng Y, Mishra
  PK, Wang Q, Wu X, Afonin KA, Grose WE, Wang Y,
  Khuder S, Fedorov A
• The Alternative Splicing Mutation Database a hub
  for investigations of alternative splicing using
  mutational evidence BMC Res Notes 2008, 13
• Bechtel JM, Rajesh P, Ilikchyan I, Deng Y, Mishra
  PK, Wang Q, Wu X, Afonin KA, Grose WE, Wang Y,
  Khuder S, Fedorov A
• Calculation of splicing potential from the
  alternative splicing mutation database
• BMC Res Notes 2008, 14

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In 2007 the class participated in the Genomic
MRI project http//mco321125.meduohio.edu/jbecht
el/gmri/

• Bechtel JM, Wittenschlaeger T, Dwyer T, Song J,
  Arunachalam S, Ramakrishnan SK, Shepard S,
  Fedorov A
• Genomic mid-range inhomogeneity correlates with
  an abundance of RNA secondary structures,
• BMC Genomics 2008, 9284

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MRI-analyzer(Mid-Range Inhomogeneity)
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2008 class continued Genomic MRI project. They
performed whole genome comparisons for human,
chimpanzee, and macaque and also analyzed
distribution of 4 million SNPs inside and outside
MRI regions. The results have been submitted for
publication in BMC Genomics with 6 students among
the authors
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INTRODUCTION TO BIOINFORMATIC COMPUTATION
2005
time
2004
2009
Videotaped lectures on-line labs
teleconferencing
Traditional lectures and seminars
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Applications of Bioinformatics and
Proteomics/Genomics
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Applications of Bioinformatics and
Proteomics/Genomics

• Dr. Neocles Leontis (BGSU)
• Dr. Sadik Khuder (UT HSC)
• Dr. Ewa Skrzypczak (UT HSC)
• Dr. John Gray (UT MAIN)
• Dr. Robert Blumenthal (UT HSC)
• Dr. Douglas Leaman (UT MAIN)
• Dr. Scott Rogers (BGSU)
• Dr. Alexei Fedorov (UT HSC)
• Dr. Paul Morris (BGSU)
• Dr. Jerzy Jankun (UT HSC)
• Dr. Khew-Voon Chin (UT HSC)
• Dr. Robert Trumbly (UT HSC)

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Applications of Bioinformatics and
Proteomics/Genomics
2005
time
2004
2009
teleconferencing
Traditional labs
Videotaped lectures