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Our Science – Schneider Website

Thomas D. Schneider, Ph.D.

Selected Publications

1)  Jeong JH, Kim HJ, Kim KH, Shin M, Hong Y, Rhee JH, Schneider TD, Choy HE.
An unusual feature associated with LEE1 P1 promoters in enteropathogenic Escherichia coli (EPEC).
Mol. Microbiol. 83: 612-22, 2012.
2)  Lou H, Li H, Yeager M, Im K, Gold B, Schneider TD, Fraumeni JF, Chanock SJ, Anderson SK, Dean M.
Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts.
Hum. Genet. 131: 1453-66, 2012.
3)  Schneider TD.
70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence.
Nucleic Acids Res. 38: 5995-6006, 2010.
4)  Schneider TD.
A brief review of molecular information theory.
Nano Commun Netw. 1: 173-180, 2010.
5)  Lyakhov IG, Krishnamachari A, Schneider TD.
Discovery of novel tumor suppressor p53 response elements using information theory.
Nucleic Acids Res. 36(11): 3828-33, 2008.
6)  Hemm MR, Paul BJ, Schneider TD, Storz G, Rudd KE.
Small membrane proteins found by comparative genomics and ribosome binding site models.
Mol. Microbiol. 70: 1487-501, 2008.
7)  Inui H, Oh K, Nadem C, Ueda T, Khan SG, Metin A, Gozukara E, Emmert S, Slor H, Busch DB, Baker CC, Digiovanna JJ, Tamura D, Seitz CS, Gratchev A, Wu WH, Chung KY, Chung HJ, Azizi E, Woodgate R, Schneider TD, Kraemer KH.
Xeroderma Pigmentosum-Variant Patients from America, Europe, and Asia.
J. Invest. Dermatol. 128(8): 2055-68, 2008.
8)  Shultzaberger RK, Chen Z, Lewis KA, Schneider TD.
Anatomy of Escherichia coli sigma70 promoters.
Nucleic Acids Res. 35: 771-88, 2007.
9)  Shultzaberger RK, Roberts LR, Lyakhov IG, Sidorov IA, Stephen AG, Fisher RJ, Schneider TD.
Correlation between binding rate constants and individual information of E. coli Fis binding sites.
Nucleic Acids Res. 35(16): 5275-83, 2007.
10)  Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD.
Discovery of Fur binding site clusters in Escherichia coli by information theory models.
Nucleic Acids Res. 35: 6762-77, 2007.
11)  Schneider TD.
Claude Shannon: biologist. The founder of information theory used biology to formulate the channel capacity.
IEEE Eng Med Biol Mag. 25: 30-3, 2006.
12)  Chen Z, Schneider TD.
Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands.
Nucleic Acids Res. 34: 1133-47, 2006.
13)  Bindewald E, Schneider TD, Shapiro BA.
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
Nucleic Acids Res. 34: W405-11, 2006.
14)  Schneider TD.
Twenty Years of Delila and Molecular Information Theory: The Altenberg-Austin Workshop in Theoretical Biology Biological Information, Beyond Metaphor: Causality, Explanation, and Unification Altenberg, Austria, 11-14 July 2002.
Biol Theory. 1: 250-260, 2006.
15)  Chen Z, Schneider TD.
Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases.
Nucleic Acids Res. 33: 6172-87, 2005.
16)  Lyakhov I, Schneider T, Lyakhov G, Suyazov N.
Orientational ordering of protein micro- and nanoparticles in A nonuniform magnetic field.
Physics of Wave Phenomena. 13: 1-14, 2005.
17)  Schneider T.
Dictionary of Bioinformatics and Computational Biology.
book: John M. Hancock and Marketa J. Zvelebil (eds), John Wiley & Sons, Inc 0-471-43622-4. (many pages), 2004.
18)  Khan SG, Metin A, Gozukara E, Inui H, Shahlavi T, Muniz-Medina V, Baker CC, Ueda T, Aiken JR, Schneider TD, Kraemer KH.
Two essential splice lariat branchpoint sequences in one intron in a xeroderma pigmentosum DNA repair gene: mutations result in reduced XPC mRNA levels that correlate with cancer risk.
Hum Mol Genet. 13: 343-52, 2004.
19)  Hengen PN, Lyakhov IG, Stewart LE, Schneider TD.
