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Biology in silico : Online tools for “ omics ” 7 th August 2013. Ansuman Chattopadhyay , PhD Carrie L Iwema , PhD, MLS, AHIP Molecular Biology Information Services Health Sciences Library System University of Pittsburgh [email protected] [email protected]

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Biology in silico online tools for omics 7 th august 2013

Biology in silico: Online tools for “omics”7th August 2013

AnsumanChattopadhyay, PhD

Carrie L Iwema, PhD, MLS, AHIP

Molecular Biology Information Services

Health Sciences Library System

University of Pittsburgh

[email protected]@pitt.edu


Hsls molecular biology information service
HSLS Molecular Biology Information Service

http://www.hsls.pitt.edu/molbio


AnsumanChattopadhyay, Ph.D.

[email protected]

  • 1990-1996

  • University of Nebraska-Lincoln

  • PhD. in Biochemistry

  • Protein synthesis initiation in eukaryotic system

  • 1997-2001

  • Vanderbilt University School of Medicine, Nashville

  • Research Fellow

  • Epidermal Growth Factor (EGF) mediated signal transduction

  • 2001-2002

  • Cellomics Inc., Pittsburgh

  • Knowledge Engineer

  • 2002- 2006

  • Information Specialist in Molecular Biology and Genetics

  • HSLS, University of Pittsburgh

  • 2006- Present

  • Head, Molecular Biology Information Service

  • HSLS, University of Pittsburgh

http://www.hsls.pitt.edu/molbio


Carrie L Iwema, PhD, MLS, AHIP

[email protected]

  • 1993-2001

  • SUNY Upstate Medical University, Syracuse

  • PhD in Neuroscience

  • Specificity of connectivity in the mammalian olfactory system

  • 2001-2005

  • Yale University School of Medicine, New Haven

  • Postdoctoral Fellow

  • Development & regeneration in the mammalian olfactory system

  • 2004-2006

  • Southern Connecticut State University, New Haven

  • Masters in Library Science

  • 2006- 2007

  • Johns Hopkins Medical Institutions, Welch Medical Library, Baltimore

  • Basic Science Librarian

  • 2007- Present

  • University of Pittsburgh, Health Sciences Library System, Pittsburgh

  • Information Specialist in Molecular Biology

http://www.hsls.pitt.edu/molbio


Topics

Literature Informatics

Bioinformatics Databases & Software

HSLS MolBio Services

http://www.hsls.pitt.edu/molbio


In silico support
In silico Support

http://www.hsls.pitt.edu/molbio


Topics
Topics

  • Literature Informatics

    • Comprehensive search:

      • MESH term based PubMed Search

      • PubMed special topics query

    • Next-generation literature search tools:

      • GoPubMed, eTBlast

      • GLAD4U, Quertle

      • HuGE Navigator

http://www.hsls.pitt.edu/molbio


Growth of pubmed citations
Growth of PubMed Citations

. p53

Lu et al. Database (Oxford). 2011: baq036

Aug 5th 2013

http://www.hsls.pitt.edu/molbio


Literature informatics
Literature Informatics

  • What genes are reported to be associated with the disease SCHIZOPHRENIA?

    • Find published literature with statistical and numerical data on DENGUE OUTBREAKS in India.

http://www.hsls.pitt.edu/molbio


Literature informatics1
Literature Informatics

Schizophrenia: 104,388

Schizophrenia gene: 8,459

Citations: 22 million

Journals: >5600

Dengue outbreaks in India: 394

Dengue outbreaks statistics India: 29

http://www.hsls.pitt.edu/molbio


Challenges
Challenges

  • Am I getting everything / the right things?

  • How to digest this?

http://www.hsls.pitt.edu/molbio


Pubmed search
PubMed Search

  • Am I getting the right things?

