Bioinformatics Research and References | Data mining collections | Workshops and Conferences | Journals | Statistics | Software | ND information | Friends | Return to home |

Bioinformatics Research and References:

• DeRiSi Lab.
• Computational Biology and Informatics Laboratory (University of Pennsylvania).
• Winzeler Lab.
• GENOME BIOINFORMATICS RESEARCH LAB.

gene specification in genomic sequences, gene prediction and annotation in genomic sequences.
• In silico experiments with complete genomes.

DNA fingerprinting, Find ORF by name, Sort sequence locator, Experiments with Eukaryotic genomes.
• PLATCOM.

Platform for Computational Comparative Genomics.
• Serafim Batzoglou.

Alignments, Comparative Genomics.
• Martin Tompa.
• Asa Ben-Hur (PPI).
• Brian Haas' home page (Comparative genomics).
• Eddy lab (computational genome sequence analysis).
• The Bulyk Lab (comparative genomics & TFBM).
• Young Lab (MIT).
• Eisen Lab.
• Dr. Eleazar Eskin (UCSD).

Statistical and Algorithmic Aspects of Motif Discovery, Regulatory Aspects of Human Disease
• Manolis Kellis.
• Jenny Bryan (statistical methods for genome-scale science).
• Steven E. Brenner (Berkeley).
• EMBL-EBI Plasmodium falciparum.
• Dr. Tibshirani.
• Dr. Martin Vingron.
• Korbinian Strimmer.
• Dr. Jun Liu.
• Dr. Michael Q. Zhang.
• Dr. Ziv Bar-Joseph.
• SMI Research Projects.
• Dr. Marco Ramoni.
• Dr. Churchill.
• Dr. Wentian Li.
• Dr. Hongzhe Li.
• Dr. Wei Pan.
• George M. Church.
• Wyeth W. Wasserman.
• Frederick Roth.
• Bioi@SCD.
• Regulatory Sequence Analysis Tools.
• Arachne: A Whole Genome Assembly Software Package.
• BIAS: Bioinformatics Integrated Application Software.

including building the position-specic scoring matrices (PSSMs).
• Swiss Institute for Experimental Cancer Research Group.

profile construction and profile search methods.
• YRSA.

Yeast Regulatory Sequence Analysis.
• PipMaker and MultiPipMaker.

PipMaker computes alignments of similar regions in two DNA sequences.
• rVista 2.0 .

rVista combines database searches with comparative sequence analysis, reducing the number of false positive predictions by ~95% while maintaining a high sensitivity of the search.
• Tools for phylogenetic footprinting purposes.

Pipmaker, Orthoseq, PromotorInspector, RepeatMasker, Ensembl (human), Ensembl (mouse), ConSite.
• JASPAR.

JASPAR is a collection of transcription factor DNA-binding preferences, modelled as position-specific weight matrices (PSSMs).
• Links for TFBS (from Chengyong Yang).

Tools for Discovery of Transcription Factor Binding Sites, Transcription Factor Binding Motifs Databases.
• Bibliography on Microarray Data Analysis.
• Data Mining, Knowledge Discovery, Genomic Mining, Web Mining .
• Bioinformatics and Functional Genomics Resource.
• The Eukaryotic Promoter Database.
• Full Malaria.
• BioBLP Server.
• Genomic Biology.

Provides an overview of the major genome resources at NCBI.
• FTP Site.

Site that allows download of genomic sequence data.
• Entrez Genome .

Graphical views and searches of genomes that are completed or in progress. Includes data from finished and unfinished genomes from all organism groups.
• MapViewer.

The Map Viewer provides special browsing and display capabilities for a subset of organisms in Entrez Genomes, including human and non-human genomes.
• GeneDB.

Search for gene by ID/description, organism BLAST, ID List Download etc.
• ArrayExpress at the EBI.

ArrayExpress is a public repository for microarray data, which is aimed at storing well annotated data in accordance with MGED recommendations.

Data mining collections:

Workshops and Conferences:

• Upcoming bioinformatics workshops and conferences.
• Data mining and knowledge discovery:Forthcoming meetings.
• Dr. Tao Li's Link.
• NIH VideoCasting.
• Bioplanet.
• Bioinformatics program FAQ @UCSC.

What is Bioinformatics, Bioinformatics job finding, Bioinformatics graduate program summary.

Journals:

• Hot papers and fast breaking papers.
• ScienceDirect.
• Bioinformatics.
• Nucleic Acids Research.
• PLoS Biology.
• Journal of Time Series Analysis.
• BMC Bioinformatics.
• PNAS.
• Genomics.
• Trends in Genetics.
• Science.
• In Silico Biology.
• Bioinformer.
• Briefings in Bioinformatics.

Statistics:

• Electronic TextBook.
• Handbook of Statistical Methods.
• Gallery of Distributions.
• Statistical Methods and Software for the Analysis of DNA Microarray Experiments.
• Statistical Genomics References.
• Statistical Methodology_Microarray Data Analysis.
• Statistical Wordwide.
• Wavelet Methods for Time Series Analy.
• job.

Software:

• Gene Plot.

Pairwise genome comparison of protein homologs (symmetrical best hits)
• sma (Statistics for Microarray Analysis) R package.
• R packages for microarray analysis.
• MicroArray Software Descriptions.
• Microarray Protocols.
• Bioconductor.
• BioPHP.
• RepeatMasker .

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
• On line analysis tools.

Search a sequence database Nucleic acids sequences, Patterns (proteins), Prediction on protein sequences, Alignments - Phylogeny, Analysis tools package
• A Pack of Molecular Analysis Tools .
DNA Analysis, DNA/Peptide Sequence Comparisons, Data Tables, Database Sequence Search & Retrieval, Oligonucleotide Analysis, Peptide Sequence & Structure Analysis, Ribosomal RNA Analysis, Sequence Formatting & Submission to NCBI
• Local Fitting Software.
• Software Tools for microarray data analysis.
• Gene Regulation.
• Molecular Informatics Resource for the Analysis of Gene Expression.

ND Information:

• University of Notre Dame.
• Department of Computer Science and Engineering.
• Office of Research.
• ND EDS Authentication (Login) Facility
• ND Webmail.
• Office of Information Technologies.
• Inside ND.
• Buy ND.
• ND Food.
• Center for Research Computing.
• ND CFA.
• ND Biology.

Friends:

• Kong, Lesheng.
• Yang, Chengyong.
• Yu, Jiaye.
• Zhou, Xiaosi.