Bacterial Functional Genomics

Note that this page is continuously modified, following reactions of the public. It is now discontinued. Obsolete links are progressively removed (july 30th 2016)

Frequently Asked Questions (in English)

Functional genomics journal watch  

The European Science Foundation Functional Genomics network

Our Centre is linked to the activity of this network through the Genetics of Bacterial Genomes Unit at the Pasteur Institute in Paris

Links

On-going bacterial genome projects (syntheses)

Microbial genome annotation

Contents

Databases
Some important results presented at meetings
Selected Literature of the Month
DNA arrays, expression profiling in bacteria
2D gel electrophoresis
Bioinformatics

Databases

Some important results presented at meetings

The selection rate has been very tough (over 80% rejection). This should be borne in mind for people making bibliometrics studies of publications in the domain of bioinformatics....

For the next meeting in Canada (2002) see here.

The China National Centre for Biotechnology Development and the European Biotechnology Node for Interaction with China organized a workshop on Bioinformatics, where several new bacterial genome sequences were presented, in particular that of a thermoresistant Bacillus (Hangzhou) and that (almost complete) of Leptospira interrogans (Shanghai).

The RECOMB 2001 Award for the Best Paper by a Young Scientist has been awarded to Mathieu Blanchette, University of Washington, for his paper Algorithms for Phylogenetic Fingerprinting. Twenty eight percent of the attendees were from industry. Thirty five selected papers focused on mathematics and algorithmics side of bioinformatics, as expected in this conference, but the keynote lectures made the link with bench lab experiments. Philip Sharp explained the recently discovered phenomenon of RNA interference. Mark Ptashne emphasized the recruitment process of activators, which select coordination of important biological pathways, thus refining progressively the interaction with their binding sites (hence the corresponding difficulty in identifying them). Matthias Wilm emphasized the importance of the study of protein complexes rather than isolated entities.

Biotechnology development in China is developing fast. The Company BioInfo Tech is setting up in Chengdu, with developments in genome analysis software and construction of DNA chips for monitoring microbial contamination. The interesting observation there is the recent involvment of the Western China authorities in the field of biotechnology, with collaboration from the Chinese community in the USA and in Canada.

Analysis of transcriptome experiments in several articles recently published in the literature: How do we make more than phenomenology (diagnostic)?

The main results presented at the meeting tend to show that the bacterial cytoplasm is a highly organised structure, much more organised than usually assumed to be.

Jeffrey Errington (Oxford, UK), demonstrated, using GFP fusions, that proteins Mbl and M of B. subtilis form helices, tightly associated to the cell membrane. The M helix has a ca 700 nm pitch, which fits exactly to the overall shape of the cell, anchored at the center of the cell (at the septum when it is formed) and at both its extremities. The Mbl helix has a shorter pitch. It is not known yet how these two helices interact, if they do, nor with which other proteins they interact. Biochemical work suggested that these proteins are actin-like. Therefore bacteria have a cytoskeleton made of tubulin-like proteins (FtsZ) and actin-like proteins

Analysis of the E. coli and B. subtilis genomes, in an entirely independent study, suggested that a strong selection pressure, most probably derived from architectural constraints (work of the HKU-Pasteur Research Centre and of the Regulation of Gene Expression Unit, was constraining the gene order and the codon bias usage in these bacteria

Finally, Noboru Sueoka (Boulder, Colorado) provided strong arguments for the existence of constraints resulting in G+C biases in DNA strands of bacterial chromosomes. This is consistent not only with some rigidity in the gene structure in genomes, but also with uneven compartmentalization of DNA inside the cell.

A Japanese team announced the completion of the sequencing of the genomeof Escherichia coli O157 H7

Pr KY Yuen presented first results of the Penicillium marneffei sequencing program (in collaboration with the GMP laboratory at the IP in Paris). Collaboration is set up with the Shanghai Genome Centre and the Bioinformatics Institute at Beijing University on this program.


Selected Literature of the Month (updated  no longer updated . You are now accessing this site at no date)