    • Construct PubMed queries with MeSH terms using MeSH browser

http://www.hsls.pitt.edu/molbio


Medical subject headings mesh
Medical Subject Headings (MeSH)

http://www.hsls.pitt.edu/molbio


Mesh vocabulary
MeSH Vocabulary

  • Headings

    • 26,853 concepts found in the biomedical literature (Body Weight, Kidney, Radioactive Waste)

  • Subheadings

    • attached to headings to describe a specific aspect of a concept (adverse effects, metabolism, diagnosis, therapy)

  • Supplementary Concept Records

    • over 214,000 terms in a separate chemical thesaurus -updated weekly (cordycepin , valspodar , tacrolimus binding protein 4)

  • Publication Types

    • (Letter, Review, Randomized Controlled Trial)

http://www.hsls.pitt.edu/molbio


Mesh tree structure
MeSH Tree Structure

  • A. AnatomyB. OrganismsC. DiseasesD. Chemicals and DrugsE. Analytical, Diagnostic and Therapeutic Techniques and EquipmentF. Psychiatry and PsychologyG. Phenomena and ProcessesH. Disciplines and OccupationsI. Anthropology, Education, Sociology and Social PhenomenaJ. Technology, Industry, AgricultureK. Humanities L. Information Science M. Named Groups N. Health CareV. Publication Characteristics Z. Geographicals

http://www.hsls.pitt.edu/molbio


Mesh indexing
MeSH Indexing

Source: NLM

http://www.hsls.pitt.edu/molbio


Mesh indexing1
MeSH Indexing

PMD: 18045777

http://www.hsls.pitt.edu/molbio


Medical subject heading mesh
Medical Subject Heading (MeSH)

http://www.hsls.pitt.edu/molbio


Mesh indexing2
MeSH Indexing

http://www.hsls.pitt.edu/molbio


PubMed Search


Pubmed search1
PubMed Search

  • Retrieve published articles on

    • Dengue outbreaks in India

      Including

    • Statistical and numerical data

http://www.hsls.pitt.edu/molbio


Pubmed query using mesh
PubMed Query Using MeSH

http://www.ncbi.nlm.nih.gov/mesh

http://www.hsls.pitt.edu/molbio


Find articles on “Dengue outbreaks

in India” by searching PubMed

using MeSH terms

  • Resources

  • Mesh Browser : http://www.ncbi.nlm.nih.gov/mesh

  • PubMed: http://www.ncbi.nlm.nih.gov/pubmed

Link to the video tutorial:

http://media.hsls.pitt.edu/media/clres2705/mesh.swf

http://www.hsls.pitt.edu/molbio


Pubmed query using mesh1
PubMed Query Using MeSH

http://www.hsls.pitt.edu/molbio


Pubmed query using mesh2
PubMed Query Using MeSH

http://www.hsls.pitt.edu/molbio


Building a pubmed query
Building a PubMed Query

http://www.hsls.pitt.edu/molbio


Building a pubmed query1
Building a PubMed Query

http://www.hsls.pitt.edu/molbio


Building a pubmed query2
Building a PubMed Query

145

http://www.hsls.pitt.edu/molbio


Building a pubmed query3
Building a PubMed Query

http://www.hsls.pitt.edu/molbio


Building a pubmed query4
Building a PubMed Query

9

http://www.hsls.pitt.edu/molbio


Building pubmed queries
Building PubMed Queries

http://www.hsls.pitt.edu/molbio


Useful links for mesh
Useful Links for MeSH

  • MeSH Browser: http://www.ncbi.nlm.nih.gov/mesh

  • 18 ways to improve your Pubmed searches by Carrie Iwema

    • http://goo.gl/B8rFf

  • Searching by using the MeSH Database. NCBI Handbook :

    • http://goo.gl/X4UAe

http://www.hsls.pitt.edu/molbio


Pubmed query
PubMed Query

  • What genes are reported to be associated with the disease SCHIZOPHRENIA ?

    • Topic-Specific PubMed Queries

http://www.hsls.pitt.edu/molbio


Topic specific pubmed queries
Topic-Specific PubMed Queries

http://www.nlm.nih.gov/bsd/special_queries.html

http://www.hsls.pitt.edu/molbio


Find genes that are reported to be

associated with the disease

SCHIZOPHRENIA by searching PubMed

  • Resources

  • PubMed Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical

Link to the video tutorial:

