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Bioinformatics: How Computer Science is Changing Biology

BIOINFORMATICS HOW COMPUTER SCIENCE IS CHANGING BIOLOGY BIOINFORMATICS is the application of statistics and computer science, including machine learning and high performance computing, to solve problems in biology COMPUTATIONAL BIOLOGY AND INFORMATICS HAVE MADE IT • map and analyze DNA and protein sequences • build models for artificial organs • design and validate pharmaceutical drugs • analyze disease and risk on an individual level AMOUNT OF DATA BEING GENERATED IN BIOLOGY TODAY EVEN THE SMALLEST KNOWN DNA SEQUENCE - FROM AN ANTARCTIC MIDGE FLY - CONTAINS 99 MILLION BASE PAIRS OF DNA The two complementary, nitrogen-rich molecules held together by weak chemical bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between their base pairs 2.8 BILLION 2.7 BILLION BASE PAIRS BASE PAIRS HUMAN GENOME CONTAINS A SEQUENCE OF 3.2 BILLION PAIRS DATA SIZES COMMONLY RUN INTO PETABYTES PUBLIC INFORMATICS REPOSITORIES ARE ALREADY HOUSING PETABYTES – MILLIONS OF GIGABYTES – OF DATA 1 PETABYTE = 58,292 MOVIES OR 13.3 YEARS OF HDTV CONTENT BENEFITS OF BIOINFORMATICS Diseases like cancer can be better understood thanks to informatics CANCER GENOME ATLAS – MAPPING THE GENOMES OF 25 TYPES OF CANCERS CANCER TUMOR GENOMES CAN BE ANALYZED FOR THEIR RESPONSES TO A PARTICULAR KIND OF DRUG BY SEQUENCING EACH PATIENT'S DNA AND THE TUMOR'S GENOME, THE BEST TREATMENT FOR PATIENTS IS TRULY INDIVIDUALIZED AND TREATMENT OUTCOMES CAN BE GREATLY IMPROVED 1.6 MILLION PEOPLE WERE DIAGNOSED WITH CANCER IN 2014 a4 Prediction of disease risk gained from genomic data is more accurate USING GENOMIC SEQUENCING TO PREDICT BREAST CANCER RISK CAN IDENTIFY PATIENTS AT HIGH RISK FOR THE DISEASE CANCER OUTCOMES CAN BE POSITIVELY IMPACTED DUE TO: • INCREASED SCREENING AND DETECTION STRATEGIES AT APPROPRIATE AGES AND INTERVALS FOR IDENTIFIED PATIENTS • REDUCED EXPOSURE TO NON-GENETIC RISK FACTORS FOR THESE PATIENTS PROJECTS LIKE GENOMEIOK STUDY SPECIES LIKE THE CICHLID, A FISH THAT EVOLVED IN FEWER THAN 10O,000 YEARS Species usually evolve over a period of tens of millions of years GENOMEIOK – SEQUENCING AND ASSEMBLING THE DNA OF 10,000 VERTEBRATE SPECIES AND ANALYZING THEIR EVOLUTIONARY RELATIONSHIP CHANGING THE WAY PHARMACEUTICAL COMPANIES DEVELOP DRUGS THESE TYPES OF ADVANCED COMPUTER MODELING AND SIMULATIONS COULD DRASTICALLY CHANGE THE WAY PHARMACEUTICAL COMPANIES DEVELOP FUTURE DRUGS RESEARCHERS FROM TEL AVIV UNIVERSITY BUILT A SUPERCOMPUTER TO SIMULATE CHANGES IN A PROTEIN'S THREE-DIMENSIONAL STRUCTURE THAT OCCUR ON A MILLISECOND TIME SCALE THE RESULTING DATA HAVE HELPED RESEARCHERS BETTER UNDERSTAND FUNDAMENTAL MOLECULAR MECHANISMS IN A NUMBER OF BIOLOGICAL PROCESSES AND DISEASES Development of novel models and methods for storing and analyzing data WATSON IS A CLOUD-BASED PROTOTYPE