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Bioinformatics and Computational Biology x clear all

A “Fundamental Theorem” of Biomedical Informatics

Charles P. Friedman.

in Journal of the American Medical Informatics Association

March 2009; p ublished online March 2009 .

Journal Article. Subjects: Medical Statistics and Methodology; Bioinformatics and Computational Biology; Biomathematics and Statistics. 1079 words.

Abstract

This paper proposes, in words and pictures, a “fundamental theorem” to help clarify what informatics is and what it is not. In words, the theorem...

A 10S galectin-3–U1 snRNP complex assembles into active spliceosomes

Kevin C. Haudek, Patricia G. Voss, John L. Wang and Ronald J. Patterson.

in Nucleic Acids Research

July 2016; p ublished online April 2016 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4810 words.

In previous studies, we reported that fractionation of HeLa cell nuclear extracts on glycerol gradients revealed an endogenous ∼10S particle that contained galectin-3 and U1 snRNP and this...

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A 16S rRNA–tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome

Wayne Huggins and Paul Wollenzien.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6644 words.

Ribosome complexes containing deacyl-[math] or biotinylvalyl-[math] and an mRNA analog have been irradiated with wavelengths specific for activation of the cmo5U nucleoside at position 34 in...

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A 1.8 kb Alternative Transcript from the Human Epidermal Growth Factor Receptor Gene Encodes a Truncated form of the Receptor

Jill L. Reiter and Nita J. Maihle.

in Nucleic Acids Research

October 1996; p ublished online October 1996 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4492 words.

The epidermal growth factor receptor (EGFR) is encoded by the c-erbB1 proto-oncogene and plays an important role in the control of cell growth and differentiation. To study the potential...

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A 21‐amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11‐like and prefers manganese ion as the cofactor

Yulong Shen, Xiao‐Feng Tang, Hideshi Yokoyama, Eriko Matsui and Ikuo Matsui.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7265 words.

Family D DNA polymerase (PolD) is a new type of DNA polymerase possessing polymerization and 3′–5′ exonuclease activities. Here we report the characterization of the nuclease activity of...

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A 2,2′-bipyridine ligand for incorporation into oligodeoxynucleotides: Synthesis, stability and fluorescence properties of ruthenium—DNA complexes

Kristin Wiederholt and Larry W. McLaughlin.

in Nucleic Acids Research

January 1999; p ublished online January 1999 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4768 words.

A non-nucleoside linker based upon the ligand 2,2′-bipyridine and ethylene glycol is prepared and placed into the backbone of a number of oligonucleo-tides. The bipyridine ligand is reacted...

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A 39 Amino Acid Fragment of the Cell Cycle Regulator p21 Is Sufficient to Bind PCNA and Partially Inhibit DNA Replication in vivo

Junjie Chen, Richard Peters, Partha Saha, Patrick Lee, Annie Theodoras, Michele Pagano, Gerhard Wagner and Anindya Dutta.

in Nucleic Acids Research

May 1996; p ublished online May 1996 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4650 words.

The cell cycle regulator p21 interacts with and inhibits the DNA replication and repair factor proliferating cell nuclear antigen (PCNA). We have defined a 39 amino acid fragment of p21...

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A 3D pattern matching algorithm for DNA sequences

Joan Hérisson, Guillaume Payen and Rachid Gherbi.

in Bioinformatics

March 2007; p ublished online January 2007 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4664 words.

Motivation: Biologists usually work with textual DNA sequences (succession of A, C, G and T). This representation allows biologists to study the syntax and other linguistic...

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A 43 kDa DNA Binding Protein from the Pea Chloroplast Interacts with and Stimulates the Cognate DNA Polymerase

Weiliang Chen, Amos Gaikwad, Sunil Kumar Mukherjee, Nirupam Roy Choudhary, Dhirendra Kumar and Krishna K. Tewari.

in Nucleic Acids Research

October 1996; p ublished online October 1996 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6663 words.

A DNA binding protein with DNA polymerase ‘accessory activity’ has been identified and purified to apparent homogeneity from pea chloroplasts. This protein consists of a single subunit of...

