http://people.cis.ksu.edu/~dcaragea/mlb/ 2009-11-22T20:23:00-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/ http://people.cis.ksu.edu/~dcaragea/mlb/lib/images/favicon.ico text/html 2009-11-06T21:57:50-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=advice&rev=1257566270&do=diff Graduate School A Guide to PhD Studies and Research (David Schmidt et al.) How to Succeed in Graduate School (by Marie desJardins) How to Have a Bad Career in Research/Academia (by Dave Patterson) Ten Simple Rules for Graduate Students (by Philip E. Bourne) text/html 2009-01-06T16:37:07-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=affiliations&rev=1231281427&do=diff K-State Affiliations Bioinformatics Center @ K-State Arthropod Genomics Center Ecological Genomics text/html 2009-06-12T22:18:46-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=blast&rev=1244863126&do=diff It's a BLAST! Bioinformatics Workshop Instructors Doina Caragea Susan J. Brown 216 Nichols Hall 239A Chalmers Hall 785-532-7908 785-532-6670 dcaragea@ksu.edu sjbrown@ksu.edu Volunteer Students text/html 2008-01-16T17:24:37-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=calendar&rev=1200525877&do=diff EST Data Analysis text/html 2009-03-14T18:50:31-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis590-798-spring-2009&rev=1237074631&do=diff Logistics Instructors Doina Caragea Susan J. Brown 216 Nichols Hall 239A Chalmers Hall 785-532-7908 785-532-6670 dcaragea@ksu.edu sjbrown@ksu.edu Office hours: W10:30-11:30 or by app. Office hours: by app. Meeting Time text/html 2008-11-25T22:44:58-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis590_798-spring-2008&rev=1227674698&do=diff CIS590/CIS798 - Introduction to Bioinformatics Logistics Instructors Susan J. Brown Doina Caragea 239A Chalmers Hall 216 Nichols Hall 785-532-6670 785-532-7908 sjbrown@ksu.edu dcaragea@ksu.edu Office hours: by app. Office hours: W10:30-11:30 or by app. Meeting Time text/html 2008-11-25T22:58:24-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis590_798-spring-2009&rev=1227675504&do=diff CIS590/CIS798 - Introduction to Bioinformatics Logistics Instructors Susan J. Brown Doina Caragea 239A Chalmers Hall 216 Nichols Hall 785-532-6670 785-532-7908 sjbrown@ksu.edu dcaragea@ksu.edu Office hours: by app. Office hours: W10:30-11:30 or by app. Meeting Time text/html 2008-11-25T21:51:23-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis798-spring-2008&rev=1227671483&do=diff CIS590/CIS798 - Introduction to Bioinformatics Logistics Instructors: Susan J. Brown Doina Caragea 239A Chalmers Hall 216 Nichols Hall 785-532-6670 785-532-7908 sjbrown@ksu.edu dcaragea@ksu.edu Office hours: by app. Office hours: W10:30-11:30 or by app. Meeting Time: Lec: MWF 1:30am-2:20pm in Nichols 127, Lab: W 2:30-4:30pm in Nichols ?. text/html 2009-01-26T10:54:27-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis798&rev=1232988867&do=diff CIS 798 Independent Study (Rohit) Computing Semantic Relatedness using Wikipedia-based Explicit Semantic Analysis Gabrilovich, Evgeniy ; Markovitch, Shaul, Proceedings of the 20th International Joint Conference on Artificial Intelligence, 2007 text/html 2009-01-26T11:00:01-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis798fall08&rev=1232989201&do=diff CIS798: Advanced Topics in IR (Ind. Study - Surya) Schedule August 29 Google Keeps Tweaking Its Search Engine September 5 K Punera, S Rajan and J Ghosh, “Automatic Construction of N-ary Tree Based Taxonomies”, MSD Workshop at ICDM '06. September 12 Suju Rajan, Kunal Punera and Joydeep Ghosh, “A Maximum Likelihood Framework for Integrating Taxonomies”, AAAI-05, pp. 856-861. text/html 2009-11-18T19:37:41-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis798fall09&rev=1258594661&do=diff CIS798: Information Retrieval and Machine Learning Meeting Time and Place Tuesday 3:30 to 5pm in Nichols 236 Schedule 09/01 Svitlana Gabrilovich, E. and Markovitch, S. (2007). Computing Semantic Relatedness using Wikipedia-based Explicit Semantic Analysis Proceedings of the 20th International Joint Conference on Artificial Intelligence (IJCAI'07). text/html 2009-01-27T22:01:54-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis798spring09&rev=1233115314&do=diff CIS798 Independent Study * Sanmitra Bhattacharya * Rohit Parimi text/html 2009-03-30T09:54:31-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis798spring09rohit&rev=1238424871&do=diff CIS798: Advanced Topics in IR (Ind. Study - Rohit) Computing Semantic Relatedness using Wikipedia-based Explicit Semantic Analysis Gabrilovich, Evgeniy ; Markovitch, Shaul, Proceedings of the 20th International Joint Conference on Artificial Intelligence, 2007 text/html 2009-04-03T11:05:29-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis798spring09sanmitra&rev=1238774729&do=diff Papers Discussed Pavesi G, Mauri G, Pesole G. In silico representation and discovery of transcription factor binding sites. Brief. Bioinform (2004) 5:217–236. Holloway, D. T., Kon, M. A., and DeLisi, C. 2006. Machine learning methods for transcription data integration. IBM J. Res. Dev. 50, 6 (Nov. 2006), 631-643. text/html 2008-03-06T15:03:35-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis890&rev=1204837415&do=diff CIS890: Independent Study * Learning