1: Tachezy J, Sanchez LB, Muller M. Related Articles
Mitochondrial Type Iron-Sulfur Cluster Assembly in the Amitochondriate Eukaryotes Trichomonas vaginalis and Giardia intestinalis, as Indicated by the Phylogeny of IscS.
Mol Biol Evol. 2001 Oct;18(10):1919-28.
PMID: 11557797 [PubMed - in process]
2: Kappler U, Dahl C. Related Articles
Enzymology and molecular biology of prokaryotic sulfite oxidation(1).
FEMS Microbiol Lett. 2001 Sep 11;203(1):1-9.
PMID: 11557133 [PubMed - in process]
3: Ogasawara Y, Lacourciere G, Stadtman TC. Related Articles
Formation of a selenium-substituted rhodanese by reaction with selenite and glutathione: Possible role of a protein perselenide in a selenium delivery system.
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9494-8.
PMID: 11493708 [PubMed - in process]
4: Masuda K, Shima H, Watanabe M, Kikuchi K. Related Articles
MKP-7, a novel MAP kinase phosphatase, functions as a shuttle protein.
J Biol Chem. 2001 Aug 6 [epub ahead of print]
PMID: 11489891 [PubMed - as supplied by publisher]
5: Kroncke KD, Haase H, Beyersmann D, Kolb-Bachofen V, Hayer-Hartl MK. Related Articles
Nitric oxide inhibits the cochaperone activity of the ring finger-like protein dnaj.
Nitric Oxide. 2001 Aug;5(4):289-95.
PMID: 11485367 [PubMed - in process]
6: Weber F, Hayer-Hartl M. Related Articles
Refolding of bovine mitochondrial rhodanese by chaperonins GroEL and GroES.
Methods Mol Biol. 2000;140:117-26. No abstract available.
PMID: 11484478 [PubMed - indexed for MEDLINE]
7: Weber F, Hayer-Hartl M. Related Articles
Prevention of rhodanese aggregation by the chaperonin GroEL.
Methods Mol Biol. 2000;140:111-5. No abstract available.
PMID: 11484477 [PubMed - indexed for MEDLINE]
8: Librando V, Tringali G, Hjorth J, Jensen N. Related Articles
Aerosol formation and reaction pathways of atmospheric oxidation of dimethylsulfide.
Ann Chim. 2001 Jul-Aug;91(7-8):415-24.
PMID: 11554180 [PubMed - in process]
9: Fahey RC. Related Articles
Novel thiols of prokaryotes.
Annu Rev Microbiol. 2001;55:333-56.
PMID: 11544359 [PubMed - in process]
10: Poirier LA, Brown AT, Fink LM, Wise CK, Randolph CJ, Delongchamp RR, Fonseca VA. Related Articles
Blood S-adenosylmethionine concentrations and lymphocyte methylenetetrahydrofolate reductase activity in diabetes mellitus and diabetic nephropathy.
Metabolism. 2001 Sep;50(9):1014-1018.
PMID: 11555831 [PubMed - as supplied by publisher]
11: Consogno E, Tiraboschi E, Iuliano E, Gennarelli M, Racagni G, Popoli M. Related Articles
Long-term treatment with s-adenosylmethionine induces changes in presynaptic cam kinase II and synapsin I.
Biol Psychiatry. 2001 Sep 1;50(5):337-44.
PMID: 11543736 [PubMed - in process]
12: Das SR, Schneller SW, Balzarini J, De Clercq E. Related Articles
5'-Nor carbocyclic 5'-deoxy-5'-(isobutylthio) adenosine and a 2',3'-dideoxy-2',3'-didehydro derivative.
Antivir Chem Chemother. 2001 Mar;12(2):119-24.
PMID: 11527043 [PubMed - in process]
13: Li YF, Hess S, Pannell LK, Tabor CW, Tabor H. Related Articles
In vivo mechanism-based inactivation of S-adenosylmethionine decarboxylases from Escherichia coli, Salmonella typhimurium, and Saccharomycescerevisiae.
Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10578-83.
PMID: 11526206 [PubMed - in process]
14: Knopman D, Patterson M. Related Articles
An open-label, 24-week pilot study of the methyl donor betaine in alzheimer disease patients.
Alzheimer Dis Assoc Disord. 2001 Jul-Sep;15(3):162-5.
PMID: 11522934 [PubMed - in process]
15: Bujnicki JM, Rychlewski L. Related Articles
Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases.
Acta Microbiol Pol. 2001;50(1):7-17.
PMID: 11518396 [PubMed - in process]
16: Csanaky I, Gregus Z. Related Articles
Effect of phosphate transporter and methylation inhibitor drugs on the disposition of arsenate and arsenite in rats.
Toxicol Sci. 2001 Sep;63(1):29-36.
PMID: 11509741 [PubMed - in process]
17: Graf WD, Unis AS, Yates CM, Sulzbacher S, Dinulos MB, Jack RM, Dugaw KA, Paddock MN, Parson WW. Related Articles
Catecholamines in patients with 22q11.2 deletion syndrome and the low-activity COMT polymorphism.
Neurology. 2001 Aug 14;57(3):410-6.
PMID: 11502905 [PubMed - in process]
18: Southern F, Eidt J, Drouilhet J, Mukunyadzi P, Williams DK, Cruz C, Wang Y, Poirier LA, Brown AT, Moursi MM.
Increasing levels of dietary homocystine with carotid endarterectomy produced proportionate increases in plasma homocysteine and intimal hyperplasia.