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A 5′, 8-cyclo-2′-deoxypurine lesion induces trinucleotide repeat deletion via a unique lesion bypass by DNA polymerase β

Meng Xu, Yanhao Lai, Zhongliang Jiang, Michael A. Terzidis, Annalisa Masi, Chryssostomos Chatgilialoglu and Yuan Liu.

in Nucleic Acids Research

December 2014; p ublished online November 2014 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 9132 words.

5′,8-cyclo-2′-deoxypurines (cdPus) are common forms of oxidized DNA lesions resulting from endogenous and environmental oxidative stress such as ionizing radiation. The lesions can only be...

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A 5′ Untranslated Region Which Directs Accurate and Robust Translation By Prokaryotic and Mammalian Ribosomes

Ahmed Al-Qahtani and Kojo Mensa-Wilmot.

in Nucleic Acids Research

March 1996; p ublished online March 1996 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 1236 words.

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A 7-methylguanosine cap commits U3 and U8 small nuclear RNAs to the nucleolar localization pathway

Marty R. Jacobson and Thoru Pederson.

in Nucleic Acids Research

February 1998; p ublished online February 1998 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2699 words.

U3 and U8 small nucleolar RNAs (snRNAs) participate in pre-rRNA processing. Like the U1, U2, U4 and U5 major spliceosomal snRNAs, U3 and U8 RNAs are transcribed by RNA polymerase II and...

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A 96-well DNase I footprinting screen for drug–DNA interactions

Tom Ellis, David A. Evans, Christopher R. H. Martin and John A. Hartley.

in Nucleic Acids Research

June 2007; p ublished online June 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5019 words.

The established protocol for DNase I footprinting has been modified to allow multiple parallel reactions to be rapidly performed in 96-well microtitre plates. By scrutinizing every aspect...

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À la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge

Colin Cherry, Xiaodan Zhu, Joel Martin and Berry de Bruijn.

in Journal of the American Medical Informatics Association

September 2013; p ublished online March 2013 .

Journal Article. Subjects: Medical Statistics and Methodology; Bioinformatics and Computational Biology; Biomathematics and Statistics. 5027 words.

Abstract

Objective An analysis of the timing of events is critical for a deeper understanding of the course of events within a patient record....

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2A peptides provide distinct solutions to driving stop-carry on translational recoding

Pamila Sharma, Fu Yan, Victoria A. Doronina, Helena Escuin-Ordinas, Martin D. Ryan and Jeremy D. Brown.

in Nucleic Acids Research

April 2012; p ublished online December 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5879 words.

Expression of viral proteins frequently includes non-canonical decoding events (‘recoding’) during translation. ‘2A’ oligopeptides drive one such event, termed ‘stop-carry on’ recoding....

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An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments

R. S. Anderssen, Y. Wu, R. Dolferus and I. Saunders.

in Bioinformatics

July 2004; p ublished online February 2004 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Motivation: Because of the high cost of sequencing, the bulk of gene discovery is performed using anonymous cDNA microarrays. Though the clones on such arrays are easier and...

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A′-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC)

Yoshiyuki Tanaka, Satoshi Fujii, Hidekazu Hiroaki, Takeshi Sakata, Toshiki Tanaka, Seiichi Uesugi, Ken-ichi Tomita and Yoshimasa Kyogoku.

in Nucleic Acids Research

February 1999; p ublished online February 1999 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3932 words.

Here we demonstrate the presence of the A′-RNA conformation using the single crystal structure of a tridecamer: r(UGAGCUUCGGCUC). The average A′-RNA conformation deduced from X-ray fiber...

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The A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyltransferase active site conformation

Mark A. Bayfield, Jill Thompson and Albert E. Dahlberg.

in Nucleic Acids Research

October 2004; p ublished online October 2004 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4346 words.

Peptide bond formation, catalyzed by the ribosomal peptidyltransferase, has long been known to be sensitive to monovalent cation concentrations and pH. More recently, we and others have...

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A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

David Coil, Guillaume Jospin and Aaron E. Darling.

in Bioinformatics

February 2015; p ublished online October 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1527 words.

Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating...

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AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases

Jianbo Pan, Sheng Liu, Heng Zhu and Jiang Qian.

in Nucleic Acids Research

January 2018; p ublished online August 2017 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3753 words.

Abstract

Autoantibodies are produced to target an individual's own antigens (e.g. proteins). They can trigger autoimmune responses and inflammation, and thus,...

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