Posted by on Aug 06 2008 |

Welcome to the Oakwood University

Bio-Quantitative Interdisciplinary Institute website.


This HHMI sponsored project offers a Faculty Quantitative Reasoning Institute

August 10-11, 2009 with a consulting session on August 12, 2009.

We’ll be meeting in the Business and Technology Complex.lggrp

Last year, a Faculty Bioinformatics Institute was held on August 11-12, 2008 at Oakwood University.

Bioinformatics and visualization are rapidly developing research approaches currently found throughout the biological, physical and mathematical sciences curriculum. Our workshop focus was on strategies for including these approaches in the development of interdisciplinary modules for undergraduates.

Faculty participants explored sequence data utilizing  a set of bioinformatics tools and datasets. We investigated resources for molecular visualization and protein structural analysis. Epidemiological modeling was included as an additional bio-quantitative approach for the development of interdisciplinary modules that touch upon medicine, epidemiology, forensics, agriculture, biotechnology, mathematical modeling, visualization and ecology.


10 comments for now

10 Responses to “About”

  1. Albert Osei

    No. I have not blogged before.

    11 Aug 2008 at 10:06 am

  2. Londa Schmidt`

    No I have not blogged before.

    11 Aug 2008 at 10:16 am

  3. Darayas

    1) 3.052 Nanomechanics of Materials and Biomaterials
    Spring 2007
    The study of forces and motion on extremely tiny (10-9 m) areas of synthetic and biological materials and structures.

    2) NCBI Tools for Bioinformatics Research
    The National Center for Biotechnology Information (NCBI) creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.
    Tools – Nucleotide Sequence Analysis
    The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases, now comes in several types including PSI-BLAST, PHI-BLAST, and BLAST 2 sequences. Specialized BLASTs are also available for human, microbial, malaria, and other genomes, as well as for vector contamination, immunoglobulins, and tentative human consensus sequences.
    Electronic PCR – allows you to search your DNA sequence for sequence tagged sites (STSs) that have been used as landmarks in various types of genomic maps. It compares the query sequence against data in NCBI’s UniSTS, a unified, non-redundant view of STSs from a wide range of sources.
    Entrez Gene – each Entrez Gene record encapsulates a wide range of information for a given gene and organism. When possible, the information includes results of analyses that have been done on the sequence data. The amount and type of information presented depend on what is available for a particular gene and organism and can include: (1) graphic summary of the genomic context, intron/exon structure, and flanking genes, (2) link to a graphic view of the mRNA sequence, which in turn shows biological features such as CDS, SNPs, etc., (3) links to gene ontology and phenotypic information, (4) links to corresponding protein sequence data and conserved domains, (5) links to related resources, such as mutation databases. Entrez Gene is a successor to LocusLink.
    Model Maker – allows you to view the evidence (mRNAs, ESTs, and gene predictions) that was aligned to assembled genomic sequence to build a gene model and to edit the model by selecting or removing putative exons. You can then view the mRNA sequence and potential ORFs for the edited model and save the mRNA sequence data for use in other programs. Model Maker is accessible from sequence maps that were analyzed at NCBI and displayed in Map Viewer.
    ORF Finder – identifies all possible ORFs in a DNA sequence by locating the standard and alternative stop and start codons. The deduced amino acid sequences can then be used to BLAST against GenBank. ORF finder is also packaged in the sequence submission software Sequin.

    Organism Specific Resources – Bee, Cat, Chicken, Cow, etc.

    SAGEmap – provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated by the Cancer Genome Anatomy Project (CGAP), which have been submitted to Gene Expression Omnibus (GEO). Gene expression profiles that compare the expression in different SAGE libraries are also available on the Entrez GEO Profiles pages. It is possible to enter a query sequence in the SAGEmap resource to determine what SAGE tags are in the sequence, then map to associated SAGEtag records and view the expression of those tags in different CGAP SAGE libraries.
    Spidey – aligns one or more mRNA sequences to a single genomic sequence. Spidey will try to determine the exon/intron structure, returning one or more models of the genomic structure, including the genomic/mRNA alignments for each exon.
    Splign – is a utility for computing cDNA-to-Genomic alignments based on a variation of the Needleman-Wunsch algorithm combined with Blast for compartment detection and greater performance.
    VecScreen – a tool for identifying segments of a nucleic acid sequence that may be of vector, linker, or adapter origin prior to sequence analysis or submission. VecScreen was developed to combat the problem of vector contamination in public sequence databases.
    Viral Genotyping Tool – a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined reference genotypes exist for three major viral pathogens: human immunodeficiency virus 1 (HIV-1), hepatitis C virus (HCV) and hepatitis B virus (HBV), as well as for poliovirus. User-defined reference sequences can be used at the same time. The query sequence is broken into segments for comparison to the reference so that the mosaic organization of recombinant sequences is revealed. The results are displayed graphically using color-coded genotypes. Therefore, the genotype(s) of any portion of the query can quickly be determined.

