Strategies in data integration to predict fish susceptibility to toxicants

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Strategies in data integration to predict fish susceptibility to toxicants"

Transcription

1 Strategies in data integration to predict fish susceptibility to toxicants Fernando Ortega and Francesco Falciani School of Biosciences The University of Birmingham

2 NERC PGP Project Kevin Chipman Mark Viant Francesco Falciani Ioanna Katsiadakis Brett Lyons Charles Tyler Identifying and defining the bases of individual and population susceptibility and adaptation to environmental pollutants in fish: An integrated 'omic' approach Steve George Mike Leaver John Taggart John Craft Colin Moffat

3 General Problem Continuous value data acquired from highthroughput experiments Small scale experiments Computational predictions Databases Problems Missing data Systematic biases in each type of data set and THE INTEGROME a long etc.

4 What makes fish populations resistant or vulnerable to environmental change and impact? Acute Exposures metal PAH estrogen Long term exposures Field Sampling Depuration Reproductive Fitness Hepatocytes Flounder Stickleback Bioinformatics Individual Biomarkers Microarrays 2D-PAGE proteomics Metabolomics Microsatellites SNPs Chemistry Data Dissemination Biomarker Development

5 Genomics - Flounder Microarrays All arrays were printed at the Birmingham University Functional Genomics Laboratory STAGE 1 Gene Picking Cloning Classical Stress Response Genes STAGE 2 Suppressive Subtractive Hybridisation (SSH) New Responders NERC STAGE 3 Amplification of random flounder clones from an induced liver cdna library Environmental SSH Tyne vs Alde Laboratory SSH Benzo(a)pyrene Cadmium 12,830 clone array Complete 160 gene array Complete 500 gene array Complete NERC PG+P

6 Type of Experiments Fish exposed to different environments Transcriptomics Multivariate statistics Analysis + GA (GALGO) Gene ontology terms + GeneSpring Gene expressions Set of genes selected Tool to classified fishes List of genes that identify each environment Toxic & detoxification pathways (Literature specific + associate measurements) Environmental chemical profiles

7 Type of Experiments Non polluted adult fishes Cu 2+, DBA, EE 2 Temporal experiments 1, 2, 4, 8 and 16 days Transcriptomics Different gene profile expressions GO terms Temporal behaviour Different pollutants Set of significant profile expressions (fingerprint)

8 Chemical treatments a) Diagnostic fingerprints of chemical effects in the environment b) Linkage of genotype & phenotype Environmental Exposures Two strategies of data integration we will follow 1. Statistical Metaanalysis strategy (combine p values from k different sets) 2. Integrated Modelling strategy

9 1. Statistical Metaanalysis strategy. Multiple data sets (different size and types) e.g. transcriptomic, proteomics and metabolomics. Minimization of the number of false positive and false negative. Different methods to combine p values from k different sets. E.g. k Fisher s weighted = 2 w i ln( p i ) i = 1

10 Test Network Environmental input

11 2. Integrated Modelling strategy. Combine Multiple data sets e.g. transcriptomic, proteomics, metabolomics, SNP, microsatellites. It is based on statistical classification tree models that evaluate the contribution of multiple for of data. If expression gen 1 > x & metabolite 37 level > y If nº SNP 14 > N & metabolite 45 level > z

12 Test Network Environmental input polluted non-polluted Simulated data: * Gene expression and * Protein levels Add Nonsense randomize data Mathematical model (ODE) Normal Mutated Ouput 1 Ouput 2 e.g. SNP Continuous variables Noise is Introduced at kinetic and conc. levels Discrete variables (presence/absence SNP)

13 ~ GEP ~ 500 metabolites ~ 20 SNP If expression gen 1 > x & metabolite 37 level > y

14 a) We consider appropriate to store the different type of data sets in spreadsheets. b) Flow diagram representation Time experiment GE Proteom Metab SNP treatment

Dr Alexander Henzing

Dr Alexander Henzing Horizon 2020 Health, Demographic Change & Wellbeing EU funding, research and collaboration opportunities for 2016/17 Innovate UK funding opportunities in omics, bridging health and life sciences Dr Alexander

More information

A Primer of Genome Science THIRD

A Primer of Genome Science THIRD A Primer of Genome Science THIRD EDITION GREG GIBSON-SPENCER V. MUSE North Carolina State University Sinauer Associates, Inc. Publishers Sunderland, Massachusetts USA Contents Preface xi 1 Genome Projects:

More information

AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE

AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE ACCELERATING PROGRESS IS IN OUR GENES AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE GENESPRING GENE EXPRESSION (GX) MASS PROFILER PROFESSIONAL (MPP) PATHWAY ARCHITECT (PA) See Deeper. Reach Further. BIOINFORMATICS

More information

Statistical Analysis. NBAF-B Metabolomics Masterclass. Mark Viant

Statistical Analysis. NBAF-B Metabolomics Masterclass. Mark Viant Statistical Analysis NBAF-B Metabolomics Masterclass Mark Viant 1. Introduction 2. Univariate analysis Overview of lecture 3. Unsupervised multivariate analysis Principal components analysis (PCA) Interpreting