Atherosclerosis. 2001 Sep;158(1):129-38.
PMID: 11500183 [PubMed - in process]
19: Law GL, Raney A, Heusner C, Morris DR. Related Articles
Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase.
J Biol Chem. 2001 Aug 6 [epub ahead of print]
PMID: 11489903 [PubMed - as supplied by publisher]
20: Schauder S, Shokat K, Surette MG, Bassler BL. Related Articles
The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule.
Mol Microbiol. 2001 Jul;41(2):463-76.
PMID: 11489131 [PubMed - in process]
21: Lindroth AM, Saarikoski P, Flygh G, Clapham D, Gronroos R, Thelander M, Ronne H, von Arnold S. Related Articles, Nucleotide, Protein
Two S-adenosylmethionine synthetase-encoding genes differentially expressed during adventitious root development in Pinus contorta.
Plant Mol Biol. 2001 Jun;46(3):335-46.
PMID: 11488480 [PubMed - indexed for MEDLINE]
22: Vahter M, Concha G. Related Articles
Role of metabolism in arsenic toxicity.
Pharmacol Toxicol. 2001 Jul;89(1):1-5.
PMID: 11484904 [PubMed - in process]
23: Bujnicki JM. Related Articles
Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation.
In Silico Biol. 1999-2000;1(4):175-82.
PMID: 11479932 [PubMed - indexed for MEDLINE]
24: Halim A, LeGros HL, Chamberlin ME, Geller A, Kotb M.
Distinct patterns of protein binding to the MAT2A promoter in normal and leukemic T cells.
Biochim Biophys Acta. 2001 Jul 25;1540(1):32-42.
PMID: 11476892 [PubMed - in process]
25: Rebeil R, Nicholson WL. Related Articles
The subunit structure and catalytic mechanism of the Bacillus subtilis DNA repair enzyme spore photoproduct lyase.
Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9038-43.
PMID: 11470912 [PubMed - indexed for MEDLINE]
26: Walters D, Meurer-Grimes B, Rovira I. Related Articles
Antifungal activity of three spermidine conjugates.
FEMS Microbiol Lett. 2001 Jul 24;201(2):255-8.
PMID: 11470370 [PubMed - in process]
27: Hurta RA. Related Articles
S-Adenosylmethionine decarboxylase gene expression is regulated by the cAMP signal transduction pathway in H-ras transformed fibrosarcoma cells capable of malignant progression.
J Cell Biochem. 2001;Suppl 36:209-21.
PMID: 11455586 [PubMed - indexed for MEDLINE]
28: Lamblin F, Saladin G, Dehorter B, Cronier D, Grenier E, Lacoux J, Bruyant P, Laine E, Chabbert B, Girault F, Monties B, Morvan C, David H, David A.
Overexpression of a heterologous sam gene encoding S-adenosylmethionine synthetase in flax (Linum usitatissimum) cells: Consequences on methylation of lignin precursors and pectins.
Physiol Plant. 2001 Jun;112(2):223-232.
PMID: 11454228 [PubMed - as supplied by publisher]
29: Medina M, Urdiales JL, Amores-Sanchez MI. Related Articles
Roles of homocysteine in cell metabolism: old and new functions.
Eur J Biochem. 2001 Jul;268(14):3871-82. Review.
PMID: 11453979 [PubMed - indexed for MEDLINE]
30: Bist P, Sistla S, Krishnamurthy V, Acharya A, Chandrakala B, Rao DN. Related Articles
S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes.
J Mol Biol. 2001 Jun 29;310(1):93-109.
PMID: 11419939 [PubMed - indexed for MEDLINE]
31: Koshiishi C, Kato A, Yama S, Crozier A, Ashihara H. Related Articles
A new caffeine biosynthetic pathway in tea leaves: utilisation of adenosine released from the S-adenosyl-L-methionine cycle.
FEBS Lett. 2001 Jun 15;499(1-2):50-4.
PMID: 11418110 [PubMed - indexed for MEDLINE]
32: Wang H, Huang ZQ, Xia L, Feng Q, Erdjument-Bromage H, Strahl BD, Briggs SD, Allis CD, Wong J, Tempst P, Zhang Y. Related Articles, OMIM
Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor.
Science. 2001 Aug 3;293(5531):853-7.
PMID: 11387442 [PubMed - indexed for MEDLINE]
33: Amachi S, Kamagata Y, Kanagawa T, Muramatsu Y. Related Articles
Bacteria mediate methylation of iodine in marine and terrestrial environments.
Appl Environ Microbiol. 2001 Jun;67(6):2718-22.
PMID: 11375186 [PubMed - indexed for MEDLINE]
34: Dirk LM, Williams MA, Houtz RL. Related Articles
Eukaryotic peptide deformylases. nuclear-encoded and chloroplast-targeted enzymes in arabidopsis.
Plant Physiol. 2001 Sep;127(1):97-107.
PMID: 11553738 [PubMed - in process]
35: Pratt LM, Beckett RP, Davies SJ, Launchbury SB, Miller A, Spavold ZM, Todd RS, Whittaker M. Related Articles
Asymmetric synthesis of bb-3497-A potent peptide deformylase inhibitor.
Bioorg Med Chem Lett. 2001 Oct 8;11(19):2585-8.
PMID: 11551755 [PubMed - in process]
36: Yuan Z, Trias J, White RJ. Related Articles
Deformylase as a novel antibacterial target.