DESIGNED TO HELP ONCOLOGISTS DELIVER MORE PERSONALIZED CARE TO CANCER PATIENTS • WATSON CAN CONTINUALLY LEARN THROUGH NEW PATIENT SCENARIOS AND NEW RESEARCH, JOURNAL ARTICLES AND CLINICAL STUDIES SPOTLIGHT ON BIOINFORMATICS PROJECTS TO00 GENOMES PROJECT THE GENOMES OF 2500 UNIDENTIFIED PEOPLE FROM 25 POPULATIONS AROUND THE WORLD WILL BE SEQUENCED USING NEXT-GENERATION SEQUENCING TECHNOLOGIES NATIONAL INSTITUTES OF HEALTH DATABASE OF GENOTYPES AND PHENOTYPES (dbGaP) DEVELOPED TO ARCHIVE AND DISTRIBUTE RESULTS OF THE FOLLOWING TYPES OF STUDIES: 12 12 12 121 * GENOME-WIDE ASSOCIATION STUDIES * MEDICAL SEQUENCING * MOLECULAR DIAGNOSTIC ASSAYS ASSOCIATIONS BETWEEN GENOTYPE AND NON-CLINICAL TRAITS 14 14 15 15 15 15 16 DIALOGUE FOR REVERSE ENGINEERING ASSESSMENTS AND METHODS (DREAM) CHALLENGES FOR THE SCIENTIFIC COMMUNITY CLOUD COMPUTING COMPANIES COMPANIES LIKE BINA TECHNOLOGIES USE THE POWER OF CLOUD COMPUTING TO MAP GENES AND VARIANT DETECTION AS WELL AS PROVIDE MORE THAN 130 WAYS TO ANNOTATE AND INTERPRET THE VARIATIONS OF GENOMIC DATA PERSONAL GENOMICS COMPANIES BRCAQTRUE BRCAOTRUE PATHWAY GENOMICS DEVELOPED A BREAST CANCER GENETIC RISK TEST, BRCA TRUE, WHICH HAS BEEN RANKED IN INC. MAGAZINE'S TOP 12 COOLEST PRODUCTS OF THE INC. S00 FOR 2014. 61.5% CLOSE TO 2 OUT OF 3 CONSUMERS WHO HAVE USED DIRECT TO CONSUMER GENETIC TESTING BELIEVE THE TEST TO BE HIGHLY USEFUL 36% SHARED THEIR RESULTS WITH THEIR PHYSICIANS NJIT. New Jersey Institute of Technology computerscience.online.njit.edu SOURCES http://cacm.acm.org/magazines/2014/5/174344-how-computers-are-changing-biology/fulltext http://cebp.aacrjournals.org/content/early/2014/10/06/1055-9965.EPI-14-0559.abstract http://commonfund.nih.gov/hmp/index http://liaison.com http://www.1000genomes.org/about http://www.bina.com http://www.cancer.org/research/cancerfactsstatistics/cancerfactsfigures2014/index http://cancergenome.nih.gov http://www.forbes.com/sites/matthewherper/2013/08/11/how-the-staggering-cost-of-inventing-new-drugs-is-shaping-the-future-of-medicine/ http://www.genome.gov/25520329 http://www.ncbi.nlm.nih.gov/gap http://www.ncbi.nlm.nih.gov/pubmed/23559530 http://www.nygenome.org/news/new-york-genome-center-ibm-watson-group-announce-collaboration-advance-genomic-medicine/ http://www.the-dream-project.org https://genome10k.soe.ucsc.edu/ https://www.pathway.com/pathway-selected-in-top-12-coolest-products-of-inc-5000-fastest-growing-companies/ http://gizmodo.com/5309889/how-large-is-a-petabyte http://ghr.nlm.nih.gov/glossary=basepair NOSIVM

Bioinformatics: How Computer Science is Changing Biology

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Bioinformatics is the careful application of computers and statistics to the field of biology. It includes things such as machine learning and computing at high rate of performance in order to help so...

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