More information

Alison Yao, Ph.D. July 2014

Alison Yao, Ph.D. July 2014 * Alison Yao, Ph.D. Program Officer, Office of Genomics and Advanced Technologies Division of Microbiology and Infectious Diseases National Institute of Allergy and Infectious Diseases National Institutes

More information

Core Facility Genomics

Core Facility Genomics Core Facility Genomics versatile genome or transcriptome analyses based on quantifiable highthroughput data ascertainment 1 Topics Collaboration with Harald Binder and Clemens Kreutz Project: Microarray

More information

University of Glasgow - Programme Structure Summary C1G5-5100 MSc Bioinformatics, Polyomics and Systems Biology

University of Glasgow - Programme Structure Summary C1G5-5100 MSc Bioinformatics, Polyomics and Systems Biology University of Glasgow - Programme Structure Summary C1G5-5100 MSc Bioinformatics, Polyomics and Systems Biology Programme Structure - the MSc outcome will require 180 credits total (full-time only) - 60

More information

dixa a data infrastructure for chemical safety Jos Kleinjans Dept of Toxicogenomics Maastricht University

dixa a data infrastructure for chemical safety Jos Kleinjans Dept of Toxicogenomics Maastricht University dixa a data infrastructure for chemical safety Jos Kleinjans Dept of Toxicogenomics Maastricht University Current protocol for chemical safety testing Short Term Tests for Genetic Toxicity Bacterial Reverse

More information

Voluntary Genomic Data Submissions at the U.S. FDA

Voluntary Genomic Data Submissions at the U.S. FDA Voluntary Genomic Data Submissions at the U.S. FDA International Conference on Harmonization Chicago, IL November 9-10, 9 2005 Felix W. Frueh, PhD Associate Director for Genomics Office of Clinical Pharmacology

More information

How many of you have checked out the web site on protein-dna interactions?

How many of you have checked out the web site on protein-dna interactions? How many of you have checked out the web site on protein-dna interactions? Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Find and be ready to discuss

More information

The Future of the Electronic Health Record. Gerry Higgins, Ph.D., Johns Hopkins

The Future of the Electronic Health Record. Gerry Higgins, Ph.D., Johns Hopkins The Future of the Electronic Health Record Gerry Higgins, Ph.D., Johns Hopkins Topics to be covered Near Term Opportunities: Commercial, Usability, Unification of different applications. OMICS : The patient

More information

BIOINFORMATICS Supporting competencies for the pharma industry

BIOINFORMATICS Supporting competencies for the pharma industry BIOINFORMATICS Supporting competencies for the pharma industry ABOUT QFAB QFAB is a bioinformatics service provider based in Brisbane, Australia operating nationwide and internationally. QFAB was established

More information

FACULTY OF MEDICAL SCIENCE

FACULTY OF MEDICAL SCIENCE Doctor of Philosophy in Biochemistry FACULTY OF MEDICAL SCIENCE Naresuan University 73 Doctor of Philosophy in Biochemistry The Biochemistry Department at Naresuan University is a leader in lower northern

More information

Lecture 11 Data storage and LIMS solutions. Stéphane LE CROM lecrom@biologie.ens.fr

Lecture 11 Data storage and LIMS solutions. Stéphane LE CROM lecrom@biologie.ens.fr Lecture 11 Data storage and LIMS solutions Stéphane LE CROM lecrom@biologie.ens.fr Various steps of a DNA microarray experiment Experimental steps Data analysis Experimental design set up Chips on catalog

More information

Introductory genetics for veterinary students

Introductory genetics for veterinary students Introductory genetics for veterinary students Michel Georges Introduction 1 References Genetics Analysis of Genes and Genomes 7 th edition. Hartl & Jones Molecular Biology of the Cell 5 th edition. Alberts

More information

PRACTICAL APPROACH TO ECOTOXICOGENOMICS

PRACTICAL APPROACH TO ECOTOXICOGENOMICS ANNOUNCEMENT PRACTICAL APPROACH TO ECOTOXICOGENOMICS Advanced Workshop Studies in Biology and Applied Biosciences Department of Biology University of Aveiro, 30 April- 4 May 2007 This one-week post-graduate

More information

Discovery and Quantification of RNA with RNASeq Roderic Guigó Serra Centre de Regulació Genòmica (CRG) roderic.guigo@crg.cat

Discovery and Quantification of RNA with RNASeq Roderic Guigó Serra Centre de Regulació Genòmica (CRG) roderic.guigo@crg.cat Bioinformatique et Séquençage Haut Débit, Discovery and Quantification of RNA with RNASeq Roderic Guigó Serra Centre de Regulació Genòmica (CRG) roderic.guigo@crg.cat 1 RNA Transcription to RNA and subsequent

More information

School of Biosciences: MRC Phenome Centre-Birmingham

School of Biosciences: MRC Phenome Centre-Birmingham University of Birmingham College of Life and Environmental Sciences School of Biosciences: MRC Phenome Centre-Birmingham Bioinformatics (Metabolomics-specific) Research Fellow 1 Salary from 28,695 to 37,394

More information

Analysis of gene expression data. Ulf Leser and Philippe Thomas

Analysis of gene expression data. Ulf Leser and Philippe Thomas Analysis of gene expression data Ulf Leser and Philippe Thomas This Lecture Protein synthesis Microarray Idea Technologies Applications Problems Quality control Normalization Analysis next week! Ulf Leser:

More information

Biologiske effekter av veiavrenning. hvordan knytte eksponering til miljørisiko?