Molecular flip-flops formed by overlapping Fis sites.
Nucleic Acids Res. 31: 6663-73, 2003.
20)  Schneider TD.
Consensus sequence Zen.
Appl Bioinformatics. 1: 111-9, 2002.
21)  Khan SG, Muniz-Medina V, Shahlavi T, Baker CC, Inui H, Ueda T, Emmert S, Schneider TD, Kraemer KH.
The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function.
Nucleic Acids Res. 30: 3624-31, 2002.
22)  Shultzaberger RK, Bucheimer RE, Rudd KE, Schneider TD.
Anatomy of Escherichia coli ribosome binding sites.
J Mol Biol. 313: 215-28, 2001.
23)  Zheng M, Wang X, Doan B, Lewis KA, Schneider TD, Storz G.
Computation-directed identification of OxyR DNA binding sites in Escherichia coli.
J Bacteriol. 183: 4571-9, 2001.
24)  Arnould I, Schriml LM, Prades C, Lachtermachter-Triunfol M, Schneider T, Maintoux C, Lemoine C, Debono D, Devaud C, Naudin L, Bauche S, Annat M, Annilo T, Allikmets R, Gold B, Denefle P, Rosier M, Dean M.
Identifying and characterizing a five-gene cluster of ATP-binding cassette transporters mapping to human chromosome 17q24: A new sub-group within the ABCA subfamily.
GeneScreen. 1: 157-64, 2001.
25)  Schneider TD.
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.
Nucleic Acids Res. 29: 4881-91, 2001.
26)  Emmert S, Schneider TD, Khan SG, Kraemer KH.
The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms.
Nucleic Acids Res. 29: 1443-52, 2001.
27)  Lyakhov IG, Hengen PN, Rubens D, Schneider TD.
The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping.
Nucleic Acids Res. 29: 4892-900, 2001.
28)  Schneider TD.
Evolution of biological information.
Nucleic Acids Res. 28: 2794-9, 2000.
29)  Kannan N, Schneider TD, Vishveshwara S.
Logos for amino-acid preferences in different backbone packing density regions of protein structural classes.
Acta Crystallogr D Biol Crystallogr. 56 ( Pt 9): 1156-65, 2000.
30)  Svojanovsky SR, Schneider TD, Rogan PK.
Redundant designations of BRCA1 intron 11 splicing mutation; c. 4216-2A>G; IVS11-2A>G; L78833, 37698, A>G.
Hum Mutat. 16: 264, 2000.
31)  Schneider TD.
The bottl.
Nature. 406: 351, 2000.
32)  Wood TI, Griffith KL, Fawcett WP, Jair KW, Schneider TD, Wolf RE.
Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters.
Mol Microbiol. 34: 414-30, 1999.
33)  Schneider TD.
Measuring molecular information.
J Theor Biol. 201: 87-92, 1999.
34)  Zheng M, Doan B, Schneider TD, Storz G.
OxyR and SoxRS regulation of fur.
J Bacteriol. 181: 4639-43, 1999.
35)  Shultzaberger RK, Schneider TD.
Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepanciesbetween natural selection and SELEX.
Nucleic Acids Res. 27: 882-7, 1999.
36)  Matten SR, Schneider TD, Ringquist S, Brusilow WS.
Identification of an intragenic ribosome binding site that affects expression of the uncB gene of the Escherichia coli proton-translocating ATPase (unc) operon.
J Bacteriol. 180: 3940-5, 1998.
37)  Rogan PK, Faux BM, Schneider TD.
Information analysis of human splice site mutations.
Hum Mutat. 12: 153-71, 1998.
38)  Allikmets R, Wasserman WW, Hutchinson A, Smallwood P, Nathans J, Rogan PK, Schneider TD, Dean M.
Organization of the ABCR gene: analysis of promoter and splice junction sequences.
Gene. 215: 111-22, 1998.
39)  Tooley PW, Salvo JJ, Schneider TD, Rogan PK.
Phylogenetic inference based on information theory-based PCR amplification.
Journal of Phytopathology. 146: 427-30, 1998.
40)  Khan SG, Levy HL, Legerski R, Quackenbush E, Reardon JT, Emmert S, Sancar A, Li L, Schneider TD, Cleaver JE, Kraemer KH.
Xeroderma pigmentosum group C splice mutation associated with autism and hypoglycinemia.
