Works matching AU Schneider, Thomas D.

Results: 30

Generalizing the isothermal efficiency by using Gaussian distributions.

Published in:

PLoS ONE, 2023, v. 18, n. 1, p. 1, doi. 10.1371/journal.pone.0279758

By:

Schneider, Thomas D.

Publication type:

Article

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.

Published in:

Molecular Microbiology, 1999, v. 34, n. 3, p. 414, doi. 10.1046/j.1365-2958.1999.01598.x

By:

Wood, Timothy I;
Griffith, Kevin L;
Fawcett, William P;
Jair, Kam-Wing;
Schneider, Thomas D;
Wolf, Richard E

Publication type:

Article

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 18, p. 5995, doi. 10.1093/nar/gkq389

By:

Schneider, Thomas D.

Publication type:

Article

Discovery of novel tumor suppressor p53 response elements using information theory.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 11, p. 3828, doi. 10.1093/nar/gkn189

By:

Lyakhov, Ilya G.;
Krishnamachari, Annangarachari;
Schneider, Thomas D.

Publication type:

Article

Discovery of Fur binding site clusters in Escherichia coli by information theory models.

Published in:

Nucleic Acids Research, 2007, v. 35, n. 20, p. 6762, doi. 10.1093/nar/gkm631

By:

Chen, Zehua;
Lewis, Karen A.;
Shultzaberger, Ryan K.;
Lyakhov, Ilya G.;
Zheng, Ming;
Doan, Bernard;
Storz, Gisela;
Schneider, Thomas D.

Publication type:

Article

Correlation between binding rate constants and individual information of E. coli Fis binding sites.

Published in:

Nucleic Acids Research, 2007, v. 35, n. 16, p. 5275, doi. 10.1093/nar/gkm471

By:

Shultzaberger, Ryan K.;
Roberts, Lindsey R.;
Lyakhov, Ilya G.;
Sidorov, Igor A.;
Stephen, Andrew G.;
Fisher, Robert J.;
Schneider, Thomas D.

Publication type:

Article

Anatomy of Escherichia coli σ70 promoters.

Published in:

Nucleic Acids Research, 2007, v. 35, n. 3, p. 771, doi. 10.1093/nar/gkl956

By:

Shultzaberger, Ryan K.;
Chen, Zehua;
Lewis, Karen A.;
Schneider, Thomas D.

Publication type:

Article

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w405, doi. 10.1093/nar/gkl269

By:

Bindewald, Eckart;
Schneider, Thomas D.;
Shapiro, Bruce A.

Publication type:

Article

Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 4, p. 1133, doi. 10.1093/nar/gkj511

By:

Chen, Zehua;
Schneider, Thomas D.

Publication type:

Article

Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 19, p. 6172, doi. 10.1093/nar/gki915

By:

Chen, Zehua;
Schneider, Thomas D.

Publication type:

Article

Molecular flip–flops formed by overlapping Fis sites.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 22, p. 6663, doi. 10.1093/nar/gkg877

By:

Hengen, Paul N.;
Lyakhov, Ilya G.;
Stewart, Lisa E.;
Schneider, Thomas D.

Publication type:

Article

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.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 16, p. 3624, doi. 10.1093/nar/gkf469

By:

Khan, Sikandar G.;
Muniz‐Medina, Vanessa;
Shahlavi, Tala;
Baker, Carl C.;
Inui, Hiroki;
Ueda, Takahiro;
Emmert, Steffen;
Schneider, Thomas D.;
Kraemer, Kenneth H.

Publication type:

Article

The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 23, p. 4892, doi. 10.1093/nar/29.23.4892

By:

Lyakhov, Ilya G.;
Hengen, Paul N.;
Rubens, Denise;
Schneider, Thomas D.

Publication type:

Article

Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 23, p. 4881, doi. 10.1093/nar/29.23.4881

By:

Schneider, Thomas D.

Publication type:

Article

Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences.

Published in:

PLoS ONE, 2019, v. 14, n. 10, p. 1, doi. 10.1371/journal.pone.0222419

By:

Schneider, Thomas D.;
Jejjala, Vishnu

Publication type:

Article

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.

Published in:

Human Molecular Genetics, 2004, v. 13, n. 3, p. 343

By:

Khan, Sikandar G.;
Metin, Ahmet;
Gozukara, Engin;
Inui, Hiroki;
Shahlavi, Tala;
Muniz-Medina, Vanessa;
Baker, Carl C.;
Ueda, Takahiro;
Aiken, Juliet R.;
Schneider, Thomas D.;
Kraemer, Kenneth H.

Publication type:

Article

Evolution of biological information.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 14, p. 2794, doi. 10.1093/nar/28.14.2794

By:

Schneider, Thomas D.

Publication type:

Article

Using sequence logos and information analysis ofLrp DNA binding sites to investigate discrepanciesbetween natural selection and SELEX.

Published in:

Nucleic Acids Research, 1999, v. 27, n. 3, p. 882, doi. 10.1093/nar/27.3.882

By:

Shultzaberger, Ryan K.;
Schneider, Thomas D.