http://media.hsls.pitt.edu/media/clres2705/scz.swf

http://www.hsls.pitt.edu/molbio


Pubmed special topic queries
PubMed Special Topic Queries

http://www.hsls.pitt.edu/molbio


Search filters
Search Filters

http://www.hsls.pitt.edu/molbio


Pubmed search filter medical genetics
PubMed Search Filter: Medical Genetics

  • ("schizophrenia"[MeSH Terms] OR "schizophrenia"[All Fields]) AND (("genetics, medical"[MeSH Terms] OR ("genetics"[All Fields] AND "medical"[All Fields]) OR "medical genetics"[All Fields] OR ("medical"[All Fields] AND "genetics"[All Fields])) OR ("genotype"[MeSH Terms] OR "genotype"[All Fields]) OR "genetics"[Subheading] AND ("genetics"[Subheading] OR "genetics"[All Fields] OR "genetics"[MeSH Terms]))

http://www.hsls.pitt.edu/molbio


Pubmed search result display
PubMed Search Result Display

How to digest

this?

http://www.hsls.pitt.edu/molbio



Latest innovations in literature searching
Latest Innovations in Literature Searching

  • GoPubMed

Display search results

sorted into meaningful

topics and subtopics

http://www.hsls.pitt.edu/molbio


Gopubmed
GoPubMed

www.gopubmed.com

http://www.hsls.pitt.edu/molbio


Find genes that are reported to be

associated with the disease

SCHIZOPHRENIA by using GoPubMed

  • Resources

  • GoPubMed: http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000

Link to the video tutorial:

http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf

http://www.hsls.pitt.edu/molbio


Gopubmed search result
GoPubMed Search Result

http://www.hsls.pitt.edu/molbio


Gopubmed search result analysis
GoPubMed Search Result Analysis

http://www.hsls.pitt.edu/molbio


Gopubmed search result analysis1
GoPubMed Search Result Analysis

http://www.hsls.pitt.edu/molbio


Latest innovations in literature searching1
Latest Innovations in Literature Searching

http://www.hsls.pitt.edu/molbio


Gopubmed1
GoPubMed

  • Noteworthy links

    GoPubMed: exploring PubMed with the Gene Ontology. DomsA,Schroeder M., Nucleic Acids Res. 2005 Jul 1; 33 (Web Server issue):W783-6. http://www.ncbi.nlm.nih.gov/pubmed/15980585

http://www.hsls.pitt.edu/molbio


Pubmed driven web tools
PubMed driven Web Tools

http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/

http://www.hsls.pitt.edu/molbio


Pubmed based tools
PubMed based Tools

http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/

Lu et al. Database (Oxford). 2011; 2011: baq036

http://www.hsls.pitt.edu/molbio


Extract gene list from literature
Extract gene list from Literature

http://www.quertle.info/

http://www.hsls.pitt.edu/molbio


Questions for quertle
Questions for Quertle

  • What genes cause Asthma?

  • What cell lines are used in diabetes research?

  • Which cell types are known to express EGFR?

  • What animals are used in studies for diabetes?

  • Which protein kinases activate TP53?

http://www.hsls.pitt.edu/molbio


A short video on Quertle

  • Resources

  • Quertle: www.quertle.info

Link to the video tutorial:

http://media.hsls.pitt.edu/media/molbiovideos/quertle-ac0212.swf

http://www.hsls.pitt.edu/molbio


Literature to gene list
Literature to gene list

  • GLAD4U

    • http://bioinfo.vanderbilt.edu/glad4u/

http://www.hsls.pitt.edu/molbio



Search engine just for human genetics
Search Engine Causing GenesJust for Human Genetics

CDC HuGENavigator : http://hugenavigator.net/

http://www.hsls.pitt.edu/molbio


  • Find Causing Geneshuman genesreported to be associated with Asthma

  • Find human SNPsreported to be associated with Asthma

  • Resources

  • HugeNavigator: http://hugenavigator.net/HuGENavigator/home.do

Link to the video tutorial:

http://media.hsls.pitt.edu/media/clres2705/asthma.swf

http://www.hsls.pitt.edu/molbio


Search engine just for human genetics1
Search Engine Causing GenesJust for Human Genetics

http://www.hsls.pitt.edu/molbio


Search engine just for human genetics2
Search Engine Causing GenesJust for Human Genetics

CDC HuGENavigator : http://hugenavigator.net/

http://www.hsls.pitt.edu/molbio


Search engine just for human genetics3
Search Engine Causing GenesJust for Human Genetics

http://hugenavigator.net/HuGENavigator/huGEPedia.do

http://www.hsls.pitt.edu/molbio


Search engine just for human genetics4
Search Engine Causing GenesJust for Human Genetics