Drug Discov Today. 2001 Sep 15;6(18):954-961.
PMID: 11546610 [PubMed - as supplied by publisher]
37: Dhandayuthapani S, Blaylock MW, Bebear CM, Rasmussen WG, Baseman JB. Related Articles
Peptide Methionine Sulfoxide Reductase (MsrA) Is a Virulence Determinant in Mycoplasma genitalium.
J Bacteriol. 2001 Oct;183(19):5645-50.
PMID: 11544227 [PubMed - in process]
38: Yang G, Kirkpatrick RB, Ho T, Zhang GF, Liang PH, Johanson KO, Casper DJ, Doyle ML, Marino JP Jr, Thompson SK, Chen W, Tew DG, Meek TD. Related Articles
Steady-state kinetic characterization of substrates and metal-ion specificities of the full-length and n-terminally truncated recombinant human methionine aminopeptidases (type 2).
Biochemistry. 2001 Sep 4;40(35):10645-54.
PMID: 11524009 [PubMed - in process]
39: Margolis P, Hackbarth C, Lopez S, Maniar M, Wang W, Yuan Z, White R, Trias J. Related Articles
Resistance of Streptococcus pneumoniae to Deformylase Inhibitors Is Due to Mutations in defB.
Antimicrob Agents Chemother. 2001 Sep;45(9):2432-5.
PMID: 11502510 [PubMed - in process]
40: Catalano A, Romano M, Robuffo I, Strizzi L, Procopio A. Related Articles
Methionine aminopeptidase-2 regulates human mesothelioma cell survival: role of Bcl-2 expression and telomerase activity.
Am J Pathol. 2001 Aug;159(2):721-31.
PMID: 11485930 [PubMed - indexed for MEDLINE]
41: Gilboa R, Spungin-Bialik A, Wohlfahrt G, Schomburg D, Blumberg S, Shoham G. Related Articles
Interactions of Streptomyces griseus aminopeptidase with amino-acid reaction products and their implications toward a catalytic mechanism.
Proteins. 2001 Sep 1;44(4):490-504.
PMID: 11484227 [PubMed - in process]
42: St John G, Brot N, Ruan J, Erdjument-Bromage H, Tempst P, Weissbach H, Nathan C.  Free in PMC , Related Articles
Peptide methionine sulfoxide reductase from Escherichia coli and Mycobacterium tuberculosis protects bacteria against oxidative damage from reactive nitrogen intermediates.
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9901-6.
PMID: 11481433 [PubMed - in process]
43: Thorarensen A, Deibel MR, Rohrer DC, Vosters AF, Yem AW, Marshall VD, Lynn JC, Bohanon MJ, Tomich PK, Zurenko GE, Sweeney MT, Jensen RM, Nielsen JW, Seest EP, Dolak LA.
Corrigendum to "Identification of novel potent hydroxamic acid inhibitors of peptidyl deformylase and the importance of the hydroxamic acid functionality on inhibition".
Bioorg Med Chem Lett. 2001 Aug 6;11(15):2053. No abstract available.
PMID: 11454479 [PubMed - in process]
44: Wiesner J, Sanderbrand S, Altincicek B, Beck E, Jomaa H. Related Articles
Seeking new targets for antiparasitic agents.
Trends Parasitol. 2001 Jan;17(1):7-8. No abstract available.
PMID: 11394347 [PubMed - indexed for MEDLINE]
45: Mitrasinovic OM, Perez GV, Zhao F, Lee YL, Poon C, Murphy GM Jr. Related Articles
Overexpression of macrophage colony-stimulating factor receptor on microglial cells induces an inflammatory response.
J Biol Chem. 2001 Aug 10;276(32):30142-9.
PMID: 11387343 [PubMed - indexed for MEDLINE]
46: Hagiwara S, Yagisawa M, Saeki K, Iki S, Urabe A, Mimura T, Miwa A, Togawa A, Higashihara M, Takaku F, Yuo A. Related Articles
Tyrosine phosphorylation of proteins in primary human myeloid leukemic cells stimulated by macrophage colony-stimulating factor: analysis by disease type and comparison with normal human hematopoietic cells.
Int J Hematol. 2001 Jan;73(1):100-7.
PMID: 11372744 [PubMed - indexed for MEDLINE]
47: Sekowska A, Mulard L, Krogh S, Tse JK, Danchin A.  Free in PMC , Related Articles
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis.
BMC Microbiol. 2001;1(1):15.
PMID: 11545674 [PubMed - as supplied by publisher]
48: Appleby TC, Mathews II, Porcelli M, Cacciapuoti G, Ealick SE. Related Articles
Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.
J Biol Chem. 2001 Aug 6 [epub ahead of print]
PMID: 11489901 [PubMed - as supplied by publisher]
49: Dai Y, Pochapsky TC, Abeles RH. Related Articles
Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae.
Biochemistry. 2001 May 29;40(21):6379-87.
PMID: 11371200 [PubMed - indexed for MEDLINE]
50: Chen S, Petersen BL, Olsen CE, Schulz A, Halkier BA. Related Articles
Long-distance phloem transport of glucosinolates in arabidopsis.
Plant Physiol. 2001 Sep;127(1):194-201.
PMID: 11553747 [PubMed - in process]
51: Bak S, Feyereisen R. Related Articles
The involvement of two p450 enzymes, cyp83b1 and cyp83a1, in auxin homeostasis and glucosinolate biosynthesis.