J Invest Dermatol. 111: 791-6, 1998.
41)  Hengen PN, Bartram SL, Stewart LE, Schneider TD.
Information analysis of Fis binding sites.
Nucleic Acids Res. 25: 4994-5002, 1997.
42)  Schneider TD.
Information content of individual genetic sequences.
J Theor Biol. 189: 427-41, 1997.
43)  Chattoraj DK, Schneider TD.
Replication control of plasmid P1 and its host chromosome: the common ground.
Prog Nucleic Acid Res Mol Biol. 57: 145-86, 1997.
44)  Schneider TD.
Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences.
Nucleic Acids Res. 25: 4408-15, 1997.
45)  Schneider TD, Mastronarde D.
Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method.
Discrete Applied Mathematics. 71: 259-68, 1996.
46)  Schneider TD.
Reading of DNA sequence logos: prediction of major groove binding by information theory.
Methods Enzymol. 274: 445-55, 1996.
47)  Rogan PK, Schneider TD.
Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites.
Hum Mutat. 6: 74-6, 1995.
48)  Barrick D, Villanueba K, Childs J, Kalil R, Schneider TD, Lawrence CE, Gold L, Stormo GD.
Quantitative analysis of ribosome binding sites in E.coli.
Nucleic Acids Res. 22: 1287-95, 1994.
49)  Toledano MB, Kullik I, Trinh F, Baird PT, Schneider TD, Storz G.
Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection.
Cell. 78: 897-909, 1994.
50)  Schneider TD.
Sequence logos, machine/channel capacity, Maxwell's demon, and molecular computers: a review of the theory of molecular machines.
Nanotechnology. 5(1): 1-18, 1994.
51)  Papp PP, Chattoraj DK, Schneider TD.
Information analysis of sequences that bind the replication initiator RepA.
J Mol Biol. 233: 219-30, 1993.
52)  Stephens RM, Schneider TD.
Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites.
J Mol Biol. 228: 1124-36, 1992.
53)  Herman ND, Schneider TD.
High information conservation implies that at least three proteins bind independently to F plasmid incD repeats.
J Bacteriol. 174: 3558-60, 1992.
54)  Arvidson DN, Youderian P, Schneider TD, Stormo GD.
Automated kinetic assay of beta-galactosidase activity.
Biotechniques. 11: 733-4, 736, 738, 1991.
55)  Schneider TD.
Theory of molecular machines. I. Channel capacity of molecular machines.
J Theor Biol. 148: 83-123, 1991.
56)  Schneider TD.
Theory of molecular machines. II. Energy dissipation from molecular machines.
J Theor Biol. 148: 125-37, 1991.
57)  Schneider TD, Stephens RM.
Sequence logos: a new way to display consensus sequences.
Nucleic Acids Res. 18: 6097-100, 1990.
58)  Schneider TD, Stormo GD.
Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique.
Nucleic Acids Res. 17: 659-74, 1989.
59)  Schneider TD, Stormo GD, Gold L, Ehrenfeucht A.
Information content of binding sites on nucleotide sequences.
J Mol Biol. 188: 415-31, 1986.
60)  Stormo GD, Schneider TD, Gold L.
Quantitative analysis of the relationship between nucleotide sequence and functional activity.
Nucleic Acids Res. 14: 6661-79, 1986.
61)  Clift B, Haussler D, McConnell R, Schneider TD, Stormo GD.
Sequence landscapes.
Nucleic Acids Res. 14: 141-58, 1986.
62)  Schneider TD, Stormo GD, Yarus MA, Gold L.
Delila system tools.
Nucleic Acids Res. 12: 129-40, 1984.
63)  Schneider TD, Stormo GD, Haemer JS, Gold L.
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation.
Nucleic Acids Res. 10: 3013-24, 1982.
64)  Stormo GD, Schneider TD, Gold LM.
Characterization of translational initiation sites in E. coli.
Nucleic Acids Res. 10: 2971-96, 1982.
65)  Stormo GD, Schneider TD, Gold L, Ehrenfeucht A.
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
Nucleic Acids Res. 10: 2997-3011, 1982.
66)  Gold L, Pribnow D, Schneider T, Shinedling S, Singer BS, Stormo G.
Translational initiation in prokaryotes.
Ann. Rev. of Microb. 35: 365-403, 1981.
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This page was last updated on 4/11/2014.