From g9055010 at mail.nchu.edu.tw Fri Nov 1 04:34:36 2002 From: g9055010 at mail.nchu.edu.tw (OuYang) Date: Sun Jun 12 19:43:24 2005 Subject: Postdoctor positions Message-ID: <20021107032626.0030C7D150@mercury.hgmp.mrc.ac.uk> Postdoctoral Positions in Transcription Regulation Three Postdoctoral positions are available immediately to explore mechanisms of transcriptional regulation in prokaryotes and eukaryotes (the latter pertaining to human diseases and cancer), using proteomics and bioinformatics. The successful candidates must have a strong background in molecular biology and biochemistry. Interested candidates should send CV and recommendation letters to: Dr. Yao, Institute of Molecular Biology, National Chung Hsing University, 250 Kuo Kuang Rd., Taichung 402, Taiwan. e-mail: yaoyl@moffitt.usf.edu Tel: 886-4-22840486 ext.246 ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From softberry at softberry.com Tue Nov 5 16:33:34 2002 From: softberry at softberry.com (Softberry Team) Date: Sun Jun 12 19:43:24 2005 Subject: Anopheles gambiae Gene finding parameters Message-ID: <20021107032717.794CA7D0C6@mercury.hgmp.mrc.ac.uk> Anopheles gambiae Gene finding parameters for FGENESH the program with parameters for major model organisms is available for on line usage at: http://www.softberry.com/berry.phtml?topic=gfind Method description: A new parameter set for gene prediction Anopheles gambiae is developed for FGENESH program. Accuracy of prediction of Plasmodium falciparum protein coding genes is about 98% on the nucleotide level. The FGENESH algorithm is based on pattern recognition of different types of signals and Markov chain models of coding regions. Optimal combination of these features is then found by dynamic programming and a set of gene models is constructed along given sequence. FGENESH is the fastest and most accurate ab initio gene prediction program available. Fgenesh output: fgenesh Tue Nov 5 16:23:15 EST 2002 FGENESH 1.1 Prediction of potential genes in Anopheles_gambiae genomic DNA Time : Tue Nov 5 16:23:16 2002 Seq name: Softberry SERVER PAST Sequence Length of sequence: 1542 Number of predicted genes 1 in +chain 1 in -chain 0 Number of predicted exons 3 in +chain 3 in -chain 0 Positions of predicted genes and exons: G Str Feature Start End Score ORF Len 1 + TSS 249 -4.78 1 + 1 CDSf 301 - 564 2.25 301 - 564 264 1 + 2 CDSi 632 - 1011 15.80 632 - 1009 378 1 + 3 CDSl 1097 - 1289 3.27 1098 - 1289 192 1 + PolA 1314 2.25 Predicted protein(s): >FGENESH: 1 3 exon (s) 301 - 1289 278 aa, chain + KQVISLVLFGLFCGNAVVTNANGQNTTEGPSHSGRIVNGIPVNISNYKYALSMRFDGEF ICGASIITYSHALTAAHCVYNYQFMSSRLTLYGGSTSASSGGVEFPVVRLLYHPSYNSYK SNLSDYDVAILTVPANSFSGKPNMAPLALQTKELPADTRCFVVGWGKRADGENEQPSVNQ LLYANMNIVSQSDCATMWANSEHRCPACKQSITSNMVCAQYGNSMDTCRGDSGGALVCGG RLTGVVSFALYCSGIWPSVFAKVTAPTIRNFIRYIAGI --- ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From rjones at mail.smu.edu Thu Nov 7 14:39:50 2002 From: rjones at mail.smu.edu (Jones, Richard) Date: Sun Jun 12 19:43:25 2005 Subject: Faculty Positions Message-ID: <20021118001232.D8B767D1C6@mercury.hgmp.mrc.ac.uk> Tenure-Track Positions Department of Biological Sciences SOUTHERN METHODIST UNIVERSITY, Dedman College, Dallas TX. The Department of Biological Sciences has recently moved into a new 68,000 sq. ft. state-of-the art facility. As part of the process to expand upon our already strong molecular biology program, two new faculty members have joined our department this year and an additional two to three positions are available for fall 2003. Candidates at the junior (ASSISTANT) or senior (ASSOCIATE OR FULL PROFESSOR) levels are invited to apply. Successful candidates must have a strong record of research accomplishments in areas that utilize molecular biology, biochemistry or cell biology and will be expected to develop vigorous, externally funded research programs. Additionally, successful candidates will have a strong commitment to undergraduate and graduate teaching. For one of the positions, preference will be given to an individual whose research examines components of oxidative stress and free radical biology. Competitive start-up funds and salaries will be offered. Candidates should forward curriculum vitae, a brief statement of research plans, and three letters of recommendation to: Dr. Larry Ruben, Chair, Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275. The positions recruited this year begin fall semester 2003. To ensure full consideration for the positions, the applications must be