Plant Physiol. 2001 Sep;127(1):108-18.
PMID: 11553739 [PubMed - in process]
52: Cheng BF, Seguin-Swartz G, Somers DJ, Rakow G. Related Articles
Low glucosinolate Brassica juncea breeding line revealed to be nullisomic.
Genome. 2001 Aug;44(4):738-41.
PMID: 11550912 [PubMed - in process]
53: Conaway CC, Getahun SM, Liebes LL, Pusateri DJ, Topham DK, Botero-Omary M, Chung FL. Related Articles
Disposition of glucosinolates and sulforaphane in humans after ingestion of steamed and fresh broccoli.
Nutr Cancer. 2000;38(2):168-78.
PMID: 11525594 [PubMed - in process]
54: Petersen BL, Andreasson E, Bak S, Agerbirk N, Halkier BA. Related Articles
Characterization of transgenic Arabidopsis thaliana with metabolically engineered high levels of p-hydroxybenzylglucosinolate.
Planta. 2001 Mar;212(4):612-8.
PMID: 11525519 [PubMed - in process]
55: Vorwerk S, Biernacki S, Hillebrand H, Janzik I, Muller A, Weiler EW, Piotrowski M. Related Articles
Enzymatic characterization of the recombinant Arabidopsis thaliana nitrilase subfamily encoded by the NIT2/NIT1/NIT3-gene cluster.
Planta. 2001 Mar;212(4):508-16.
PMID: 11525507 [PubMed - in process]
56: Agerbirk N, Olsen CE, Nielsen JK. Related Articles
Seasonal variation in leaf glucosinolates and insect resistance in two types of Barbarea vulgaris ssp. arcuata.
Phytochemistry. 2001 Sep;58(1):91-100.
PMID: 11524118 [PubMed - in process]
57: Steinkellner H, Rabot S, Freywald C, Nobis E, Scharf G, Chabicovsky M, Knasmuller S, Kassie F. Related Articles
Effects of cruciferous vegetables and their constituents on drug metabolizing enzymes involved in the bioactivation of DNA-reactive dietary carcinogens.
Mutat Res. 2001 Sep 1;480-481(1-2):285-97.
PMID: 11506821 [PubMed - in process]
58: Moyes CL, Raybould AF.
The role of spatial scale and intraspecific variation in secondary chemistry in host-plant location by Ceutorhynchus assimilis (Coleoptera: Curculionidae).
Proc R Soc Lond B Biol Sci. 2001 Aug 7;268(1476):1567-73.
PMID: 11487403 [PubMed - in process]
59: Thangstad OP, Bones AM, Holtan S, Moen L, Rossiter JT. Related Articles
Microautoradiographic localisation of a glucosinolate precursor to specific cells in Brassica napus L. embryos indicates a separate transport pathway into myrosin cells.
Planta. 2001 Jun;213(2):207-13.
PMID: 11469585 [PubMed - in process]
60: Ibarreta D, Daxenberger A, Meyer HH. Related Articles
Possible health impact of phytoestrogens and xenoestrogens in food.
APMIS. 2001 Mar;109(3):161-84. Review.
PMID: 11430495 [PubMed - indexed for MEDLINE]
1: Mane J, Fernandez-Banares F, Ojanguren I, Castella E, Bertran X, Bartoli R, Alvarez M, Gassull MA. Related Articles
Effect of L-arginine on the course of experimental colitis.
Clin Nutr. 2001 Oct;20(5):415-22.
PMID: 11534936 [PubMed - in process]
2: Chen Y, Kramer DL, Diegelman P, Vujcic S, Porter CW. Related Articles
Apoptotic signaling in polyamine analogue-treated SK-MEL-28 human melanoma cells.
Cancer Res. 2001 Sep 1;61(17):6437-44.
PMID: 11522638 [PubMed - indexed for MEDLINE]
3: Suppola S, Heikkinen S, Parkkinen JJ, Uusi-Oukari M, Korhonen VP, Keinanen T, Alhonen L, Janne J. Related Articles
Concurrent overexpression of ornithine decarboxylase and spermidine/spermine N1-acetyltransferase further accelerates the catabolism of hepatic polyamines in transgenic mice.
Biochem J. 2001 Sep 1;358(Pt 2):343-8.
PMID: 11513732 [PubMed - in process]
4: Feith DJ, Shantz LM, Pegg AE. Related Articles
Targeted antizyme expression in the skin of transgenic mice reduces tumor promoter induction of ornithine decarboxylase and decreases sensitivity to chemical carcinogenesis.
Cancer Res. 2001 Aug 15;61(16):6073-81.
PMID: 11507056 [PubMed - indexed for MEDLINE]
5: Li L, Rao JN, Guo X, Liu L, Santora R, Bass BL, Wang JY. Related Articles
Polyamine depletion stabilizes p53 resulting in inhibition of normal intestinal epithelial cell proliferation.
Am J Physiol Cell Physiol. 2001 Sep;281(3):C941-53.
PMID: 11502571 [PubMed - indexed for MEDLINE]
6: Cayre M, Malaterre J, Strambi C, Charpin P, Ternaux JP, Strambi A. Related Articles
Short- and long-chain natural polyamines play specific roles in adult cricket neuroblast proliferation and neuron differentiation in vitro.
J Neurobiol. 2001 Sep 15;48(4):315-24.
PMID: 11500844 [PubMed - indexed for MEDLINE]
7: Heilman-Miller SL, Pan J, Thirumalai D, Woodson SA. Related Articles
Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics.