Ontologies and Mappings between Ontologies * Information Retrieval and Text Classification Students: Aaron Chavez Michael Marlen Claudia Martin text/html 2009-08-18T21:23:06-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis890fall08&rev=1250648586&do=diff Information Retrieval and Text Mining Logistics Instructor: Dr. Doina Caragea (dcaragea@ksu.edu) Meeting Time: TU 11:30am-12:45pm in Nichols 236 Prerequisites: Basic knowledge in probability and statistics, data structures and algorithms. Prior knowledge of either Java or C++. text/html 2009-09-09T22:18:32-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=cis890fall09&rev=1252552712&do=diff Information Retrieval and Text Mining Logistics Instructor: Dr. Doina Caragea (dcaragea@ksu.edu) Meeting Time: TU 11:30am-12:45pm in Nichols 236 Prerequisites: Basic knowledge in probability and statistics, data structures and algorithms. Prior knowledge of either Java or C++. text/html 2009-06-06T08:39:17-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=conferences&rev=1244295557&do=diff Conferences * umbc-various * sg-various * kmining.com * dbworld * computer-science * iscb-bioinfo * SIAM: Conference Calendar * bioinformatics * Bioinformatics Calendar * Conferences acceptance ratio statistics * Computer Science Conference Ranking text/html 2008-11-25T23:22:03-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=course_description&rev=1227676923&do=diff Course Description The course provides fundamental background in bioinformatics, both theoretical (bioinformatics algorithms) and practical (databases and web-based tools used to study problems in biology), to students in computer science or in biological sciences. It is designed for both undergrad and graduate students. The class requirements for the undergrad students are a strict subset of the requirements for graduate students. Introduction to the biological problems addressed in this cours… text/html 2009-08-26T22:43:49-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=courses&rev=1251344629&do=diff Spring 2008 CIS 890 Fall 2008 CIS 890 CIS 798 Spring 2009 CIS 590/798 CIS 798 Summer 2009 It's a BLAST! Bioinformatics Workshop Fall 2009 CIS 890 CIS 798 text/html 2009-02-06T22:00:32-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=dlmont&rev=1233979232&do=diff Learning link-based classifiers from ontology-extended data sources text/html 2009-02-26T16:02:29-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=est&rev=1235685749&do=diff Genomics Data Analysis * Project Members * References text/html 2008-01-16T00:10:33-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=est_data_analysis&rev=1200463833&do=diff text/html 2008-01-16T00:35:05-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=fall_2007&rev=1200465305&do=diff Members Calendar text/html 2008-01-16T00:11:08-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=gene_regulatory_networks&rev=1200463868&do=diff GRN Calendar text/html 2008-09-12T19:27:06-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=grn-fall08&rev=1221265626&do=diff GRN Fall 2008 References Protein Function Prediction Building transcription factor classifiers and discovering relevant biological features, D. Holloway, Mark Kon and C. DeLisi, preprint, 2008. ADJ van Dijk, Ter, RG Immink, GC Angenent, RCHJ van Ham (2008). Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control. Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 26-33. text/html 2008-09-12T17:38:28-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=grn-spring08&rev=1221259108&do=diff Spring 2008 Meeting Time and Place Fridays from 10:00AM to 11:30AM in Nichols 236. New This Semester Every other Friday we will discuss chapters from Michael Lynch's book on: The Origins of the Genome Architecture. Schedule * 01/25/08 Lynch Chapter 1: The Origin of Eukaryotes * 02/01/08 Rescheduled Chapter 1. * 02/08/08 Lynch Chapter 2: Genome Size and Organismal Complexity * 02/15/08 Identifying regulatory networks by combinatorial analysis of promoter elements. Pilpel Y, Su… text/html 2008-09-12T17:38:07-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=grn&rev=1221259087&do=diff Spring 2008 Fall 2008 text/html 2008-12-09T11:25:53-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=here&rev=1228843553&do=diff Course Description The course provides fundamental background in bioinformatics, both theoretical (bioinformatics algorithms) and practical (databases and web-based tools used to study problems in biology), to students in computer science or in biological sciences. It is designed for both undergrad and graduate students. The requirements for the undergrad students are a strict subset of the requirements for graduate students. Introduction to the biological problems addressed in this course will… text/html 2009-06-22T10:38:49-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=home&rev=1245685129&do=diff Machine Learning and Bioinformatics (MLB) Group [Summer 09 Graduation Picnic] The MLB Group aims to design algorithms and to develop tools for analyzing large amounts of data, in particular, molecular sequence and gene expression data. Our main projects are focused on: text/html 2009-03-07T23:22:51-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=indus&rev=1236489771&do=diff