postmarked by December 1, 2002, but the committee will continue to accept applications until the positions are filled. The committee will notify applicants of its employment decisions after the positions are filled. SMU will not discriminate on the basis of race, color, religion, national origin, sex, age, disability, or veteran status. SMU also is committed to nondiscrimination on the basis of sexual orientation. --- ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From rjones at mail.smu.edu Thu Nov 7 14:39:50 2002 From: rjones at mail.smu.edu (Jones, Richard) Date: Sun Jun 12 19:43:25 2005 Subject: Faculty Positions Message-ID: <20021118001243.189A57D1EB@mercury.hgmp.mrc.ac.uk> Tenure-Track Positions Department of Biological Sciences SOUTHERN METHODIST UNIVERSITY, Dedman College, Dallas TX. The Department of Biological Sciences has recently moved into a new 68,000 sq. ft. state-of-the art facility. As part of the process to expand upon our already strong molecular biology program, two new faculty members have joined our department this year and an additional two to three positions are available for fall 2003. Candidates at the junior (ASSISTANT) or senior (ASSOCIATE OR FULL PROFESSOR) levels are invited to apply. Successful candidates must have a strong record of research accomplishments in areas that utilize molecular biology, biochemistry or cell biology and will be expected to develop vigorous, externally funded research programs. Additionally, successful candidates will have a strong commitment to undergraduate and graduate teaching. For one of the positions, preference will be given to an individual whose research examines components of oxidative stress and free radical biology. Competitive start-up funds and salaries will be offered. Candidates should forward curriculum vitae, a brief statement of research plans, and three letters of recommendation to: Dr. Larry Ruben, Chair, Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275. The positions recruited this year begin fall semester 2003. To ensure full consideration for the positions, the applications must be postmarked by December 1, 2002, but the committee will continue to accept applications until the positions are filled. The committee will notify applicants of its employment decisions after the positions are filled. SMU will not discriminate on the basis of race, color, religion, national origin, sex, age, disability, or veteran status. SMU also is committed to nondiscrimination on the basis of sexual orientation. --- ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From strauerman at lycos.com Fri Nov 15 03:24:09 2002 From: strauerman at lycos.com (Mark Strauerman) Date: Sun Jun 12 19:43:25 2005 Subject: FW: CFP: Graphical Models for Computational Message-ID: <20021118001451.8F8547D1C6@mercury.hgmp.mrc.ac.uk> First CFP: IJCAI-2003 Workshop -- Learning Graphical Models for Computational Genomics Saturday, 9 August 2003 Acapulco, Mexico http://www.kddresearch.org/KDD/Workshops/IJCAI-2003-Bioinformatics/ Recent advances in experimental tools for computational genomics have led to sharp growth in data resources for bioinformatics problems such as modeling of gene expression and gene-protein interaction. This provides an interesting application domain for intelligent systems that learn graphical models from data for causal modeling, time series simulation and prediction, and classification and regression problems in computational life sciences. In response, we propose a workshop to bring together researchers in intelligent systems who are interested in: * probabilistic reasoning and learning with the primary focus of: - learning the structure of graphical models from data, - new graphical models such as types of dynamic Bayesian networks, stochastic and other approximation algorithms for inference, - structure learning; * constraint-based knowledge representation; * parameter estimation on graphical models and dynamical systems. ---Topics Active research topics that are relevant to learning graphical models for computational genomics include: * functional genomics, which includes: - modeling of gene regulatory dynamics, - data mining from DNA hybridization microarrays, - other gene modeling tools such as northern blots; * building simulation models for metabolomics on: - biochemical pathways, - environmental stress-response, - cellular process regulation; * proteomics, such as: - secondary and tertiary fold prediction - gene-protein interaction; * other contemporary bioinformatics