Biologiske effekter av veiavrenning. hvordan knytte eksponering til miljørisiko? Biologiske effekter av veiavrenning hvordan knytte eksponering til miljørisiko? Knut Erik Tollefsen 1,2 1 NIVA-Norwegian Institute for Water Research, Oslo (NO) 2 UMB-University of Life Sciences (isotope

More information

School of Nursing. Presented by Yvette Conley, PhD

School of Nursing. Presented by Yvette Conley, PhD Presented by Yvette Conley, PhD What we will cover during this webcast: Briefly discuss the approaches introduced in the paper: Genome Sequencing Genome Wide Association Studies Epigenomics Gene Expression

More information

> Semantic Web Use Cases and Case Studies

> Semantic Web Use Cases and Case Studies > Semantic Web Use Cases and Case Studies Case Study: Applied Semantic Knowledgebase for Detection of Patients at Risk of Organ Failure through Immune Rejection Robert Stanley 1, Bruce McManus 2, Raymond

More information

EMBL-EBI Industry Programme Workshop, 26th to 27th November 2012. Data Infrastructure for Omics-based Chemical Safety.

EMBL-EBI Industry Programme Workshop, 26th to 27th November 2012. Data Infrastructure for Omics-based Chemical Safety. EMBL-EBI Industry Programme Workshop, 26th to 27th November 2012. Data Infrastructure for Omics-based Chemical Safety Danyel Jennen The systems toxicology approach Cf. Waters & Fostel. Toxicogenomics and

More information

Draft NIEHS Strategic Plan. Mission, Vision, Strategic Pillars, Strategic Goals. Draft Mission Statement

Draft NIEHS Strategic Plan. Mission, Vision, Strategic Pillars, Strategic Goals. Draft Mission Statement Draft NIEHS Strategic Plan Mission, Vision, Strategic Pillars, Strategic Goals Draft Mission Statement The mission of the National Institute of Environmental Health Sciences is to discover how the environment

More information

BBSRC TECHNOLOGY STRATEGY: TECHNOLOGIES NEEDED BY RESEARCH KNOWLEDGE PROVIDERS

BBSRC TECHNOLOGY STRATEGY: TECHNOLOGIES NEEDED BY RESEARCH KNOWLEDGE PROVIDERS BBSRC TECHNOLOGY STRATEGY: TECHNOLOGIES NEEDED BY RESEARCH KNOWLEDGE PROVIDERS 1. The Technology Strategy sets out six areas where technological developments are required to push the frontiers of knowledge

More information

Introduction To Real Time Quantitative PCR (qpcr)

Introduction To Real Time Quantitative PCR (qpcr) Introduction To Real Time Quantitative PCR (qpcr) SABiosciences, A QIAGEN Company www.sabiosciences.com The Seminar Topics The advantages of qpcr versus conventional PCR Work flow & applications Factors

More information

Molecular mechanisms of carcinogenesis. Nik Hodges School of Biosciences

Molecular mechanisms of carcinogenesis. Nik Hodges School of Biosciences Molecular mechanisms of carcinogenesis Nik Hodges School of Biosciences N.Hodges@bham.ac.uk Aims What is cancer at the cellular level? How do chemical and physical agents cause cancer? How do we test for

More information

Data Integration. Lectures 16 & 17. ECS289A, WQ03, Filkov

Data Integration. Lectures 16 & 17. ECS289A, WQ03, Filkov Data Integration Lectures 16 & 17 Lectures Outline Goals for Data Integration Homogeneous data integration time series data (Filkov et al. 2002) Heterogeneous data integration microarray + sequence microarray

More information

Big Data for Population Health and Personalised Medicine through EMR Linkages

Big Data for Population Health and Personalised Medicine through EMR Linkages Big Data for Population Health and Personalised Medicine through EMR Linkages Zheng-Ming CHEN Professor of Epidemiology Nuffield Dept. of Population Health, University of Oxford Big Data for Health Policy

More information

Electronic Medical Records and Genomics: Possibilities, Realities, Ethical Issues to Consider

Electronic Medical Records and Genomics: Possibilities, Realities, Ethical Issues to Consider Electronic Medical Records and Genomics: Possibilities, Realities, Ethical Issues to Consider Daniel Masys, M.D. Affiliate Professor Biomedical and Health Informatics University of Washington, Seattle

More information

The National Institute of Genomic Medicine (INMEGEN) was

The National Institute of Genomic Medicine (INMEGEN) was Genome is...... the complete set of genetic information contained within all of the chromosomes of an organism. It defines the particular phenotype of an individual. What is Genomics? The study of the