CDC HuGENavigator : http://hugenavigator.net/

http://www.hsls.pitt.edu/molbio


Gwas catalog
GWAS Catalog Causing Genes

  • http://www.genome.gov/multimedia/illustrations/GWAS_2010_2nd.pdf

http://www.hsls.pitt.edu/molbio


Gwa studies catalog
GWA Studies Catalog Causing Genes

http://www.genome.gov/gwastudies/

http://www.hsls.pitt.edu/molbio


Find disease causing snps
Find Disease Causing SNPs Causing Genes

http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do

What SNPs are associated

  • with “Schizophrenia”?

http://www.hsls.pitt.edu/molbio



Text based similarity search tools
Text-based Similarity Search Tools Literature

Search Box:

http://www.hsls.pitt.edu/molbio


Text similarity search tools
Text Similarity Search Tools Literature

  • eTBLAST

http://etest.vbi.vt.edu/etblast3/

http://www.hsls.pitt.edu/molbio


Text similarity search tools1
Text Similarity Search Tools Literature

  • eTBLAST

http://www.hsls.pitt.edu/molbio


Text similarity search tools2
Text Similarity Search Tools Literature

http://www.hsls.pitt.edu/molbio


D j vu a database of highly similar citations
Déjà Vu: a Database of Highly Similar Citations Literature

http://dejavu.vbi.vt.edu/dejavu/duplicate/

http://www.hsls.pitt.edu/molbio


Journal author name estimator
Journal Author Name Estimator Literature

http://www.biosemantics.org/jane/

http://www.hsls.pitt.edu/molbio



Automated email notification tool
Automated email Notification Tool Literature

http://www.ncbi.nlm.nih.gov/sites/myncbi/

Save your searches at My NCBI and set up an email notification on new publication based on your search query

http://www.hsls.pitt.edu/molbio


My ncbi
My NCBI Literature

1

2

3

http://www.hsls.pitt.edu/molbio


My ncbi1
My NCBI Literature

4

http://www.hsls.pitt.edu/molbio


My ncbi email notification
My NCBI email Notification Literature

http://www.hsls.pitt.edu/molbio


Reference management tools
Reference Management Tools Literature

Connotea

CiteULike

Mendeley

Zotero

Web pages

online

Scientific Research

Papers

downloadable

EndNote

http://www.hsls.pitt.edu/molbio



Post publications metrics
Post Publications Metrics Literature

  • Journal level : Impact Factor

  • Author level: H-Index

  • Article level:

  • Article usage statistics: HTML pageviews, PDF downloads  and XML downloads

  • Citations from the scholarly literature: PubMed Central, Scopus and CrossRef

  • Social bookmarks: CiteULikeand Connotea

  • Comments: left by readers of each article

  • Notes: left by readers of each article

  • Blog posts: aggregated from Postgenomic, Nature Blogs, Bloglines, andResearch Blogging

  • Ratings: left by readers of each article

http://www.hsls.pitt.edu/molbio


Impact factor
Impact Factor Literature

  • a measure reflecting the average number of citations to articles published in science and social science journals.

  • a proxy for the relative importance of a journal within its field

  • developed by Eugene Garfield, the founder of the Institute for Scientific Information (ISI)

    • A = the number of times articles published in 2006 and 2007 were cited by indexed journals during 2008

    • B = the total number of "citable items" published in 2006 and 2007. ("Citable items" are usually articles, reviews, proceedings, or notes; not editorials or Letters-to-the-Editor.)