    Tools – Protein Sequence Analysis and Proteomics
    The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases, now comes in several types including PSI-BLAST, PHI-BLAST, and BLAST 2 sequences. Specialized BLASTs are also available for human, microbial, malaria, and other genomes, as well as for vector contamination, immunoglobulins, and tentative human consensus sequences.
    BLink – (“BLAST Link”) displays the results of BLAST searches that have been done for every protein sequence in the Entrez Proteins data domain.
    CD Search – search the Conserved Domain Database with Reverse Position Specific BLAST.

    CDART – when given a protein query sequence, CDART displays the functional domains that make up the protein and lists proteins with similar domain architectures.
    Open Mass Spectrometry Search Algorithm (OMSSA) – The OMSSA search service allows proteomics researchers to submit the mass spectra of peptides and proteins for identification. OMSSA then compares these mass spectra to theoretical ions generated from data libraries of known protein sequences and ranks the results using a score derived from classical hypothesis testing.
    TaxPlot – a tool for 3-way comparisons of genomes on the basis of the protein sequences they encode. To use TaxPlot, one selects a reference genome to which two other genomes are compared. Pre-computed BLAST results are then used to plot a point for each predicted protein in the reference genome, based on the best alignment with proteins in each of the two genomes being compared.

    Tools – Structures
    Cn3D – Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI’s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix.
    VAST Search – VAST Search is NCBI’s structure-structure similarity search service. It compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database.
    CD Search – search the Conserved Domain Database with Reverse Position Specific BLAST.

    11 Aug 2008 at 3:51 pm

  4. Shushannah

    I have not blogged before and didn’t really know what it was.

    11 Aug 2008 at 3:51 pm

  5. Kathleen Dobbins

    1. Related Articles, Links
    Sadygov RG, Yates JR 3rd.

    A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases.
    Anal Chem. 2003 Aug 1;75(15):3792-8.
    PMID: 14572045 [PubMed – indexed for MEDLINE]
    2. Related Articles, Links
    Gygi SP, Rochon Y, Franza BR, Aebersold R.

    Correlation between protein and mRNA abundance in yeast.
    Mol Cell Biol. 1999 Mar;19(3):1720-30.
    PMID: 10022859 [PubMed – indexed for MEDLINE]
    3. Related Articles, Links
    Vaillant M, Olliaro P.

    Geometric least squares means ratios for the analysis of Plasmodium falciparum in vitro susceptibility to antimalarial drugs.
    Malar J. 2007 Nov 26;6:156.
    PMID: 18039388 [PubMed – indexed for MEDLINE]

    11 Aug 2008 at 3:57 pm

  6. Shushannah

    Found two more:


    5. http://www.ajtmh.org/cgi/content/abstract/62/5/535

    11 Aug 2008 at 4:05 pm

  7. Shushannah

    4 did not come up correctly. Here it is
    4. http://www.informaworld.com/smpp/content~db=all~content=a781283205~tab=citation

    11 Aug 2008 at 4:07 pm

  8. Kathleen Dobbins

    4. Related Articles, Links
    Sergiev VP, Orlov VS, Boev BV, Grinchenko SN, SabgaÄ­da TP.

    [The mathematical modelling of tropical malaria]
    Parazitologiia. 1995 May-Jun;29(3):159-66. Russian.
    PMID: 7567076 [PubMed – indexed for MEDLINE]

    11 Aug 2008 at 4:09 pm

  9. Kathleen Dobbins

    5. [Mathematical model for the analysis of vaccination and vector control in malaria incidence]
    Rev Salud Publica (Bogota). 2003 May-Aug;5(2):172-9. Spanish.
    PMID: 14661350 [PubMed – indexed for MEDLINE]

    11 Aug 2008 at 4:16 pm

  10. Shushannah

    Here are my resources on Calculus and Malaria, although most of these are just about applying Calculus and not about Malaria. Only the third one actually uses Malaria to teach modeling.

    1. The Calculus of “I Love You”

    2. Calculus for Biology II

    3. How to Mathematically Model

    11 Aug 2008 at 3:53 pm

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