More information

Regulatory Issues in Genetic Testing and Targeted Drug Development

Regulatory Issues in Genetic Testing and Targeted Drug Development Regulatory Issues in Genetic Testing and Targeted Drug Development Janet Woodcock, M.D. Deputy Commissioner for Operations Food and Drug Administration October 12, 2006 Genetic and Genomic Tests are Types

More information

Introduction to mass spectrometry (MS) based proteomics and metabolomics

Introduction to mass spectrometry (MS) based proteomics and metabolomics Introduction to mass spectrometry (MS) based proteomics and metabolomics Tianwei Yu Department of Biostatistics and Bioinformatics Rollins School of Public Health Emory University September 10, 2015 Background

More information

Molecular Genetics: Challenges for Statistical Practice. J.K. Lindsey

Molecular Genetics: Challenges for Statistical Practice. J.K. Lindsey Molecular Genetics: Challenges for Statistical Practice J.K. Lindsey 1. What is a Microarray? 2. Design Questions 3. Modelling Questions 4. Longitudinal Data 5. Conclusions 1. What is a microarray? A microarray

More information

Biomarkers for Vitamins and Minerals

Biomarkers for Vitamins and Minerals Biomarkers for Vitamins and Minerals Eleanor Brindle Center for Studies in Demography and Ecology University of Washington Biomarkers for Vitamins and Minerals Current methods New methods for use now and

More information

Model Selection. Introduction. Model Selection

Model Selection. Introduction. Model Selection Model Selection Introduction This user guide provides information about the Partek Model Selection tool. Topics covered include using a Down syndrome data set to demonstrate the usage of the Partek Model

More information

Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS)

Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) A typical RNA Seq experiment Library construction Protocol variations Fragmentation methods RNA: nebulization,

More information

Nazneen Aziz, PhD. Director, Molecular Medicine Transformation Program Office

Nazneen Aziz, PhD. Director, Molecular Medicine Transformation Program Office 2013 Laboratory Accreditation Program Audioconferences and Webinars Implementing Next Generation Sequencing (NGS) as a Clinical Tool in the Laboratory Nazneen Aziz, PhD Director, Molecular Medicine Transformation

More information

Total Test Questions: 71 Levels: Grades 10-12 Units of Credit: 1.0 STANDARD 1 STUDENTS WILL INVESTIGATE THE PAST, PRESENT, AND FUTURE APPLICATIONS OF

Total Test Questions: 71 Levels: Grades 10-12 Units of Credit: 1.0 STANDARD 1 STUDENTS WILL INVESTIGATE THE PAST, PRESENT, AND FUTURE APPLICATIONS OF DESCRIPTION Biotechnology is designed to create an awareness of career possibilities in the field of biotechnology. Students are introduced to diagnostic and therapeutic laboratory procedures that support

More information

Medical Informatics II

Medical Informatics II Medical Informatics II Zlatko Trajanoski Institute for Genomics and Bioinformatics Graz University of Technology http://genome.tugraz.at zlatko.trajanoski@tugraz.at Medical Informatics II Introduction

More information

Hacking Brain Disease for a Cure

Hacking Brain Disease for a Cure Hacking Brain Disease for a Cure Magali Haas, CEO & Founder #P4C2014 Innovator Presentation 2 Brain Disease is Personal The Reasons We Fail in CNS Major challenges hindering CNS drug development include:

More information

Basics of microarrays. Petter Mostad 2003

Basics of microarrays. Petter Mostad 2003 Basics of microarrays Petter Mostad 2003 Why microarrays? Microarrays work by hybridizing strands of DNA in a sample against complementary DNA in spots on a chip. Expression analysis measure relative amounts

More information

Factors for success in big data science

Factors for success in big data science Factors for success in big data science Damjan Vukcevic Data Science Murdoch Childrens Research Institute 16 October 2014 Big Data Reading Group (Department of Mathematics & Statistics, University of Melbourne)

More information

Ingenuity Pathway Analysis (IPA )

Ingenuity Pathway Analysis (IPA ) ProductProfile Ingenuity Pathway Analysis (IPA ) For the analysis and interpretation of omics data IPA is a web-based software application for the analysis, integration, and interpretation of data derived

More information

Knowledge Discovery and Data Mining

Knowledge Discovery and Data Mining Knowledge Discovery and Data Mining Lecture 15 - ROC, AUC & Lift Tom Kelsey School of Computer Science University of St Andrews http://tom.home.cs.st-andrews.ac.uk twk@st-andrews.ac.uk Tom Kelsey ID5059-17-AUC

More information

Presentation by: Ahmad Alsahaf. Research collaborator at the Hydroinformatics lab - Politecnico di Milano MSc in Automation and Control Engineering

Presentation by: Ahmad Alsahaf. Research collaborator at the Hydroinformatics lab - Politecnico di Milano MSc in Automation and Control Engineering Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen 9-October 2015 Presentation by: Ahmad Alsahaf Research collaborator at the Hydroinformatics lab - Politecnico di