problems, such as: - intelligent systems for pharmacology, - plant science and crop simulation, - decision support systems for human and veterinary medicine, - phylogenetic modeling. ---Format The one day workshop will include one or more invited talks and specialized tutorials on state-of-the-art research problems and methodologies, presentations by selected participants, and a panel and open discussion on key topics. ---Attendance This workshop is intended for researchers and practitioners in the area of bioinformatics and uncertain reasoning using graphical models for computational genomics. Researchers with an interest in machine learning, medical informatics, microbiology, biophysics, and knowledge discovery in databases (KDD) will also find this workshop of interest. ---Paper Submissions Participants are encouraged to submit papers (up to 8 pages in length) on recent and continuing research, formatted according to IJCAI guidelines. Experimental results are also encouraged, especially on fielded applications, even if they are only preliminary. Papers should be submitted electronically in Postscipt, PDF, MS Word format via e-mail. To encourage participation but focus discussions on key topics, we also invite 2-page research synopses and position papers from attendants who do not submit full papers. Each submission shall be accompanied by a short statement, up to 500 words or one page in length from each participants. This should describe your interest in and perspectives on this workshop topic. DUAL SUBMISSION POLICY: Submission of short (2-page OR 6-8 page) synopses of articles currently in preparation, under review, or accepted for publication as journals or book chapters is permitted. Submission of full-length papers currently under review for other conferences and workshops is also permitted. However, these papers shall be published in the working notes for this workshop if and only if they are compliant with the dual-submission guidelines of the other conference or workshop. Please consult the workshop web page for formatting instructions. All submissions should be sent to: ijcai2003-bioinformatics(AT)kddresearch.org. (Please replace "(AT)" with the appropriate symbol.) ---Important Dates Mar 01, 2003 Submission deadline Mar 21, 2003 Acceptance notification May 16, 2003 Camera-ready version of papers ---Organizing Chairs William H. Hsu (primary contact) Department of Computing and Information Sciences Kansas State University 234 Nichols Hall Manhattan, KS 66506-2302 t: (785) 532-6350 ext. 29 f: (785) 539-7180 e: bhsu-AT-cis.ksu.edu w: http://www.cis.ksu.edu/~bhsu Roby Joehanes (primary contact) Department of Computing and Information Sciences Kansas State University 234 Nichols Hall Manhattan, KS 66506-2302 t: (785) 532-6350 ext. 55 f: (785) 537-9927 e: robbyjo-AT-cis.ksu.edu w: http://www.cis.ksu.edu/~robbyjo C. David Page, Jr. Department of Biostatistics and Medical Informatics (Medical School) and Department of Computer Sciences University of Wisconsin-Madison Medical Science Center, Room 6743 1300 University Avenue Madison, WI 53706 t: (608) 265-6168 f: (608) 263-0415 e: page-AT-biostat.wisc.edu w: http://www.cs.wisc.edu/~dpage ---Program Committee - Mark Craven, University of Wisconsin-Madison - Dan Geiger, Technion, Israel - David Gilbert, University of Glasgow - Haipeng Guo, Kansas State University - Lei Liu, University of Illinois at Urbana-Champaign - Irene Ong, University of Wisconsin-Madison - Jude Shavlik, University of Wisconsin-Madison - Stephen M Welch, Kansas State University ---Additional information Please consult the following web page: http://www.kddresearch.org/KDD/Workshops/IJCAI-2003-Bioinformatics/ for more information. --- ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From matthew.oconnell at mssm.edu Wed Nov 20 12:47:19 2002 From: matthew.oconnell at mssm.edu (Matthew O'Connell) Date: Sun Jun 12 19:43:28 2005 Subject: Postdoc positions - cell cycle checkpoints Message-ID: <20021217135247.BF6227D0C7@mercury.hgmp.mrc.ac.uk> Positions are available for highly motivated people to join the group of Dr Matthew OΉConnell and study G2 checkpoint signalling through the Chk1 protein kinase. Available projects are part of a larger effort within the lab that studies checkpoint signalling at the G2/M transition. Our laboratory widely uses fission yeast as a model for gene and pathway discovery, and these findings then direct experiments in mammalian systems. The projects below build on a body of data from an ongoing effort within the laboratory to dissect Chk1 in the fission yeast system. 