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<i>Ab initio</i> identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq

Yi Liu, Dali Han, Yixing Han, Zheng Yan, Bin Xie, Jing Li, Nan Qiao, Haiyang Hu, Philipp Khaitovich, Yuan Gao and Jing-Dong J. Han.

in Nucleic Acids Research

March 2011; p ublished online October 2010 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5901 words.

Rhesus macaque is a widely used primate model organism. Its genome annotations are however still largely comparative computational predictions derived mainly from human genes, which...

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<i>Ab initio</i> thermodynamic modeling of distal multisite transcription regulation

Leonor Saiz and Jose M. G. Vilar.

in Nucleic Acids Research

February 2008; p ublished online December 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4380 words.

Transcription regulation typically involves the binding of proteins over long distances on multiple DNA sites that are brought close to each other by the formation of DNA loops. The...

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Abasic Site Binding by the Human Apurinic Endonuclease, Ape, and Determination of the DNA Contact Sites

David M. Wilson, Masaru Takeshita and Bruce Demple.

in Nucleic Acids Research

March 1997; p ublished online March 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4712 words.

The mutagenic and lethal effects of abasic sites in DNA are averted by repair initiated by ‘class II’ apurinic (AP) endonucleases, which cleave immediately 5′; to abasic sites. We examined...

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<i>AbeI</i>, a restriction endonuclease from <i>Azotobacter beijerinckii</i>, which recognizes the asymmetric heptanucleotide sequence 5′-CCTCAGC-3′(−5/−2)

J. Vitkute, Z. Maneliene and A. Janulaitis.

in Nucleic Acids Research

November 1998; p ublished online November 1998 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 1494 words.

A new restriction endonuclease AbeI has been isolated from Azotobacter beijerinckii. This enzyme recognizes the asymmetric heptanucleotide sequence 5′-CCTCAGC-3′ and cleaves within it...

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Aberrant 5′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization

Emanuele Buratti, Martin Chivers, Jana Královičová, Maurizio Romano, Marco Baralle, Adrian R. Krainer and Igor Vořechovský.

in Nucleic Acids Research

July 2007; p ublished online June 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 9407 words.

Despite a growing number of splicing mutations found in hereditary diseases, utilization of aberrant splice sites and their effects on gene expression remain challenging to predict. We...

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Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers

Zhenbao Yu, Zhen Li, Normand Jolicoeur, Linhua Zhang, Yves Fortin, Edwin Wang, Meiqun Wu and Shi-Hsiang Shen.

in Nucleic Acids Research

July 2007; p ublished online June 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4780 words.

MicroRNAs (miRNAs) are a class of noncoding small RNAs that regulate gene expression by base pairing with target mRNAs at the 3′-terminal untranslated regions (3′-UTRs), leading to mRNA...

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Aberrant growth and lethality of <i>Arabidopsis</i> deficient in nonsense-mediated RNA decay factors is caused by autoimmune-like response

Nina Riehs-Kearnan, Jiradet Gloggnitzer, Bettina Dekrout, Claudia Jonak and Karel Riha.

in Nucleic Acids Research

July 2012; p ublished online February 2012 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5626 words.

Nonsense-mediated RNA decay (NMD) is an evolutionarily conserved RNA quality control mechanism that eliminates transcripts containing nonsense mutations. NMD has also been shown to affect...

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Aberrant repair initiated by mismatch-specific thymine-DNA glycosylases provides a mechanism for the mutational bias observed in CpG islands

Ibtissam Talhaoui, Sophie Couve, Laurent Gros, Alexander A. Ishchenko, Bakhyt Matkarimov and Murat K. Saparbaev.

in Nucleic Acids Research

June 2014; p ublished online April 2014 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 10399 words.

The human thymine-DNA glycosylase (TDG) initiates the base excision repair (BER) pathway to remove spontaneous and induced DNA base damage. It was first biochemically characterized for its...

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Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines

Ayako Suzuki, Hideki Makinoshima, Hiroyuki Wakaguri, Hiroyasu Esumi, Sumio Sugano, Takashi Kohno, Katsuya Tsuchihara and Yutaka Suzuki.

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. 10540 words.

Here we conducted an integrative multi-omics analysis to understand how cancers harbor various types of aberrations at the genomic, epigenomic and transcriptional levels. In order to...

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An Abf1p C-terminal region lacking transcriptional activation potential stimulates a yeast origin of replication

Steven Wiltshire, Santanu Raychaudhuri and Shlomo Eisenberg.

in Nucleic Acids Research

November 1997; p ublished online November 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4812 words.

Although it has been demonstrated that eukaryotic cellular origins of DNA replication may harbor stimulatory elements that bind transcription factors, how these factors stimulate origin...

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