More information

Genomics Services @ GENterprise

Genomics Services @ GENterprise Genomics Services @ GENterprise since 1998 Mainz University spin-off privately financed 6-10 employees since 2006 Genomics Services @ GENterprise Sequencing Service (Sanger/3730, 454) Genome Projects (Bacteria,

More information

Preparing the scenario for the use of patient s genome sequences in clinic. Joaquín Dopazo

Preparing the scenario for the use of patient s genome sequences in clinic. Joaquín Dopazo Preparing the scenario for the use of patient s genome sequences in clinic Joaquín Dopazo Computational Medicine Institute, Centro de Investigación Príncipe Felipe (CIPF), Functional Genomics Node, (INB),

More information

Data integration in systems biology: characterization of biological phenomena from structural and functional information

Data integration in systems biology: characterization of biological phenomena from structural and functional information Data integration in systems biology: characterization of biological phenomena from structural and functional information Ronaldo Fumio Hashimoto Institute of Mathematics and Statists University of Sao

More information

Biophysical and biochemical mechanisms of the biological effects of mobile phone radiation

Biophysical and biochemical mechanisms of the biological effects of mobile phone radiation Biophysical and biochemical mechanisms of the biological effects of mobile phone radiation Dariusz Leszczynski Research Professor; STUK - Radiation and Nuclear Safety Authority Helsinki, Finland & Guangbiao

More information

Genevestigator Training

Genevestigator Training Genevestigator Training Gent, 6 November 2012 Philip Zimmermann, Nebion AG Goals Get to know Genevestigator What Genevestigator is for For who Genevestigator was created How to use Genevestigator for your

More information

Environmental Research and Innovation ( ERIN )

Environmental Research and Innovation ( ERIN ) RDI Department Environmental Research and Innovation ( ERIN ) LIST s Environmental Research & Innovation (ERIN) department develops strategies, technologies and tools to better monitor, assess, use and

More information

Cardiff University MSc in Bioinformatics - MSc in Genetic Epidemiology & Bioinformatics

Cardiff University MSc in Bioinformatics - MSc in Genetic Epidemiology & Bioinformatics Cardiff University MSc in Bioinformatics - MSc in Genetic Epidemiology & Bioinformatics http://bbu.cardiff.ac.uk/html/training/msc.htm What is Bioinformatics? Bioinformatics applies principles of information

More information

PSS 6424 - Spring 2014

PSS 6424 - Spring 2014 Structural Genomics of Plants and Animals PSS 6424 - Spring 2014 Instructor: Dr. Mark D. Burow, Associate Professor, Department of Plant and Soil Science Office: Room 204D Food Science, email:md.burow@ttu.edu,

More information

FACULTY OF MEDICAL SCIENCE

FACULTY OF MEDICAL SCIENCE Doctor of Philosophy Program in Microbiology FACULTY OF MEDICAL SCIENCE Naresuan University 171 Doctor of Philosophy Program in Microbiology The time is critical now for graduate education and research

More information

Twincore - Zentrum für Experimentelle und Klinische Infektionsforschung Institut für Molekulare Bakteriologie

Twincore - Zentrum für Experimentelle und Klinische Infektionsforschung Institut für Molekulare Bakteriologie Twincore - Zentrum für Experimentelle und Klinische Infektionsforschung Institut für Molekulare Bakteriologie 0 HELMHOLTZ I ZENTRUM FÜR INFEKTIONSFORSCHUNG Technische Universität Braunschweig Institut

More information

2019 Healthcare That Works for All

2019 Healthcare That Works for All 2019 Healthcare That Works for All This paper is one of a series describing what a decade of successful change in healthcare could look like in 2019. Each paper focuses on one aspect of healthcare. To

More information

Defining the genetic component of thyroid cancer. risk at low doses

Defining the genetic component of thyroid cancer. risk at low doses FI6R-CT-2006-36495 GENRISK-T Defining the genetic component of thyroid cancer risk at low doses PROJECT DELIVERABLE A: Coordinator: Prof. Michael J. Atkinson Institut für Strahlenbiologie Helmholtz-Zentrum

More information

Clinical Research Infrastructure

Clinical Research Infrastructure Clinical Research Infrastructure Enhancing UK s Clinical Research Capabilities & Technologies At least 150m to establish /develop cutting-edge technological infrastructure, UK wide. to bring into practice

More information

WG5: Informatics. Martin Dugas, Jaakko Hollmen. European Genomics and Epigenomics Study on MDS and AML

WG5: Informatics. Martin Dugas, Jaakko Hollmen. European Genomics and Epigenomics Study on MDS and AML WG5: Informatics Martin Dugas, Jaakko Hollmen EuGESMA European Genomics and Epigenomics Study on MDS and AML Presentations from WG5 members Hans Ulrich Klein Detection of Fusion Genes by Targeted Roche

More information

(1-p) 2. p(1-p) From the table, frequency of DpyUnc = ¼ (p^2) = #DpyUnc = p^2 = 0.0004 ¼(1-p)^2 + ½(1-p)p + ¼(p^2) #Dpy + #DpyUnc

