Yeondae Kwon - Academia.edu (original) (raw)

Papers by Yeondae Kwon

Research paper thumbnail of Checking Pattern Query Containment Under Shape Expression

Research paper thumbnail of Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery

Journal of Structural and Functional Genomics, Dec 1, 2016

genetically, structurally and functionally using the structural life science data cloud VaProS, s... more genetically, structurally and functionally using the structural life science data cloud VaProS, so as to evaluate their potential as next targets in drug discovery.

Research paper thumbnail of Genome-Wide Analysis of Long Noncoding RNA Turnover

Methods in molecular biology, Dec 5, 2014

Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that exami... more Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that examines the specific half-life of nuclear noncoding RNA (ncRNA). In particular, a pulse-labeling method using uridine analogs enables the determination of RNA stability under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromo-uridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing. The method is called BrU immunoprecipitation chase assay (BRIC) or BRIC through deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

Research paper thumbnail of Computational Complexity of Finding Meaningful Association Rules

IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Sep 25, 1999

Research paper thumbnail of A New Approach and Knowledge Integration to Proposing Perspectives on Aging Research Based on Literature Mining

The Molecular Biology Society of Japan, Nov 8, 2016

Research paper thumbnail of A Novel Measure for Finding Disease-Specific Genes from the Biomedical Literature

QP-PQ, quantum probability and white noise analysis, Mar 1, 2013

Research paper thumbnail of On-the-fly Link Generation for Workflows in Biology

A number of biological data resources such as databases and analytical tools can be accessible th... more A number of biological data resources such as databases and analytical tools can be accessible through the Internet. However, it is laborious and sometimes impossible to write a computer program that finds a useful data source, sends a proper query and processes its output. Therefore, it becomes a serious obstacle to the

Research paper thumbnail of RESEARCH Open Access Two-way AIC: detection of differentially

expressed genes from large scale microarray meta-dataset

Research paper thumbnail of Workflow and Its Navigation System Using

We present an overview of workflow and its navigation system using Web API for biology (WABI) dev... more We present an overview of workflow and its navigation system using Web API for biology (WABI) developed by DNA Data Bank of Japan (DDBJ). The system helps non-programming biologists perform analysis tasks which use multiple software tools and databases only by following links on Web browsers. The services are available at

Research paper thumbnail of A New Approach and Knowledge Integration to Proposing Perspectives on Aging Research Based on Literature Mining

The Molecular Biology Society of Japan, 2016

Research paper thumbnail of Computational Complexity of Finding Meaningful Association Rules

Ieice Transactions on Fundamentals of Electronics Communications and Computer Sciences, Sep 25, 1999

Research paper thumbnail of Protein synthesis using partially protected peptide thioesters as building blocks

Peptide Chemistry 1992, 1993

Research paper thumbnail of A Novel Measure for Finding Disease-Specific Genes from the Biomedical Literature

QP-PQ: Quantum Probability and White Noise Analysis, 2013

Research paper thumbnail of Genome-Wide Analysis of Long Noncoding RNA Turnover

Methods in Molecular Biology, 2014

Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that exami... more Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that examines the specific half-life of nuclear noncoding RNA (ncRNA). In particular, a pulse-labeling method using uridine analogs enables the determination of RNA stability under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromo-uridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing. The method is called BrU immunoprecipitation chase assay (BRIC) or BRIC through deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

Research paper thumbnail of Preparation of Partially Protected Peptide Thioesters Containing a Cysteine Residue and Their Segment Condensation

Research paper thumbnail of Development of a Linker with an Enhanced Stability for the Preparation of Peptide Thioesters and Its Application to the Synthesis of a Stable-Isotope-Labelled HU-Type DNA-Binding Protein

Bulletin of the Chemical Society of Japan, 1993

Research paper thumbnail of Identification of a novel human UDP-GalNAc transferase with unique catalytic activity and expression profile

Biochemical and Biophysical Research Communications, 2010

A novel member of the human ppGalNAc-T family, ppGalNAc-T20, was identified and characterized. Am... more A novel member of the human ppGalNAc-T family, ppGalNAc-T20, was identified and characterized. Amino acid alignment revealed a high sequence identity between ppGalNAc-T20 and-T10. In the GalNAc transfer assay towards mucin-derived peptide substrates, the recombinant ppGalNAc-T20 demonstrated to be a typical glycopeptide GalNAc-transferase that exhibits activity towards mono-GalNAc-glycosylated peptide EA2 derived from rat submandibular gland mucin but no activity towards non-modified EA2. The in vitro catalytic property of ppGalNAc-T20 was compared with that of ppGalNAc-T10 to show different acceptor substrate specificities and kinetic constants. The ppGalNAc-T20 transcript was found exclusively in testis and brain. In situ hybridization further reveals that ppGalNAc-T20 was specifically localized in primary and secondary spermatocytes of the two meiotic periods, suggesting that it may involve in O-glycosylation during mouse spermatogenesis.

