Pointers and Meta-pointers to resources
Following is a list of pointers and meta-pointers
to resources (papers, softwares, etc.)
related to this course that is mostly available in the web. As the
class progresses I will
identify particular papers from this that are necessary for
the class. The pointers and
meta-pointers are also good starting points for doing literature survey
for the projects.
- Pointers to similar course pages at other universities
- Microarray pointers and meta-pointers
- http://ihome.cuhk.edu.hk/~b400559/arraysoft_pathway.html
Microarray Software Comparison - Network/pathway Reconstruction.
(a meta-pointer)
- http://linkage.rockefeller.edu/wli/microarray/
This site has a collection of papers with emphasis on analysis of
microarray (a.k.a. DNA chip) data. General reviews on microarray may be
included. Analysis of gene network is only occasionally included. However,
papers on microarray technology itself are not usually in. Papers on
results of microarray experiments are also not emphasized here.
- http://www-stat.stanford.edu/~tibs/lab/
Laboratory for the analysis of microarray data in Stanford. Their publications
page is at http://www-stat.stanford.edu/~tibs/lab/publications.html.
- http://www.ebi.ac.uk/microarray/ The microarray
informatics group at the European Bioinformatic institute (EBI) addresses
the problem(s) of managing, storing and analysing microarray data.
- http://www.statsci.org/micrarra/ A good
microarray site with pointers to Conferences, Microarray tutorials, Microarray
Technology Resources, etc; including the following
- http://www.bio.davidson.edu/courses/genomics/chip/chipreal.html
Pat Brown's microarray web pages at Davidson college, NC, USA. A nice
animation is at http://www.bio.davidson.edu/courses/genomics/chip/chip.html
- http://www.molgen.mpg.de/~heydebre/explit.html
Literature on Microarray Data Analysis
- http://www.stat.wisc.edu/~yandell/statgen/reference/array.html
Microarray Expression Data Analysis References (Has pointers to many important
papers such as:
- Eisen MB, Chiang DY, Brown PO (2001) Discovery of regulatory
elements from microarray data using genome mean expression profiles. 9th
International Conf on Intelligent Systems for Molecular Biology, Copenhagen.
- Zien A, Kuffner R, Zimmer R, Lenguaer T (2000) Analysis of gene
expression data with pathway scores. In Proceedings of the 8th International
Conference on Intelligent Systems for Molecular Biology. AAAI Press.
- http://sysopmind.com/archive-sl4/0106/0204.html
Brief business plan of a company on AI and Biology. The company website
is http://www.intelligenesiscorp.com/cognitivebio/
The founder's personal website is http://goertzel.org/work.html.
- http://bioinf.wehi.edu.au/marray/ Another
microarray group.
- http://research.nhgri.nih.gov/microarray/image_analysis.html
Microarrays site at NIH.
- http://discover.nci.nih.gov/arraytools/
Another NIH site.
- http://www.dnachip.org/
Stanford microarray database
- http://ihome.cuhk.edu.hk/~b400559/array.html
Another microarray site with lots of pointers.
- http://oz.berkeley.edu/users/terry/zarray/html/
Terry Speed's Microarray Data Analysis Group Page at Berkeley.
- http://www.hgmp.mrc.ac.uk/Research/Microarray/dataanalysis.jsp
The Microarray Programme at the Medical Research Council's Resource Centre,
is a new initiative funded by the MRC and BBS aimed at developing and disseminating
microarray technology to UK academics.
- http://www.biomath.medsch.ucla.edu/~dab/DARPA/webpage/home.html
DNA-Microarray-assisted Regulatory Network Modeling
- http://www.cse.ucsc.edu/research/compbio/genex/genexTR2html/genex.html
Support Vector Machine Classification of Microarray Gene Expression Data.
UCSC-CRL-99-09 Michael P. S. Brown, William Noble Grundy, David Lin,
Nello Cristianini, Charles Sugnet, Manuel Ares Jr., David Haussler. (their
bibliography is at http://www.cse.ucsc.edu/research/compbio/genex/genexTR2html/node18.html)
- http://citeseer.nj.nec.com/brown00knowledgebased.html
Knowledge-based Analysis of Microarray Gene Expression Data By Using Support
Vector Machines. Michael P. S. Brown, William Noble Grundy, David Lin, Nello
Cristianini, Charles Sugnet, Manuel Ares Jr., David Haussler.
- Cluster analysis and display of genome-wide expression patterns Eisen
et al., 1998 Eisen, M., Spellman, P., Brown, P., and Botstein, D. (1998).
Proceedings of the National Academy of Sciences (PNAS), 95:14863-14868.
- Use of a cDNA microarray to analyse gene expression patterns in
human cancer DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray
M, Chen Y, Su YA, Trent JM. Nature Genet. 14, 457-460 (1996).
- Exploring the metabolic and genetic control of gene expression
on a genomic scale.DeRisi et al., 1997 DeRisi, J., Iyer, V., and Brown,
P. (1997). Science, 278:680-686.
- Yeast microarrays for genome wide parallel genetic and gene expression
analysis Lashkari et al., 1997 Lashkari, D. A., L., J., DeRisi,
McCusker, J. H., Namath, A. F., Gentile, C., Hwang, S. Y., Brown, P. O.,
and Davis, R. W. (1997). Proceedings of the National Academy of Sciences
(PNAS), 94:13057-13062
- Interpreting patterns of gene expression with self-organizing maps.
Tamayo et al., 1999 Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan,
S., Dmitrovsky, E., Lander, E., and Golub, T. (1999). Proceedings of the
National Academy of Sciences (PNAS), 96:2907-2912.