Project Summary Advances in networks, sensors, storage, computing, and high throughput data acquisition, have led to a proliferation of autonomous, distributed data sources in many areas of human activity. New discoveries in biological, physical, and social sciences and engineering are being driven by our ability to discover, share, integrate and analyze disparate types of data. Statistically-based machine learning algorithms offer some of the most cost-effective approaches to discovery of exp… text/html 2008-12-09T22:38:30-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=links_for_students&rev=1228883910&do=diff Graduate School A Guide to PhD Studies and Research (David Schmidt et al.) How to Succeed in Graduate School (by Marie desJardins) How to Have a Bad Career in Research/Academia (by Dave Patterson) Ten Simple Rules for Graduate Students (by Philip E. Bourne) text/html 2009-02-26T16:02:56-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=meetings&rev=1235685776&do=diff Bioinformatics Meetings at K-State Genomics Data Analysis Gene Regulatory Networks Meeting text/html 2009-10-15T16:51:38-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=members&rev=1255643498&do=diff Director Doina Caragea Students Ph.D. Students * Ezzat El-Sherif M.S. Students * Vishal Bahirwani * Roshan Chetry * Surbhi Mungre * Rohit Parimi * Shruti Phanse * Sandeep Solanki * Karthik Tangirala * Swapnil Nagar text/html 2008-04-23T22:54:19-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=ontology_learning&rev=1209009259&do=diff Schedule January 24 Ontology Learning from Text: An Overview. Paul Buitelaar, Philipp Cimiano and Bernardo Magnini. Book Introduction. January 31 P. Cimiano, S. Staab. Learning by Googling. SIGKDD Explorations. 6(2), pp. 24-33, 2004. February 7 K. Dellschaft, S. Staab. On How to Perform a Gold Standard based Evaluation of Ontology Learning. In: Proc. of ISWC-2006 –International Semantic Web Conference, Athens, GA, USA, Springer, LNCS, November 2006. text/html 2009-01-15T22:09:11-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=policy&rev=1232078951&do=diff CIS 590/798 - Assignments and Grading Policies Class Reading Assigned chapters in the textbook & supplemental materials provided in class or on the course website should be read prior to lecture (see Schedule on K-State online). Reading Assignments Students will be required to read assigned journal articles & answer discussion questions that emphasize critical evaluation of experiments & results presented, including fundamental concepts, experimental design, and interpretation of results. text/html 2008-01-16T16:48:16-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=project_members&rev=1200523696&do=diff EST Data Analysis Project Members * Faculty * Sue Brown * Doina Caragea * Yoonseong Park ---------- * Bioinformatics Staff * Sanjay Chellapilla * Hee Shin Kim * Nanyan Wang ---------- * Students * Surya Kallumadi * Jing Xia text/html 2009-02-06T21:13:27-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=projects&rev=1233976407&do=diff Knowledge Discovery from Semantically Heterogeneous Data The goal of this project is to design algorithms for learning classifiers from semantically heterogeneous data sources, classifiers that offer rigorous performance guarantees (relative to their centralized or batch counterparts). Our recent work has focused on theoretically sound approaches to this problem, under fairly general assumptions. Several sets of experiments for evaluating the robustness of this approach in real world scenari… text/html 2009-02-26T16:08:35-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=references&rev=1235686115&do=diff References Tiling Arrays J Robert Manak et al. (2006) Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genetics - 38, 1151 - 1158. Gene Structure DeCaprio D, Vinson J, Pearson M, Montgomery P, Doherty M, Galagan J. (2007) “Conrad: Gene prediction using conditional random fields” Genome Research, 17(9):1389-98. text/html 2009-01-06T16:43:02-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=resources&rev=1231281782&do=diff Random Links Genomics and Bioinformatics Resources The OpenHelix Reference Sources Cell Press DTU Machine Learning Resources Homepage of Marcus Hutter Graph Visualization Graph Visualization Semantic Web Jennifer Golbeck Feature Selection text/html 2009-01-27T22:36:18-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=schedule&rev=1233117378&do=diff # Date Day Topic Chapter 1 Jan 16 F What is Bioinformatics? - Jan 19 M University Holiday - No class 2 Jan 21 W Nucleic Acids and Protein Structures (I) 1 & 2 3 Jan 23 F Protein Structures (II) & Intro Databases 3 4 Jan 26 M Types of Databases 3 5 Jan 28 W Biological Databases 3 6 Jan 28 F Probability Review 7 Jan 30 M P… text/html 2009-01-06T16:43:38-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=sidebar&rev=1231281818&do=diff * Home * Members * Projects * Courses * Affiliations * Meetings * Conferences * Resources * Advice ---------- * Doina's Page text/html 2008-01-16T00:35:31-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=spring_2008&rev=1200465331&do=diff Members Calendar text/html 2008-01-15T19:10:33-06:00 http://people.cis.ksu.edu/~dcaragea/mlb/doku.php?id=start&rev=1200445833&do=diff test