(1-p) 2. p(1-p) From the table, frequency of DpyUnc = ¼ (p^2) = #DpyUnc = p^2 = 0.0004 ¼(1-p)^2 + ½(1-p)p + ¼(p^2) #Dpy + #DpyUnc Advanced genetics Kornfeld problem set_key 1A (5 points) Brenner employed 2-factor and 3-factor crosses with the mutants isolated from his screen, and visually assayed for recombination events between

More information

Superior TrueMAB TM monoclonal antibodies for the recognition of proteins native epitopes

Superior TrueMAB TM monoclonal antibodies for the recognition of proteins native epitopes Superior TrueMAB TM monoclonal antibodies for the recognition of proteins native epitopes Outlines Brief introduction of OriGene s mission on gene-centric product solution. TrueMAB monoclonal antibody

More information

White Paper. Yeast Systems Biology - Concepts

White Paper. Yeast Systems Biology - Concepts White Paper Yeast Systems Biology - Concepts Stefan Hohmann, Jens Nielsen, Hiroaki Kitano (see for further contributers at end of text) Göteborg, Lyngby, Tokyo, February 2004 1 Executive Summary Systems

More information

Introduction to Proteomics

Introduction to Proteomics Introduction to Proteomics Åsa Wheelock, Ph.D. Division of Respiratory Medicine & Karolinska Biomics Center asa.wheelock@ki.se In: Systems Biology and the Omics Cascade, Karolinska Institutet, June 9-13,

More information

BSc (Hons) Biology (Minor: Forensic Science or Marine & Coastal Environmental Science)/MSc Biology SC516 (Subject to Approval) SC516

BSc (Hons) Biology (Minor: Forensic Science or Marine & Coastal Environmental Science)/MSc Biology SC516 (Subject to Approval) SC516 BSc (Hons) Biology (Minor: Forensic Science or Marine & Coastal Environmental Science)/MSc Biology SC516 (Subject to Approval) SC516 1. Mission, Aims and Objectives The new BSc (Hons)/ MSc course is a

More information

Genomic Analysis Solutions from SAS

Genomic Analysis Solutions from SAS Genomic Analysis Solutions from SAS Russell Wolfinger Gerhard Held Development Director Solutions Manager Genomics Analytical Applications SAS Institute Inc. SAS International Pictures: Human Genome Program

More information

Protein Protein Interaction Networks

Protein Protein Interaction Networks Functional Pattern Mining from Genome Scale Protein Protein Interaction Networks Young-Rae Cho, Ph.D. Assistant Professor Department of Computer Science Baylor University it My Definition of Bioinformatics

More information

escience and Post-Genome Biomedical Research

escience and Post-Genome Biomedical Research escience and Post-Genome Biomedical Research Thomas L. Casavant, Adam P. DeLuca Departments of Biomedical Engineering, Electrical Engineering and Ophthalmology Coordinated Laboratory for Computational

More information

The Human Genome Project

The Human Genome Project The Human Genome Project Brief History of the Human Genome Project Physical Chromosome Maps Genetic (or Linkage) Maps DNA Markers Sequencing and Annotating Genomic DNA What Have We learned from the HGP?

More information

Plant Metabolomics. For BOT 6516

Plant Metabolomics. For BOT 6516 Plant Metabolomics For BOT 6516 Introduction Modern metabolomics began about ten years ago and yet many continue to question the relative performance of this area of technology in advancing plant biology.

More information

Software Description Technology

Software Description Technology Software applications using NCB Technology. Software Description Technology LEX Provide learning management system that is a central resource for online medical education content and computer-based learning

More information

Licht ins Dunkel BLACKBOX

Licht ins Dunkel BLACKBOX Licht ins Dunkel BLACKBOX 1 Hypothesis-driven Research Hypothesis 1 Hypothesis 2 Hypothesis 1 Hypothesis 2 Hypothesis Focus 3 3 Hypothesis 3 Hypothesis 4 Hypothesis 5 2 Light into the Blackbox Answers

More information

Noise Exposure and Serious Injury in British Columbia Sawmills

Noise Exposure and Serious Injury in British Columbia Sawmills Noise Exposure and Serious Injury in British Columbia Sawmills Rakel N. Kling, Hugh W. Davies, Hasanat Alamgir, & Paul A. Demers University of British Columbia AIHce,, Philadelphia, June 6 th, 2007 Presentation

More information

(3) UNRAVELING PEACH FRUIT MEALINESS AND COLD STORAGE BROWNING WITH GENOMIC TOOLS

(3) UNRAVELING PEACH FRUIT MEALINESS AND COLD STORAGE BROWNING WITH GENOMIC TOOLS (3) UNRAVELING PEACH FRUIT MEALINESS AND COLD STORAGE BROWNING WITH GENOMIC TOOLS Ebenezer A. Ogundiwin 1, Antonio Granell 2, Thomas M. Gradziel 1, and Carlos H. Crisosto 1 1 Department of Plant Sciences,

More information

Statistics Graduate Courses

Statistics Graduate Courses Statistics Graduate Courses STAT 7002--Topics in Statistics-Biological/Physical/Mathematics (cr.arr.).organized study of selected topics. Subjects and earnable credit may vary from semester to semester.