J Mol Biol. 2001 May 25;309(1):57-68.
PMID: 11491301 [PubMed - indexed for MEDLINE]
8: Stoner MC, Kellum JM. Related Articles
Both serotonin and a nitric-oxide donor cause chloride secretion in rat colonocytes by stimulating cGMP.
Surgery. 2001 Aug;130(2):236-41.
PMID: 11490355 [PubMed - indexed for MEDLINE]
9: Law GL, Raney A, Heusner C, Morris DR. Related Articles
Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase.
J Biol Chem. 2001 Aug 6 [epub ahead of print]
PMID: 11489903 [PubMed - as supplied by publisher]
10: Coleman CS, Pegg AE. Related Articles
Polyamine analogues inhibit the ubiquitination of spermidine/spermine N1-acetyltransferase and prevent its targeting to the proteasome for degradation.
Biochem J. 2001 Aug 15;358(Pt 1):137-45.
PMID: 11485561 [PubMed - in process]
11: Shantz LM, Feith DJ, Pegg AE. Related Articles
Targeted overexpression of ornithine decarboxylase enhances beta-adrenergic agonist-induced cardiac hypertrophy.
Biochem J. 2001 Aug 15;358(Pt 1):25-32.
PMID: 11485548 [PubMed - in process]
12: Jansen AP, Dreckschmidt NE, Verwiebe EG, Wheeler DL, Oberley TD, Verma AK. Related Articles
Relation of the induction of epidermal ornithine decarboxylase and hyperplasia to the different skin tumor-promotion susceptibilities of protein kinase C alpha, -delta and -epsilon transgenic mice.
Int J Cancer. 2001 Sep 1;93(5):635-43.
PMID: 11477572 [PubMed - indexed for MEDLINE]
13: Wei LH, Wu G, Morris SM Jr, Ignarro LJ.  Free in PMC , Related Articles
Elevated arginase I expression in rat aortic smooth muscle cells increases cell proliferation.
Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9260-4.
PMID: 11470919 [PubMed - indexed for MEDLINE]
14: Robert V, Mouille B, Mayeur C, Michaud M, Blachier F. Related Articles
Effects of the garlic compound diallyl disulfide on the metabolism, adherence and cell cycle of HT-29 colon carcinoma cells: evidence of sensitive and resistant sub-populations.
Carcinogenesis. 2001 Aug;22(8):1155-61.
PMID: 11470743 [PubMed - indexed for MEDLINE]
15: Rodriguez-Sallaberry C, Simmen FA, Simmen RC.
Polyamine- and insulin-like growth factor-i-mediated proliferation of porcine uterine endometrial cells: a potential role for spermidine/spermine n(1)-acetyltransferase during peri-implantation.
Biol Reprod. 2001 Aug;65(2):587-94.
PMID: 11466230 [PubMed - in process]
16: Bauer PM, Buga GM, Fukuto JM, Pegg AE, Ignarro LJ. Related Articles
Nitric Oxide Inhibits Ornithine Decarboxylase via S-Nitrosylation of Cysteine 360 in the Active Site of the Enzyme.
J Biol Chem. 2001 Sep 14;276(37):34458-64.
PMID: 11461922 [PubMed - in process]
17: Hurta RA. Related Articles
S-Adenosylmethionine decarboxylase gene expression is regulated by the cAMP signal transduction pathway in H-ras transformed fibrosarcoma cells capable of malignant progression.
J Cell Biochem. 2001;Suppl 36:209-21.
PMID: 11455586 [PubMed - indexed for MEDLINE]
18: Bergeron RJ, Muller R, Huang G, McManis JS, Algee SE, Yao H, Weimar WR, Wiegand J. Related Articles
Synthesis and evaluation of hydroxylated polyamine analogues as antiproliferatives.
J Med Chem. 2001 Jul 19;44(15):2451-9.
PMID: 11448227 [PubMed - indexed for MEDLINE]
19: Basle A, Delcour AH. Related Articles
Effect of two polyamine toxins on the bacterial porin OmpF.
Biochem Biophys Res Commun. 2001 Jul 13;285(2):550-4.
PMID: 11444879 [PubMed - indexed for MEDLINE]
20: Bachrach U, Wang YC, Tabib A. Related Articles
Polyamines: new cues in cellular signal transduction.
News Physiol Sci. 2001 Jun;16:106-9. Review.
PMID: 11443226 [PubMed - indexed for MEDLINE]
21: Ray RM, Viar MJ, McCormack SA, Johnson LR. Related Articles
Focal adhesion kinase signaling is decreased in polyamine-depleted IEC-6 cells.
Am J Physiol Cell Physiol. 2001 Aug;281(2):C475-85.
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Tissue transglutaminase selectively modifies proteins associated with truncated mutant huntingtin in intact cells.
Neurobiol Dis. 2001 Jun;8(3):391-404.
PMID: 11442349 [PubMed - indexed for MEDLINE]
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Pulm Pharmacol Ther. 2001;14(4):297-305.
PMID: 11440558 [PubMed - indexed for MEDLINE]
24: Shore L, McLean P, Gilmour SK, Hodgins MB, Finbow ME. Related Articles
Polyamines regulate gap junction communication in connexin 43-expressing cells.
Biochem J. 2001 Jul 15;357(Pt 2):489-95.
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DNA arrays, expression profiling in bacteria