Research paper thumbnail of Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery

Journal of structural and functional genomics, 2016

More than 800 G protein-coupled receptor (GPCR) genes have been discovered in the human genome. T... more More than 800 G protein-coupled receptor (GPCR) genes have been discovered in the human genome. Towards the next step in GPCR research, we performed a knowledge-driven analysis of orphan class-A GPCRs that may serve as novel targets in drug discovery. We examined the relationship between 61 orphan class-A GPCR genes and diseases using the Online Mendelian Inheritance in Man (OMIM) database and the DDSS tool. The OMIM database contains data on disease-related variants of the genes. Particularly, the variants of GPR101, GPR161, and GPR88 are related to the genetic diseases: growth hormone-secreting pituitary adenoma 2, pituitary stalk interruption syndrome (not confirmed), and childhood-onset chorea with psychomotor retardation, respectively. On the other hand, the Drug Discovery and Diagnostic Support System (DDSS) tool suggests that 48 out of the 61 orphan receptor genes are related to diseases, judging from their co-occurrences in abstracts of biomedical literature. Notably, GPR50 ...

Research paper thumbnail of Detecting unsatisfiable CSS rules in the presence of DTDs

Cascading Style Sheets (CSS) is a popular language for describing the styles of XML documents as ... more Cascading Style Sheets (CSS) is a popular language for describing the styles of XML documents as well as HTML documents. For a DTD D and a list R of CSS rules, due to specificity R may contain “unsatisfiable” rules under D, e.g., rules that are not applied to any element of any document valid to D. In this paper, we consider the problem of detecting unsatisfiable CSS rules under DTDs. We focus on CSS fragments in which descendant, child, adjacent sibling, and general sibling combinators are allowed. We show that the problem is coNP-hard in most cases, even if only one of the four combinators is allowed. We also show that the problem is in coNP or PSPACE depending on restrictions on DTDs and CSS. Finally, we present two conditions under which the problem can be solved in polynomial time.

Research paper thumbnail of An External Memory Algorithm for All-Pairs Regular Path Problem

Lecture Notes in Computer Science, 2015

In this paper, we consider solving the all-pairs regular path problem on large graphs efficiently... more In this paper, we consider solving the all-pairs regular path problem on large graphs efficiently. Let G be a graph and r be a regular path query, and consider finding the answers of r on G. If G is so small that it fits in main memory, it suffices to load entire G into main memory and traverse G to find paths matching r. However, if G is too large and cannot fit in main memory, we need another approach. In this paper, we propose an external memory algorithm for solving all-pairs regular path problem on large graphs. Our algorithm finds the answers matching r by scanning the node list of G sequentially, which avoids random accesses to disk and thus makes regular path query processing I/O efficient.

Research paper thumbnail of Checking Pattern Query Containment Under Shape Expression

Research paper thumbnail of Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery

Journal of Structural and Functional Genomics, Dec 1, 2016

genetically, structurally and functionally using the structural life science data cloud VaProS, s... more genetically, structurally and functionally using the structural life science data cloud VaProS, so as to evaluate their potential as next targets in drug discovery.

Research paper thumbnail of Genome-Wide Analysis of Long Noncoding RNA Turnover

Methods in molecular biology, Dec 5, 2014

Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that exami... more Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that examines the specific half-life of nuclear noncoding RNA (ncRNA). In particular, a pulse-labeling method using uridine analogs enables the determination of RNA stability under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromo-uridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing. The method is called BrU immunoprecipitation chase assay (BRIC) or BRIC through deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

Research paper thumbnail of Computational Complexity of Finding Meaningful Association Rules

IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Sep 25, 1999

Research paper thumbnail of A New Approach and Knowledge Integration to Proposing Perspectives on Aging Research Based on Literature Mining

The Molecular Biology Society of Japan, Nov 8, 2016

Research paper thumbnail of A Novel Measure for Finding Disease-Specific Genes from the Biomedical Literature

QP-PQ, quantum probability and white noise analysis, Mar 1, 2013

Research paper thumbnail of On-the-fly Link Generation for Workflows in Biology

A number of biological data resources such as databases and analytical tools can be accessible th... more A number of biological data resources such as databases and analytical tools can be accessible through the Internet. However, it is laborious and sometimes impossible to write a computer program that finds a useful data source, sends a proper query and processes its output. Therefore, it becomes a serious obstacle to the

Research paper thumbnail of RESEARCH Open Access Two-way AIC: detection of differentially

expressed genes from large scale microarray meta-dataset

Research paper thumbnail of Workflow and Its Navigation System Using

We present an overview of workflow and its navigation system using Web API for biology (WABI) dev... more We present an overview of workflow and its navigation system using Web API for biology (WABI) developed by DNA Data Bank of Japan (DDBJ). The system helps non-programming biologists perform analysis tasks which use multiple software tools and databases only by following links on Web browsers. The services are available at

Research paper thumbnail of A New Approach and Knowledge Integration to Proposing Perspectives on Aging Research Based on Literature Mining

The Molecular Biology Society of Japan, 2016

Research paper thumbnail of Computational Complexity of Finding Meaningful Association Rules

Ieice Transactions on Fundamentals of Electronics Communications and Computer Sciences, Sep 25, 1999