Publication type:

Article

Information Analysis of Fis Binding Sites.

Published in:

Nucleic Acids Research, 1997, v. 25, n. 24, p. 4994, doi. 10.1093/nar/25.24.4994

By:

Hengen, Paul N.;
Bartram, Stacy L.;
Stewart, Lisa E.;
Schneider, Thomas D.

Publication type:

Article

Sequence walkers: A graphical method to display how binding proteins interact with DNA or RNA sequences.

Published in:

Nucleic Acids Research, 1997, v. 25, n. Supplement, p. 4408, doi. 10.1093/nar/25.21.4408

By:

Schneider, Thomas D.

Publication type:

Article

Xeroderma Pigmentosum Group C Splice Mutation Associated with Autism and Hypoglycinemia<sup>1</sup>.

Published in:

Journal of Investigative Dermatology, 1998, v. 111, n. 5, p. 791, doi. 10.1046/j.1523-1747.1998.00391.x

By:

Khan, Sikandar G.;
Levy, Harvey L.;
Legerski, Randy;
Quackenbush, Elizabeth;
Reardon, Joyce T.;
Emmert, Steffen;
Sancar, Aziz;
Li, Lei;
Schneider, Thomas D.;
Cleaver, James E.;
Kraemer, Kenneth H.

Publication type:

Article

Redundant designations of BRCA1 intron 11 splicing mutation; c. 4216-2A>G; IVS11-2A>G; L78833, 37698, A>G.

Published in:

Human Mutation, 2000, v. 16, n. 3, p. 264, doi. 10.1002/1098-1004(200009)16:3<264::AID-HUMU9>3.0.CO;2-1

By:

Svojanovsky, Stan R.;
Schneider, Thomas D.;
Rogan, Peter K.

Publication type:

Article

Rogan PK, Faux BM, Schneider TD. 1998. Information analysis of human splice site mutations. Hum Mutat 12:153-171.

Published in:

Human Mutation, 1999, v. 13, n. 1, p. 82, doi. 10.1002/(SICI)1098-1004(1999)13:1<82::AID-HUMU10>3.0.CO;2-E

By:

Rogan, Peter K.;
Faux, Brian M.;
Schneider, Thomas D.

Publication type:

Article

Information analysis of human splice site mutations.

Published in:

Human Mutation, 1998, v. 12, n. 3, p. 153, doi. 10.1002/(SICI)1098-1004(1998)12:3<153::AID-HUMU3>3.0.CO;2-I

By:

Rogan, Peter K.;
Faux, Brian M.;
Schneider, Thomas D.

Publication type:

Article

Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites.

Published in:

Human Mutation, 1995, v. 6, n. 1, p. 74, doi. 10.1002/humu.1380060114

By:

Rogan, Peter K.;
Schneider, Thomas D.

Publication type:

Article

Elements in the λ immunity region regulate phage development: beyond the 'Genetic Switch'.

Published in:

Molecular Microbiology, 2019, v. 112, n. 6, p. 1798, doi. 10.1111/mmi.14394

By:

Thomason, Lynn C.;
Morrill, Kathleen;
Murray, Gillian;
Court, Carolyn;
Shafer, Brenda;
Schneider, Thomas D.;
Court, Donald L.

Publication type:

Article

An unusual feature associated with LEE1 P1 promoters in enteropathogenic Escherichia coli (EPEC).

Published in:

Molecular Microbiology, 2012, v. 83, n. 3, p. 612, doi. 10.1111/j.1365-2958.2011.07956.x

By:

Jeong, Jae-Ho;
Kim, Hyun-Ju;
Kim, Kun-Hee;
Shin, Minsang;
Hong, Yeongjin;
Rhee, Joon Haeng;
Schneider, Thomas D.;
Choy, Hyon E.

Publication type:

Article

Small membrane proteins found by comparative genomics and ribosome binding site models.

Published in:

Molecular Microbiology, 2008, v. 70, n. 6, p. 1487, doi. 10.1111/j.1365-2958.2008.06495.x

By:

Hemm, Matthew R.;
Paul, Brian J.;
Schneider, Thomas D.;
Storz, Gisela;
Rudd, Kenneth E.

Publication type:

Article

Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 8, p. 3970, doi. 10.1093/nar/gkz159

By:

Sun, Zhe;
Cagliero, Cedric;
Izard, Jerome;
Chen, Yixiong;
Zhou, Yan Ning;
Heinz, William F;
Schneider, Thomas D;
Jin, Ding Jun

Publication type:

Article

Identification of a Cryptic Bacterial Promoter in Mouse (mdr1a) P-Glycoprotein cDNA.

Published in:

PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0136396

By:

Pluchino, Kristen M.;
Esposito, Dominic;
Moen, Janna K.;
Hall, Matthew D.;
Madigan, James P.;
Shukla, Suneet;
Procter, Lauren V.;
Wall, Vanessa E.;
Schneider, Thomas D.;
Pringle, Ian;
Ambudkar, Suresh V.;
Gill, Deborah R.;
Hyde, Steven C.;
Gottesman, Michael M.

Publication type:

Article