Most WWW sites and publications dealing with this subject are devoted to eukaryotes, where cDNA preparation is much easier than in bacteria. The references provided here deal with the specific problems posed by bacteria.

Role of cDNA preparation and statistical analysis: A short review on expression profiling in bacteria

The following references gives interesting standard approaches in statistics for extracting information from DNA filters:

Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P.
Gene Expression Profiling in Escherichia coli K12: Improved statistical inference from DNA microarray data using analysis of
variance and a Bayesian statistical framework.
J Biol Chem. 2001 Mar 20

Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis
GenomeBiology (2001) 2: 19.1-19.12.

see also BioI@Sista for clustering gene expression profiles

For comparison: Human Genome arrays

Data processing (from the group "microarrays" at the Ecole Normale Supérieure, Paris)

Terry speed's microarray data analysis group page
Whitehead/MIT Genome Center's Molecular Pattern Recognition web site
Data mining in yeast genome expression data and functional classes (EBI)
NHGRI Microarray Project: Query the 15K Set
Pacific Symposium on Biocomputing reprints
GenomeJobs Home Page for jobs in genomics bioinformatics biotech computers DNAChips Databases
A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression, pdf
Genome-wide analysis relating expression levels with protein subcellular localization, pdf
Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome, pdf
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins, pdf
The current excitement in bioinformatics, analysis of whole-genome expression data: How does it relate to protein structure and function?, pdf
Useful things from Chris Seidel:
16 pin Array Deconvoluter, Block Row Column list generator, GenePix GAL file header generator
Mutual information analysis as a tool to assess the role of aneuploidy in the generation of cancer-associated differential gene expression patterns, free pdf
     Klus G.T., Pacific Symposium on Biocomputing 2001