Research paper thumbnail of Protein synthesis using partially protected peptide thioesters as building blocks

Peptide Chemistry 1992, 1993

Research paper thumbnail of A Novel Measure for Finding Disease-Specific Genes from the Biomedical Literature

QP-PQ: Quantum Probability and White Noise Analysis, 2013

Research paper thumbnail of Genome-Wide Analysis of Long Noncoding RNA Turnover

Methods in Molecular Biology, 2014

Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that exami... more Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that examines the specific half-life of nuclear noncoding RNA (ncRNA). In particular, a pulse-labeling method using uridine analogs enables the determination of RNA stability under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromo-uridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing. The method is called BrU immunoprecipitation chase assay (BRIC) or BRIC through deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

Research paper thumbnail of Preparation of Partially Protected Peptide Thioesters Containing a Cysteine Residue and Their Segment Condensation

Research paper thumbnail of Development of a Linker with an Enhanced Stability for the Preparation of Peptide Thioesters and Its Application to the Synthesis of a Stable-Isotope-Labelled HU-Type DNA-Binding Protein

Bulletin of the Chemical Society of Japan, 1993

Research paper thumbnail of Identification of a novel human UDP-GalNAc transferase with unique catalytic activity and expression profile

Biochemical and Biophysical Research Communications, 2010

A novel member of the human ppGalNAc-T family, ppGalNAc-T20, was identified and characterized. Am... more A novel member of the human ppGalNAc-T family, ppGalNAc-T20, was identified and characterized. Amino acid alignment revealed a high sequence identity between ppGalNAc-T20 and-T10. In the GalNAc transfer assay towards mucin-derived peptide substrates, the recombinant ppGalNAc-T20 demonstrated to be a typical glycopeptide GalNAc-transferase that exhibits activity towards mono-GalNAc-glycosylated peptide EA2 derived from rat submandibular gland mucin but no activity towards non-modified EA2. The in vitro catalytic property of ppGalNAc-T20 was compared with that of ppGalNAc-T10 to show different acceptor substrate specificities and kinetic constants. The ppGalNAc-T20 transcript was found exclusively in testis and brain. In situ hybridization further reveals that ppGalNAc-T20 was specifically localized in primary and secondary spermatocytes of the two meiotic periods, suggesting that it may involve in O-glycosylation during mouse spermatogenesis.

Research paper thumbnail of Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery

Journal of structural and functional genomics, 2016

More than 800 G protein-coupled receptor (GPCR) genes have been discovered in the human genome. T... more More than 800 G protein-coupled receptor (GPCR) genes have been discovered in the human genome. Towards the next step in GPCR research, we performed a knowledge-driven analysis of orphan class-A GPCRs that may serve as novel targets in drug discovery. We examined the relationship between 61 orphan class-A GPCR genes and diseases using the Online Mendelian Inheritance in Man (OMIM) database and the DDSS tool. The OMIM database contains data on disease-related variants of the genes. Particularly, the variants of GPR101, GPR161, and GPR88 are related to the genetic diseases: growth hormone-secreting pituitary adenoma 2, pituitary stalk interruption syndrome (not confirmed), and childhood-onset chorea with psychomotor retardation, respectively. On the other hand, the Drug Discovery and Diagnostic Support System (DDSS) tool suggests that 48 out of the 61 orphan receptor genes are related to diseases, judging from their co-occurrences in abstracts of biomedical literature. Notably, GPR50 ...

Research paper thumbnail of Detecting unsatisfiable CSS rules in the presence of DTDs

Cascading Style Sheets (CSS) is a popular language for describing the styles of XML documents as ... more Cascading Style Sheets (CSS) is a popular language for describing the styles of XML documents as well as HTML documents. For a DTD D and a list R of CSS rules, due to specificity R may contain “unsatisfiable” rules under D, e.g., rules that are not applied to any element of any document valid to D. In this paper, we consider the problem of detecting unsatisfiable CSS rules under DTDs. We focus on CSS fragments in which descendant, child, adjacent sibling, and general sibling combinators are allowed. We show that the problem is coNP-hard in most cases, even if only one of the four combinators is allowed. We also show that the problem is in coNP or PSPACE depending on restrictions on DTDs and CSS. Finally, we present two conditions under which the problem can be solved in polynomial time.

Research paper thumbnail of An External Memory Algorithm for All-Pairs Regular Path Problem

Lecture Notes in Computer Science, 2015

In this paper, we consider solving the all-pairs regular path problem on large graphs efficiently... more In this paper, we consider solving the all-pairs regular path problem on large graphs efficiently. Let G be a graph and r be a regular path query, and consider finding the answers of r on G. If G is so small that it fits in main memory, it suffices to load entire G into main memory and traverse G to find paths matching r. However, if G is too large and cannot fit in main memory, we need another approach. In this paper, we propose an external memory algorithm for solving all-pairs regular path problem on large graphs. Our algorithm finds the answers matching r by scanning the node list of G sequentially, which avoids random accesses to disk and thus makes regular path query processing I/O efficient.