More information

BIOINF 525 Winter 2016 Foundations of Bioinformatics and Systems Biology http://tinyurl.com/bioinf525-w16

BIOINF 525 Winter 2016 Foundations of Bioinformatics and Systems Biology http://tinyurl.com/bioinf525-w16 Course Director: Dr. Barry Grant (DCM&B, bjgrant@med.umich.edu) Description: This is a three module course covering (1) Foundations of Bioinformatics, (2) Statistics in Bioinformatics, and (3) Systems

More information

OECD FELLOWSHIP SUMMARY REPORT

OECD FELLOWSHIP SUMMARY REPORT OECD FELLOWSHIP SUMMARY REPORT Name: Rolf Altenburger Subject: Status and research need in toxicogenomic mixture toxicity analysis Host Institution: University of Queensland, Brisbane, QLD Host Supervisor:

More information

6 ELIXIR Domain Specific Services

6 ELIXIR Domain Specific Services 6 ELIXIR Domain Specific Services Work stream leads: Alfonso Valencia (ES), Inge Jonassen (NO), Jose Leal (PT) Work stream members: Nils-Peder Willassen (NO), Finn Drablos (NO), Mark Viant (UK), Ferran

More information

An EVIDENCE-ENHANCED HEALTHCARE ECOSYSTEM for Cancer: I/T perspectives

An EVIDENCE-ENHANCED HEALTHCARE ECOSYSTEM for Cancer: I/T perspectives An EVIDENCE-ENHANCED HEALTHCARE ECOSYSTEM for Cancer: I/T perspectives Chalapathy Neti, Ph.D. Associate Director, Healthcare Transformation, Shahram Ebadollahi, Ph.D. Research Staff Memeber IBM Research,

More information

The growing challenges of big data in the agricultural and ecological sciences

The growing challenges of big data in the agricultural and ecological sciences The growing challenges of big data in the agricultural and ecological sciences chris.rawlings@rothamsted.ac.uk Head of Computational and Systems Biology Food Security Demand for food is projected to increase

More information

Understanding the dynamics and function of cellular networks

Understanding the dynamics and function of cellular networks Understanding the dynamics and function of cellular networks Cells are complex systems functionally diverse elements diverse interactions that form networks signal transduction-, gene regulatory-, metabolic-

More information

Beaming in your answers

Beaming in your answers Bio 112 Handout for Evolution 4 This handout contains: Today s iclicker Question Figures for today s lecture iclicker Question #1 - after lecture Which of the following statements are false: A. If the

More information

Gene Expression Analysis

Gene Expression Analysis Gene Expression Analysis Jie Peng Department of Statistics University of California, Davis May 2012 RNA expression technologies High-throughput technologies to measure the expression levels of thousands

More information

CCR Biology - Chapter 9 Practice Test - Summer 2012

CCR Biology - Chapter 9 Practice Test - Summer 2012 Name: Class: Date: CCR Biology - Chapter 9 Practice Test - Summer 2012 Multiple Choice Identify the choice that best completes the statement or answers the question. 1. Genetic engineering is possible

More information

What s New in Pathway Studio Web 11.1

What s New in Pathway Studio Web 11.1 1 1 What s New in Pathway Studio Web 11.1 Elseiver is pleased to announce the release of Pathway Studio Web 11.1 for all database subscriptions (Mammal, Mammal+ChemEffect+DiseaseFx, Plant). This release

More information

Name Class Date. KEY CONCEPT Mutations are changes in DNA that may or may not affect phenotype. frameshift mutation

Name Class Date. KEY CONCEPT Mutations are changes in DNA that may or may not affect phenotype. frameshift mutation Unit 7 Study Guide Section 8.7: Mutations KEY CONCEPT Mutations are changes in DNA that may or may not affect phenotype. VOCABULARY mutation point mutation frameshift mutation mutagen MAIN IDEA: Some mutations

More information

Deterministic computer simulations were performed to evaluate the effect of maternallytransmitted

Deterministic computer simulations were performed to evaluate the effect of maternallytransmitted Supporting Information 3. Host-parasite simulations Deterministic computer simulations were performed to evaluate the effect of maternallytransmitted parasites on the evolution of sex. Briefly, the simulations

More information

SYMPOSIUM. June 15, 2013. Photonics Center Colloquium Room (906) 8 Saint Mary's St., Boston, MA 02215 Boston University

SYMPOSIUM. June 15, 2013. Photonics Center Colloquium Room (906) 8 Saint Mary's St., Boston, MA 02215 Boston University SYMPOSIUM June 15, 2013 Photonics Center Colloquium Room (906) 8 Saint Mary's St., Boston, MA 02215 Bette Korber Los Alamos National Labs HIV evolution and the neutralizing antibody response We have recently

