Mini course to understand the biological pathway Yong Jiang(Frank)

Slides:

Advertisements

Similar presentations

Parallel BioInformatics Sathish Vadhiyar. Parallel Bioinformatics  Many large scale applications in bioinformatics – sequence search, alignment, construction.

Advertisements

Doug Raiford Lesson 13 5/10/20151Gene networks and pathways.

iNtegrating Technology for inQuery

+ Phylogenetic Trees AP Biology Evolution. + Phylogenetic Trees By Bob Cooper and Mark Eberhard.

Gene Ontology John Pinney

Bioinformatics for biomedicine Seminar: Sequence analysis of a favourite gene Lecture 5, Per Kraulis

BIOINFORMATICS Ency Lee.

Bioinformatics for biomedicine Summary and conclusions. Further analysis of a favorite gene Lecture 8, Per Kraulis

Democratizing Bioinformatics Research in a High School Biology Classroom Bertram C. Bruce, Umesh Thakkar, Eric G. Jakobsson, Jo Williamson, Paul R. Lock.

KEGG: Kyoto Encyclopedia of Genes and Genomes Susan Seo Intro to Bioinformatics Fall 2004.

Projects Key dates lists of suggested projects published * *You are highly encouraged to choose a project yourself or find a relevant project.

1 Data Integration and Extraction over Molecular Biological Data Cui Tao supported by NSF.

August 29, 2002InforMax Confidential1 Vector PathBlazer Product Overview.

Biology Workbench Introduction. What is it used for? It is a web-browser to use bioinformatics tools to analyze and visualize nucleotide and protein sequences.

We are developing a web database for plant comparative genomics, named Phytome, that, when complete, will integrate organismal phylogenies, genetic maps.

Bioinformatics Unit 1: Data Bases and Alignments Lecture 3: “Homology” Searches and Sequence Alignments (cont.) The Mechanics of Alignments.

Signaling Pathways and Summary June 30, 2005 Signaling lecture Course summary Tomorrow Next Week Friday, 7/8/05 Morning presentation of writing assignments.

Welcome to Introduction to Bioinformatics Computing aka BIC1.

ExPASy - Expert Protein Analysis System The bioinformatics resource portal and other resources An Overview.

Gyrase Mutation in Various Bacteria Leading to Fluoroquinolone (“Cipro”) Resistance By: Nancy Halliday Wesley Hanson Brenda Breeding.

EECS 395/495 Algorithmic Techniques for Bioinformatics General Introduction 9/27/2012 Ming-Yang Kao 19/27/2012.

Final GK-12 Presentation Participant: Anuradha Datta Murphy, Dept. of Molecular & Integrative Physiology, UIUC Mentor: Deanna Raineri, Assoc.. Dean, Dept.

341: Introduction to Bioinformatics Dr. Natasa Przulj Deaprtment of Computing Imperial College London

Ch10. Intermolecular Interactions and Biological Pathways

Role of Rubisco in Photosynthesis Anu Murphy Dept. of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign.

Bioinformatics Dr. Víctor Treviño BT4007

Data and Dissemination Core 1. Overview and EFI Website – Heidi Imker, UIUC 2. EFI LabDB LIMS – Wladek Minor, UVA 3. SFLD – Patsy Babbitt, UCSF (post lunch)

An Introduction to the Inquiry Page and the Biology Workbench An Introduction to the Inquiry Page and the Biology Workbench Anu Murphy Department of Molecular.

EBI is an Outstation of the European Molecular Biology Laboratory. Avazeh Ghanbarian Paul Kersey Alessandro Vullo EBI Microme Annotation Meeting June 2011.

Research Methods in Computer Science James Gain

Integrating the Bioinformatic Technology Group into your research programme Introduction People and Skills Examples Integrating the BTG Contacts BHRC Away.

Gene set analysis by using CPDB By NFU Biology Algorithm lab.

ARE THESE ALL BEARS? WHICH ONES ARE MORE CLOSELY RELATED?

Bioinformatics for Human Biologists Rasmus Wernersson, Associate Professor Center for Biological Sequence Analysis, DTU [ -

Mining Biological Data. Protein Enzymatic ProteinsTransport ProteinsRegulatory Proteins Storage ProteinsHormonal ProteinsReceptor Proteins.

Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST INVESTIGATION 3 BIG IDEA 1.

CTCAAGGGGTNAGNNNTNTNAAAGNTGCCNTTCCAAAGNTNNGNNNANNACNNTTGGCCGAGAACTTNGNNG GGGNTNANTNNNATATTCCNATTTTGCCTAATACNANGCTTGATANTTTCCGTTTNNTCNCACCTGGGNNCNNNT AATCGGATGNNGGACANANCAANGCGGGCCTTCACCCCATCNTGGNGGNCCNTNNGNCCNTTTNGCCANTCNC.