- Gene networks
- Gene http://doegenomestolife.org/roadmap/models.html
Dept of Energy sites. http://doegenomestolife.org/roadmap/goal2.html
- http://www.psrg.lcs.mit.edu/publications.html
Computational functional Genomics at MIT. Includes pointers
to
- A Transcriptional Regulatory Network Map for Saccharomyces cerevisiae."
T.I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber,
D. K. Gifford and R. A. Young. Science, 2002
- Combining Location and Expression Data for Principled Discovery
of Genetic Regulatory Network Models.Alexander J. Hartemink, David K. Gifford,
Tommi S. Jaakkola, and Richard A. Young. Pacific Symposium on Biocomputing
2002, Kauai, January 2002
- Bayesian Methods for Elucidating Genetic Regulatory Networks. Hartemink,
A. J., Gifford, D. K., Jaakkola, T. S., Young, R. A IEEE Intelligent Systems
in Biology, Vol. 17, No. 2, pp. 37-43.
- Using Graphical Models and Genomic Expression Data to Statistically
Validate Models of Genetic Regulatory Networks. Alexander J. Hartemink, David
K. Gifford, Tommi S. Jaakkola, and Richard A. Young Pacific Symposium on
Biocomputing 2001, Hawaii, January 2001.
- http://www.goertzel.org/papers/regnet1.htmInferring
Genetic Regulatory Patterns with Integrative AI Part I: Quantitative
Pattern Recognition. Ben Goertzel1, Cassio Pennachin, Andre Senna,
Thiago Maia, Takuo Henmi, Guilherme Lamacie, Saulo Pinto.
- http://www.botany.iastate.edu/~mash/metnetex/NAFIPS01v3a.pdf
Creating Metabolic and Regulatory Network Models using Fuzzy Cognitive Maps
JA Dickerson and Z. Cox ES Wurtele AW Fulmer Electrical Engineering Dept.
Iowa State University.
- http://www.ki.se/icsb2002/pdf/ICSB_234.pdf
Using Bayesian Network Inference Algorithms to Recover Molecular Genetic
Regulatory Networks. Jing Yu et al.
- http://clue.eng.iastate.edu/~julied/publications/Chapter9.pdf
Creating Metabolic Network Models using Text Mining and Expert Knowledge.
J.A. Dickerson, D. Berleant, Z. Cox, W. Qi, D. Ashlock, E. Wurtele and A.W.
Fulmer. In Computational Biology and Genome Informatics.
- http://capb.dbi.udel.edu/main/seminar/student-talk/2002-summer/yanwei-n/niuJuly3.pdf
Nice slides on regulatory network models. Talks about why boolean networks
may be better than Bayesian networks.
- On-line journal, conferences, books, and some newspaper articles.
- Biochemical Pathways and Networks
- Genome Sequencing
- http://www.bioinformatik.de/cgi-bin/browse/Catalog/Databases/Genome_Projects/
List of Genome projects
- http://bcs.whfreeman.com/mga2e/pages/bcs-main.asp?v=category&s=002&n=020&i=002&o=
Exploring Genomes: Web based tutorial
- Gene Myers, "Toward
simplifying and accurately formulating fragment assembly", Journal
of Computational Biology, 2:2, 1995.
- S. Batzoglou, D. Jaffe, K. Stanley,
J. Butler, S. Gnerre, E. Mauceli, B. Berger, J.P. Mesirov, and E.S. Lander.
“ARACHNE: A
Whole Genome Shotgun Assembler.” Genome Research 12:177-189,
2002.
- http://mbl.katewood.com/lecture5/index.shtml
- http://www.tigr.org/~mariae/comp_gen.html
- http://nema.cap.ed.ac.uk/teaching/genomics/geneprediction.html
- http://www.nslc.wustl.edu/courses/Bio4342/lectures.html
- http://www-biology.ucsd.edu/classes/bimm100.FA00/lectures.html
- http://www.ucl.ac.uk/~ucbhjow/b200/b200.html
- http://sun5.liveonline.net/amnh/event.html
- http://www.tigr.org/tdb/edb2/pfa1/htmls/intro.shtml
- http://www-genome.wi.mit.edu/wga/manual.html
- http://www.genome.org/cgi/reprint/13/1/91.pdf
- http://216.239.57.100/search?q=cache:-080jozPqQQC:www.zi.biologie.uni-muenchen.de/~parsch/evogen/Lecture4.pdf+paired+forward+and+reverse+reads&hl=en&ie=UTF-8
- http://www.dnastar.com/dat/pdf/dual_end_naming.pdf
- http://www.paracel.com/publications/cap4_092200.pdf
- http://216.239.53.100/search?q=cache:mJa6LM0rzfwC:www.bii.a-star.edu.sg/docs/notes/0918.pdf+paired+forward+and+reverse+reads&hl=en&ie=UTF-8
- http://www.bii.a-star.edu.sg/docs/notes/0918.pdf
- www.cs.arizona.edu/people/gene/PAPERS/wholegenes.ps
``Is Whole Genome Sequencing Feasible?'' in Computational Methods in Genome
Research (S. Suhai, ed.) Plenum Press (New York, 1997), 73-89.
- http://www.cs.arizona.edu/people/gene/PAPERS/whole.IEEE.pdf
- http://www.cs.arizona.edu/people/gene/PAPERS/dros.asm.pdf
- http://www.cs.arizona.edu/people/gene/
- http://www.sciencemag.org/cgi/reprint/291/5507/1304.pdf