More information

Biological importance of metabolites. Safety and efficacy aspects

Biological importance of metabolites. Safety and efficacy aspects Biological importance of metabolites Safety and efficacy aspects Bernard Walther Technologie Servier Biological importance of metabolites Safety testing of drug metabolites Bioanalytical strategy Structural

More information

Master's projects at ITMO University. Daniil Chivilikhin PhD Student @ ITMO University

Master's projects at ITMO University. Daniil Chivilikhin PhD Student @ ITMO University Master's projects at ITMO University Daniil Chivilikhin PhD Student @ ITMO University General information Guidance from our lab's researchers Publishable results 2 Research areas Research at ITMO Evolutionary

More information

OMICs TECHNOLOGY PLATFORM (GENOMICS, PROTEOMICS AND METABOLOMICS). Coordinators: Prof. Marcello Maggiolini, Prof. Maria Beatrice Bitonti

OMICs TECHNOLOGY PLATFORM (GENOMICS, PROTEOMICS AND METABOLOMICS). Coordinators: Prof. Marcello Maggiolini, Prof. Maria Beatrice Bitonti OMICs TECHNOLOGY PLATFORM (GENOMICS, PROTEOMICS AND METABOLOMICS). Coordinators: Prof. Marcello Maggiolini, Prof. Maria Beatrice Bitonti 0 The OMICA Technology Platform (Genomics, Proteomics and Metabolomics)

More information

STANDARD 2 Students will demonstrate appropriate safety procedures and equipment use in the laboratory.

STANDARD 2 Students will demonstrate appropriate safety procedures and equipment use in the laboratory. BIOTECHNOLOGY Levels: 11-12 Units of Credit: 1.0 CIP Code: 51.1201 Prerequisite: Biology or Chemistry Skill Certificates: #708 COURSE DESCRIPTION is an exploratory course designed to create an awareness

More information

TECHNOLOGIES, PRODUCTS & SERVICES for MOLECULAR DIAGNOSTICS, MDx ABA 298

TECHNOLOGIES, PRODUCTS & SERVICES for MOLECULAR DIAGNOSTICS, MDx ABA 298 DIAGNOSTICS BUSINESS ANALYSIS SERIES: TECHNOLOGIES, PRODUCTS & SERVICES for MOLECULAR DIAGNOSTICS, MDx ABA 298 By ADAMS BUSINESS ASSOCIATES MAY 2014. May 2014 ABA 298 1 Technologies, Products & Services

More information

Genetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis

Genetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis Genetic Analysis Phenotype analysis: biological-biochemical analysis Behaviour under specific environmental conditions Behaviour of specific genetic configurations Behaviour of progeny in crosses - Genotype

More information

IMPLEMENTING BIG DATA IN TODAY S HEALTH CARE PRAXIS: A CONUNDRUM TO PATIENTS, CAREGIVERS AND OTHER STAKEHOLDERS - WHAT IS THE VALUE AND WHO PAYS

IMPLEMENTING BIG DATA IN TODAY S HEALTH CARE PRAXIS: A CONUNDRUM TO PATIENTS, CAREGIVERS AND OTHER STAKEHOLDERS - WHAT IS THE VALUE AND WHO PAYS IMPLEMENTING BIG DATA IN TODAY S HEALTH CARE PRAXIS: A CONUNDRUM TO PATIENTS, CAREGIVERS AND OTHER STAKEHOLDERS - WHAT IS THE VALUE AND WHO PAYS 29 OCTOBER 2015 DR. DIRK J. EVERS BACKGROUND TreatmentMAP

More information

Healthcare Analytics. Aryya Gangopadhyay UMBC

Healthcare Analytics. Aryya Gangopadhyay UMBC Healthcare Analytics Aryya Gangopadhyay UMBC Two of many projects Integrated network approach to personalized medicine Multidimensional and multimodal Dynamic Analyze interactions HealthMask Need for sharing

More information

Translational Technologies Resources (TTR)

Translational Technologies Resources (TTR) Translational Technologies Resources (TTR) TTR at CWRU Bioinformatics and Biostatistics Core This core can provide services on typical data which are focused on large scale information datasets (a.k.a.

More information

200631 - ADO - Omics Data Analysis

200631 - ADO - Omics Data Analysis Coordinating unit: Teaching unit: Academic year: Degree: ECTS credits: 2016 200 - FME - School of Mathematics and Statistics 1004 - UB - (ENG)Universitat de Barcelona MASTER'S DEGREE IN STATISTICS AND

More information

A truly robust Expression analyzer

A truly robust Expression analyzer Genowiz A truly robust Expression analyzer Abstract Gene expression profiles of 10,000 tumor samples, disease classification, novel gene finding, linkage analysis, clinical profiling of diseases, finding

More information

Big Data and Data Analysis for Personalized Medicine

Big Data and Data Analysis for Personalized Medicine Big Data and Data Analysis for Personalized Medicine Dr. Paul Terry Ambassador Agenda Information and Data The Technology The Promise Personalized Medicine 2 CEO/CTO of PHEMI Board of Life Sciences BC

More information