    • 2008 impact factor = A/BFrom Wikipedia

http://www.hsls.pitt.edu/molbio


Scopus journal analyzer
Scopus Journal Analyzer Literature

http://www.hsls.pitt.edu/molbio


Isi journal impact factor
ISI Journal Impact Factor Literature

http://www.hsls.pitt.edu/molbio


Journal impact factor
Journal Impact Factor Literature

http://admin-apps.isiknowledge.com/JCR/JCR?RQ=RECORD&rank=1&journal=ACTA+CRYSTALLOGR+A

http://www.hsls.pitt.edu/molbio


H index
H Index Literature

  • proposed by J.E. Hirsch of UCSD

  • an index to quantify an individual's scientific research output

  • provides a single-number metric of an academic's impact

  • combining quality with quantity

http://www.hsls.pitt.edu/molbio


Article level metrics
Article Level Metrics Literature

http://www.hsls.pitt.edu/molbio


Retrieve Journal Impact Factor Literature

by searching Scopus and

ISI Web of Science

  • Resources

  • Scopus: http://www.scopus.com/source/eval.url

  • ISI Web of Science: http://admin-apps.isiknowledge.com/JCR/JCR?RQ=HOME

Link to the video tutorial:

http://media.hsls.pitt.edu/media/clres2705/impact.swf

http://www.hsls.pitt.edu/molbio



Molecular databases
Molecular Databases Literature

  • Nucleic Acids Research : Annual databases Issue

  • NAR: Annual Web Server Issue

  • Oxford Journal : Bioinformatics

  • BioMedCentral: BMC Bioinformatics

http://www.hsls.pitt.edu/molbio


Biomedical life sciences search engines
Biomedical & Life Sciences Search Engines Literature

  • OBRC : University of Pittsburgh

    http://www.hsls.pitt.edu/molbio/obrc

  • Vadlo

    http://vadlo.com/

  • OReFil : University of Tokyo

    http://orefil.dbcls.jp/

http://www.hsls.pitt.edu/molbio


Search for bioinformatics Resources Literature

Locate online tools that predict phosphorylation sites

in a protein sequence.

  • Resources

  • Search.HSLS.MolBio :

Link to the video tutorial:

http://media.hsls.pitt.edu/media/Search%20Bioinfo%20Resoursec.swf

http://www.hsls.pitt.edu/molbio


Life sciences search engine
Life Sciences Search Engine Literature

http://www.hsls.pitt.edu/obrc/

http://www.hsls.pitt.edu/molbio


Life sciences search engine1
Life Sciences Search Engine Literature

http://www.hsls.pitt.edu/molbio


Hsls obrc
HSLS OBRC Literature

http://www.hsls.pitt.edu/molbio


Molecular databases catalog
Molecular Databases Catalog Literature

http://www.hsls.pitt.edu/molbio


Search hsls molbio
Search.HSLS.MolBio Literature

http://www.hsls.pitt.edu/molbio/

http://www.hsls.pitt.edu/molbio


Search hsls molbio1
Search.HSLS.MolBio Literature

  • Integrated search system

    • Databases & Software

    • Articles on Databases & Software

    • Genes/Proteins

    • Pathways

    • Protocols

    • Seminar/Talks Videos

    • Recommended Articles

  • Tabbed browsing

  • Clustered search results

http://www.hsls.pitt.edu/molbio


Search term phosphorylation
Search term: “ Literaturephosphorylation”

http://www.hsls.pitt.edu/molbio


Molecular databases and software search term phosphorylation
Molecular Databases and Software: Literaturesearch term: “Phosphorylation”

http://www.hsls.pitt.edu/molbio


Search result page
Search Result Page Literature

http://www.hsls.pitt.edu/molbio


Citation trackers
Citation Trackers Literature

http://www.hsls.pitt.edu/molbio


Search pubmed articles on databases and software phosphorylation
Search LiteraturePubMed Articles on Databases and Software : “phosphorylation”

http://www.hsls.pitt.edu/molbio


Articles on databases and software
Articles on Databases and Software Literature

http://www.hsls.pitt.edu/molbio


Articles on prediction of phosphorylation sites
Articles on Prediction of LiteraturePhosphorylation Sites

http://www.hsls.pitt.edu/molbio


Protocols
Protocols Literature:

http://www.hsls.pitt.edu/molbio


Seminar talks video
Seminar Talks Video Literature

http://www.hsls.pitt.edu/molbio


Seminar talks video1
Seminar Talks Video Literature

http://www.hsls.pitt.edu/molbio


Recommended articles
Recommended Articles Literature

Faculty of 1000 Biology: a literature awareness tool that

highlights and reviews the most interesting papers published

in the biological sciences, based on the recommendations of a

faculty of well over 2300 selected leading researchers.

