Introduction to bioin as long as matics (I617) Textbook Grading Bioin as long as matics = BIOlogy + in as long as matics The birth of bioin as long as matics

Introduction to bioin as long as matics (I617) Textbook Grading Bioin as long as matics = BIOlogy + in as long as matics The birth of bioin as long as matics www.phwiki.com

Introduction to bioin as long as matics (I617) Textbook Grading Bioin as long as matics = BIOlogy + in as long as matics The birth of bioin as long as matics

Cox, Beverly, Food Editor has reference to this Academic Journal, PHwiki organized this Journal Introduction to bioin as long as matics (I617) Haixu Tang School of In as long as matics Email: hatang@indiana.edu Office: EIG 1008 Tel: 812-856-1859 Textbook A Primer of Genome Science (2nd Edition) by Greg Gibson, Spencer V. Muse, Sinauer Associates, 2004 Suggested reading materials will be posted on the class wiki page: http://cheminfo.in as long as matics.indiana.edu/djwild/I617-2006-wiki/index.php/Main-Page Office Hour: MW 11:00-12:00, EIG 1008 or appointment Grading Class project: selected from one of four covered areas (bioin as long as matics, Chemical in as long as matics, Laboratory in as long as matics in addition to Health in as long as matics) 25% Suggested Bioin as long as matics topics will be posted on the class wiki page Homework: 25% in Bioin as long as matics 4, each 6.25%

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Bioin as long as matics = BIOlogy + in as long as matics Not really: it is a term (somehow arbitrarily chosen) to define a multi-disciplinary area that combines life sciences, physical sciences in addition to computer science / in as long as matics; It addresses biological problems using theoretical in as long as matics approaches, not vice versa; It is trans as long as ming classical Biology into a In as long as mation Science. The birth of bioin as long as matics A revolution in biology research: the emergence of Genome Science Technology advancement in both biology in addition to in as long as mation science Genome science: a revolution of biology Classical Biology Genome Science Hypothesis Hypothesis driven approach Data Data driven approach

Bioin as long as matics: from data analysis to data mining Classical Biology Hypothesis Low throughput data Genome Science Data High throughput data Hypothesis confirmation / rejection Hypothesis generation Bioin as long as matics: in the driver’s seat Classical Biology Hypothesis Genome Science Data Data analysis Data mining Key technology advancements High throughput biotechnologies Genome sequencing techniques DNA microarray Mass spectrometry Large-scale experiments HGP, HapMap Omics / Systems Biology Massive data generation, storage, exchange in addition to analysis CPU, storage, etc. High speed network (Internet) Bioin as long as matics

Bioin as long as matics: mutually beneficial For biologists Fragment assembly in genome sequencing Genome comparison Gene clustering in DNA microarray analysis Protein identification in proteomics For computer scientists String algorithms / Tree algorithms Alternative Eulerian path (BEST theorem) Reversal distances Probabilistic graphic models (HMMs, BNs, etc.) Two origins of bioin as long as matics Combinatorial pattern matching in theoretical computer science DNA in addition to protein sequence analysis Physical in addition to analytical chemistry of Biomolecules Protein structure analysis Structural bioin as long as matics Bio-analytical chemistry Proteomics Bioin as long as matics addresses computational challenges in life in addition to medical sciences New computational problems as long as automatic data analysis Re as long as mulation of old problems using new high throughput data Formulating new problems using high throughput data

Bioin as long as matics addresses computational challenges in life in addition to medical sciences New computational problems as long as automatic data analysis Genome sequencing Proteomics Transcriptomics Data representation in addition to visualization Genome Browser Solving biological problems by in silico approaches Re as long as mulation of old problems using new high throughput data Gene finding Protein structure in addition to function Formulating new problems using high throughput data Comparative genomics Polymorphisms / Population genetics Systems Biology Bioin as long as matics resources Databases Nucleic Acid Research (NAR) annual database issue Organization ISCB (International Society in Computational Biology) Conferences ISMB RECOMB Many other smaller or regional conferences, e.g. ECCB, CSB, PSB, etc, including local Indiana Bioin as long as matics conference A case study How bioin as long as matics help in addition to trans as long as m classical biological topics Molecular evolutionary studies: from anatomical features to molecular evidences Genome evolution: comparison of gene orders

Early Evolutionary Studies Anatomical features were the dominant criteria used to derive evolutionary relationships between species since Darwin till early 1960s Early Evolutionary Studies Anatomical features were the dominant criteria used to derive evolutionary relationships between species since Darwin till early 1960s The evolutionary relationships derived from these relatively subjective observations were often inconclusive. Some of them were later proved incorrect Evolution in addition to DNA Analysis: the Giant P in addition to a Riddle For roughly 100 years scientists were unable to figure out which family the giant p in addition to a belongs to Giant p in addition to as look like bears but have features that are unusual as long as bears in addition to typical as long as raccoons, e.g., they do not hibernate

Evolution in addition to DNA Analysis: the Giant P in addition to a Riddle In 1985, Steven O’Brien in addition to colleagues solved the giant p in addition to a classification problem using DNA sequences in addition to bioin as long as matics algorithms Evolutionary Tree of Bears in addition to Raccoons Evolutionary Trees: DNA-based Approach 40 years ago: Emile Zuckerk in addition to l in addition to Linus Pauling brought reconstructing evolutionary relationships with DNA into the spotlight In the first few years after Zuckerk in addition to l in addition to Pauling proposed using DNA as long as evolutionary studies, the possibility of reconstructing evolutionary trees by DNA analysis was hotly debated Now it is a dominant approach to study evolution.

Evolutionary Trees How are these trees built from DNA sequences Evolutionary Trees How are these trees built from DNA sequences leaves represent existing species internal vertices represent ancestors root represents the common evolutionary ancestor Rooted in addition to Unrooted Trees In the unrooted tree the position of the root (“common ancestor”) is unknown. Otherwise, they are like rooted trees

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Distances in Trees Edges may have weights reflecting: Number of mutations on evolutionary path from one species to another Time estimate as long as evolution of one species into another In a tree T, we often compute dij(T) – the length of a path between leaves i in addition to j dij(T) – tree distance between i in addition to j Distance in Trees: an Exampe d1,4 = 12 + 13 + 14 + 17 + 12 = 68 Distance Matrix Given n species, we can compute the n x n distance matrix Dij Dij may be defined as the edit distance between a gene in species i in addition to species j, where the gene of interest is sequenced as long as all n species. Dij – edit distance between i in addition to j

Fitting Distance Matrix Given n species, we can compute the n x n distance matrix Dij Evolution of these genes is described by a tree that we don’t know. We need an algorithm to construct a tree that best fits the distance matrix Dij Reconstructing a 3 Leaved Tree Tree reconstruction as long as any 3×3 matrix is straight as long as ward We have 3 leaves i, j, k in addition to a center vertex c Observe: dic + djc = Dij dic + dkc = Dik djc + dkc = Djk Turnip vs Cabbage: Look in addition to Taste Different Although cabbages in addition to turnips share a recent common ancestor, they look in addition to taste different

Turnip vs Cabbage: Different mtDNA Gene Order Gene order comparison: Trans as long as ming Cabbage into Turnip Reversal distance History of Chromosome X Rat Consortium, Nature, 2004

Cox, Beverly Food Editor

Cox, Beverly is from United States and they belong to Native Peoples Magazine and they are from  Phoenix, United States got related to this Particular Journal. and Cox, Beverly deal with the subjects like Cooking; Ethnic Interest; Food; Native American Interest; Wine

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