November 18, 2000ICTCM 2000 Introductory Biological Sequence Analysis Through Spreadsheets Stephen J. Merrill Sandra E. Merrill Marquette University Milwaukee,

Structural Models Lecture 11. Structural Models: Introduction Structural models display relationships among entities and have a variety of uses, such.

Bioinformatics Curriculum Issues, goals, curriculum.

An overview of Bioinformatics. Cell and Central Dogma.

Portfolios for TAs. PI34 “Students must complete a portfolio of evidence for the teaching standards” to be certified Review.

Copyright OpenHelix. No use or reproduction without express written consent1 1.

Automatic and manual sequence alignment Inferring phylogenetic trees Mining web-based databases Estimating rates of molecular evolution Testing evolutionary.

Bioinformatics Research Overview Li Liao Develop new algorithms and (statistical) learning methods > Capable of incorporating domain knowledge > Effective,

Tools in Bioinformatics Ontologies and pathways. Why are ontologies needed? A free text is the best way to describe what a protein does to a human reader.

Integration of BioInformatics tools at NUS. GenBank Growth Chart Year Bases.

Biotechnology and Bioinformatics: Bioinformatics Essential Idea: Bioinformatics is the use of computers to analyze sequence data in biological research.

L ESSON A IMS & O BJECTIVES Two part lab: First part will be completed in class today. (1) Use the online Bioinformatics tool ClustalW to analyze DNA sequences.

Course Overview This course encourages candidates to develop their knowledge and understanding of computer systems, the principles of computing (including.

PROTEIN IDENTIFIER IAN ROBERTS JOSEPH INFANTI NICOLE FERRARO.

Introducing Bioinformatics Using the Nitrogen Cycle Alyssa Bumbaugh Ron Peck Mark Radosevich.

Using BLAST to Identify Species from Proteins

INVESTIGATION 3 BIG IDEA 1

Biological Databases By: Komal Arora.

Bioinformatics Capstone Project

Using BLAST to Identify Species from Proteins

Predict Protein Sequence by Fuzzy-Association Rules

INVESTIGATION 3 BIG IDEA 1

Bioinformatics and BLAST

INVESTIGATION 3 BIG IDEA 1

Overview Bioinformatics: Analyzing biological data using statistics, math modeling, and computer science BLAST = Basic Local Alignment Search Tool Input.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Explore Evolution: Instrument for Analysis

Evolution Test Wednesday

INVESTIGATION 3 BIG IDEA 1

Multiple sequence alignment & Phylogenetics Analysis

Using BLAST to Identify Species from Proteins

Introduction to Bioinformatics

SUBMITTED BY: DEEPTI SHARMA BIOLOGICAL DATABASE AND SEQUENCE ANALYSIS.

Presentation transcript:

Mini course to understand the biological pathway Yong Jiang(Frank)

Purpose of the course  Provide basic knowledge of biological reaction path to student that may not have rich biological background.  Provide online database that students are able to extract valuable information of reaction path.  Help students to integrate they knowledge in the context of bioinformatics  Promote students ’ interests to use possible tools to explore unknown problems.

Students will learn …  How to use bio-pathway database (KEGG, Ecocyc) to search for a specific biological reaction or enzyme.  Observing the structure of enzyme in 3D software  Find similar enzyme in different species.  Do sequence and structure alignment and find phygenetic relationship between different species.  Modeling the kinetics of the reaction

Case study “ glucose-6-phosphate isomerase “ alpha-D-Glucose 6-phosphate glucose-6- phosphate isomerase beta-D-Fructose 6-phosphate

glucose-6- phosphate isomerase Observing 3D structure Sequence and structure alignment Find similar sequence in different species Find phylogenetic tree of different species Modeling kinetics

Before the class … Students are divided into groups. Discussion within group is encouraged. Students are divided into groups. Discussion within group is encouraged. Each group will find literatures that relates to the specific biological reaction they are interested in. Each group will find literatures that relates to the specific biological reaction they are interested in. Each group will prepare a proposal talk before class Each group will prepare a proposal talk before class

In the class … One student representing each group will give a proposal talk and answer questions from other groups. One student representing each group will give a proposal talk and answer questions from other groups. Find similar enzymes that exist in other species in bioquest workbench. Find similar enzymes that exist in other species in bioquest workbench. Download pdb files of these proteins from pdb databank. Download pdb files of these proteins from pdb databank. Do sequence and structure alignment and find phygenetic relationship between different species. Propose the candidate active site that is crucial for the enzyme function. Do sequence and structure alignment and find phygenetic relationship between different species. Propose the candidate active site that is crucial for the enzyme function. Modeling the process and find the reaction order. Modeling the process and find the reaction order.

After the class … Each group will prepare a poster session reporting their finding Each group will prepare a poster session reporting their finding Encourage inter-group discussion. Encourage inter-group discussion. Award will be given to top 3 posters. Award will be given to top 3 posters.