1. Regulation and function of Chk1 in human cells: From our studies in fission yeast, we have identified a number of proteins that either modulate Chk1 function, or are themselves targets of Chk1. Human homologs of these proteins have been identified, and we now aim to use molecular, biochemical and cell biological approaches to investigate the functional interactions between these and human Chk1. Through extensive mutagenesis of Chk1 in fission yeast we have generated a library of mutations that either inactivate or constitutively activate Chk1. Several of these have been shown to function similarly when introduced into Human Chk1, and will be important tools in these experiments. 2. Chk1 as a target for anti-cancer therapy: Studies in vitro implicate Chk1 as a prime target for anti-cancer therapies. From a number of different approaches to block Chk1 activation, there is evidence for a synergy with common tumor mutations in promoting cell death. This project will further explore this approach, and define tumor genotypes most susceptible to anti-Chk1 based therapies. Experiments will be carried out both in culture and in primary animal tumor models. Our lab has recentlyrelocated from Australia to Mt Sinai School of Medicine, located on Manhattans Upper East Side. Successful candidates should have relevant experience and will receive competitive salary support and housing assistance. Please email you CV and details for at least three referees, or email for further details to: matthew.oconnell@mssm.edu > -- > Matthew J. OΉConnell, Ph.D. > Mount Sinai School of Medicine > Derald H. Ruttenberg Cancer Center > One Gustave L. Levy Place - Box 1130 > New York, New York 10029 > > matthew.oconnell@mssm.edu > > Express Mail/FedEx: > 1425 Madison Ave - Room 15-70 > New York, New York 10029 > > > ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From softberry at softberry.com Tue Nov 19 15:32:37 2002 From: softberry at softberry.com (Victor Solovyev) Date: Sun Jun 12 19:43:28 2005 Subject: Genes/Operons in pathogenic organisms: Message-ID: <20021217135606.1B31E7D0C7@mercury.hgmp.mrc.ac.uk> Genes/Operons in pathogenic organisms: Mycobacterium tuberculosis, Yersinia pestis and others Applying Softberry fgenesB-annotator script that predicts genes and find similar proteins in public databases, we present annotations for several pathogenic organisms at: http://www.softberry.com/berry.phtml?topic=fgenesb_ann Mycobacterium tuberculosis H37Rv, complete genome Mycobacterium tuberculosis CDC1551, complete genome Yersinia pestis strain CO92, complete genome Yersinia pestis KIM, complete genome Bacillus anthracis A2012 main chromosome Example of annotation of Yersinia pestis KIM Prediction of potential operons and genes in microbial genomes Time: Mon Nov 18 11:07:36 2002 Seq name: gi|22123922|ref|NC_004088.1| Yersinia pestis KIM, complete genome Length of sequence - 4600755 bp Number of predicted genes - 4011, with homology - 3927 Number of transcription units - 2364, operons – 799 N Tu/Op Conserved S Start End Score pairs(N/Pv) 1 1 Op 1 2/0.311 - CDS 21 - 461 375 ## COG0716 Flavodoxins 2 1 Op 2 . - CDS 554 - 1015 362 ## COG1522 Transcriptional regulators 3 2 Tu 1 . + CDS 1185 - 2177 1148 ## COG2502 Asparagine synthetase A … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … New FgenesB is the fastest (E.coli genome analyzed in ~14 sec) and most accurate ab initio Bacterial gene prediction program available. http://www.softberry.com/berry.phtml?topic=fgenesb It uses parameters learned for different bacteria by FgenesB-train script, which input is just new bacterial sequence. It will automatically create file with gene prediction parameters for the analyzed organism. It takes only ~10 minutes to create such file for such genome as E.coli using its sequence. If you need parameters for your new bacteria, please contact Softberry Inc., we can include them in the WEB list. Algorithm based on pattern recognition of different types of signals and Markov chain models of coding regions. Optimal combination of these features is then found by dynamic programming and a set of gene models is constructed along given sequences. In the current FgenesB version operon prediction model is realized based on gene distances. It can recognize accurately 70% of single transcription units and define exactly about 43% of operons (~92% partially). --- ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com