Image analysis

CrazyQuant: Java quantification (Université de Washington)
NHGRI Microarray Project: Image Analysis
Dapple: image analysis software for cDNA microarrays
ImageJ: image analysis and analysis in Java
FSCAN: Fluorescently Probed cDNA Microarray Analysis
(MATLAB package)
Comparison of methods for image analysis on cDNA microarray data, pdf


Statistical analysis of data

Analysis of variance for gene expression data
    
Kerr, Martin, and Churchill (jullet 2000) programme ANOVA
On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data
        M.A. Newton , C.M. Kendziorski, C.S. Richmond, F.R. Blattner, and K.W. Tsui (Juin 2000 accepted for Journal of Computational Biology) sources Splus
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments, pdf
Microsoft Excel template for microarrays analysis from Chih Long
Determining significant fold differences in gene expression analysis, free pdf
  
Butte A.J., Pacific Symposium on Biocomputing 2001
A nonparametric scoring algorithm for identifying informative genes from microarray data, free pdf
     Park P.J., Pacific Symposium on Biocomputing 2001
Statistical ideas or mathematical models glossarie
CyberT: find variation using Bayesian statistical approach 
Spectral statistics of instantaneous normal modes in liquids and random matrices , free ps
Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data, free html, pdf
Using Non-Parametric Methods in the Context of Multiple Testing to Identify Differentially Expressed Genes, free pdf.
Grant, G., Manduchi, E., Stoeckert, C. (2001) Winner of best presentation award, CAMDA00


Clustering

Jexpress: pairwise, SOM, PCA in java. great! (free for academics)
Stanford software: ScanAlyse, Cluster, Treeview (password required)
CLEAVER: online classification of microarray data at Stanford university
A survey of computational algorithms to analyze patterns of gene expression from cDNA/DNA chip Microarray data
Generation of patterns from gene expression data by assigning confidence to differentially expressed genes
Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines
Plaid model for gene expression data
Biclustering of expression data 
Comparison of discrimination methods for the classification of tumors using gene expression data , pdf
Singular value decomposition for genome-wide expression data processing and modeling
Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns 
Bayesian Classification of DNA Array Expression Data, abstract, free pdf
Validating Clustering for Gene Expression Data, abstract, ps, free pdf
Coupled Two-Way Clustering Analysis of Gene Microarray Data
A Simple Introduction to Principal Component and Cluster Analysis
Fist steps in analysis of microarray data and clustering
Support vector machine book from Cambridge University Press 
Supervised harvesting of expression trees
Unsupervised learning from complex data: the matrix incision tree algorithm
Combining microarray expression data and phylogenetic profiles to learn gene functional categories using support vector machines, free pdf
     Kim J.H., Pacific Symposium on Biocomputing 2001
Percolation clustering: a novel algorithm applied to the clustering of gene expression patterns in dictyostelium development
     Sasik R., Pacific Symposium on Biocomputing 2001
Bootstrapping Cluster Analysis: Assessing the Reliability of Conclusions fromMicroarray Experiments
  
Kerr K. manuscript from Gary Churchill's Statistical Genetics Group
Bioinformatics Software: AMADA (Analyzing Microarray Data)
Windows 98/NT/2000 with pentium III
2HAPI a web-based microarray data analysis system
Theoretical Aspects of Pattern Analysis: A Simple Introduction to Principal Component and Cluster Analysis
 


Motif finding in co-regulated genes

Regulatory Sequence Analysis Tools (Belgique) (S. cerevisiae + 16 bacteria supported)
Weblogo: to create visual logo of your consensus sequences
Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences Clustered by Whole-Genome mRNA Quantitation
Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces, pdf
Predicting regulons and their cis-regulatory motifs by comparative genomics
 
Cluster, function and promoter: analysis of yeast expression array
Explore the motif universe (emotif)

Gene Networks
Mining the gene expression matrix: inferring gene relationships from large scale gene expression data
Systematic determination of genetic network architecture
Gene Networks from Microarray Data, html, pdf, gz ps
Tracing genetic information flow from gene expression to pathways and molecular networks, free pdf
Gene Expression Analysis and Genetic Network Modeling, free pdf
    D'haeseleer, P. Pacific Symposium on Biocomputing 1999, Tutorial session on Gene Expression and Genetic Networks. 
Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering.
Gene network inference using a linear, additive regulation model. 
Discovering Functional Relationships Between RNA Expression and Chemotherapeutic Susceptibility Using Relevance Networks.
Using Bayesian Networks to Analyze Gene Expression Data
Reconstructing Gene Networks from Large Scale Gene Expression Data, free pdf


Microarray discussion group
Pat Brown microarray forum 
Meetings
Microarray bibliography


2D gel electrophoresis


Bioinformatics

Fast computation can be performed using clusters of PCs. Did you know that one of the easiest, cheapest (and fastest) way is to use clusters of G4 Macintoshes?

 


History

Publications

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