http://www.hsls.pitt.edu/molbio


Recommended articles1
Recommended Articles Literature

http://www.hsls.pitt.edu/molbio


Licensed Tools Literature


Microarray data analysis
Microarray Data Analysis Literature

GeneSpring/Partek

Statistical packages

  • Ingenuity IPA

  • GeneGOMetacore

  • Explain

Literature findings

Biology

http://www.hsls.pitt.edu/molbio


Discovery step pathway analysis
Discovery Step: Pathway Analysis Literature

Gene List

http://www.hsls.pitt.edu/molbio


Discovery step
Discovery Step Literature

  • Gene List

    • Biological functions

    • Canonical Pathways

    • Interaction Networks

http://www.hsls.pitt.edu/molbio


Common functions and pathways ipa analysis
Common Functions and Pathways: IPA Analysis Literature

http://www.hsls.pitt.edu/molbio


Common functions and pathways ipa analysis1
Common Functions and Pathways: IPA Analysis Literature

http://www.hsls.pitt.edu/molbio


Common pathways ipa
Common Pathways: IPA Literature

http://www.hsls.pitt.edu/molbio


Pathway map p53
Pathway Map: p53 Literature

Red:

Green:

http://www.hsls.pitt.edu/molbio


Pathway map nfkb and tgf beta
Pathway Map: NFkB and TGF beta Literature

http://www.hsls.pitt.edu/molbio


Interaction network maps ipa
Interaction Network Maps: IPA Literature

http://www.hsls.pitt.edu/molbio


Interaction map with data overlay ipa
Interaction Map with Data Overlay: IPA Literature

http://www.hsls.pitt.edu/molbio


Pathway analysis genego metacore
Pathway Analysis: GeneGo Metacore Literature

http://www.hsls.pitt.edu/molbio



Metacore transcription regulation
Metacore: Transcription Regulation Literature

http://www.hsls.pitt.edu/molbio


BioBase Literature Explain: Key Molecules Prediction

Key Molecules

Over representation of

TF Binding site

Promoter

Microarray

http://www.hsls.pitt.edu/molbio


Biobase Literature Explain: Key Mols Prediction

Common:

KM:108

TF:4

Key Molecules :677

TF: 12

2072

32 >2 fold up

583: NC

Over representation of

TF Binding site

Promoter

Microarray

http://www.hsls.pitt.edu/molbio


Use of ingenuity genego and biobase
Use of Ingenuity, GeneGO and BioBase Literature

  • DNA microarrays

  • Protein arrays

  • CHIP-chip

  • Search for

    • Gene/protein info (human, mouse, rat, yeast)

    • Drug/small molecule

    • Disease info

    • Promoter sequences

    • Transcription factors binding sites

http://www.hsls.pitt.edu/molbio


Finding disease causing genes
Finding Disease Causing Genes Literature

http://www.hsls.pitt.edu/molbio


Most relevant disease networks for alzheimer genes
Most Relevant Disease Networks for Alzheimer Genes Literature

http://www.hsls.pitt.edu/molbio


Metacore atherosclerosis core network
Metacore Literature: Atherosclerosis (core network)

http://www.hsls.pitt.edu/molbio


Most relevant pathway maps for alzheimers genes
Most Relevant Pathway Maps for LiteratureAlzheimers Genes

http://www.hsls.pitt.edu/molbio


Atherosclerosis and alzheimers
Atherosclerosis And LiteratureAlzheimers

From Wikipedia, the free encyclopedia

http://www.hsls.pitt.edu/molbio


Pubmed search on atherosclerosis majr and alzheimer disease majr
PubMed Literature Search on"Atherosclerosis"[Majr] AND "Alzheimer Disease"[Majr]

http://www.hsls.pitt.edu/molbio


Atherosclerosis and alzheimers1
Atherosclerosis And LiteratureAlzheimers

http://www.hsls.pitt.edu/molbio


Hsls molecular biology information service1
HSLS Molecular Biology Information Service Literature

http://www.hsls.pitt.edu/molbio


Thank you any questions

Thank you! LiteratureAny questions?

Carrie IwemaAnsumanChattopadhyay

[email protected]@pitt.edu

412-383-6887 412-648-1297

http://www.hsls.pitt.edu/molbio


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