Search Results - "Kim, RyangGuk"

Assessment of programs for ligand binding affinity prediction by Kim, Ryangguk, Skolnick, Jeffrey

“…The prediction of the binding free energy between a ligand and a protein is an important component in the virtual screening and lead optimization of ligands…”
Get full text

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit by Masica, David L, Douville, Christopher, Tokheim, Collin, Bhattacharya, Rohit, Kim, RyangGuk, Moad, Kyle, Ryan, Michael C, Karchin, Rachel

“…Cancer sequencing studies are increasingly comprehensive and well powered, returning long lists of somatic mutations that can be difficult to sort and…”
Get full text

Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle by Fu, Haiqing, Maunakea, Alika K, Martin, Melvenia M, Huang, Liang, Zhang, Ya, Ryan, Michael, Kim, RyangGuk, Lin, Chii Meil, Zhao, Keji, Aladjem, Mirit I

“…Mammalian DNA replication starts at distinct chromosomal sites in a tissue-specific pattern coordinated with transcription, but previous studies have not yet…”
Get full text

The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage by Fu, Haiqing, Martin, Melvenia M., Regairaz, Marie, Huang, Liang, You, Yang, Lin, Chi-Mei, Ryan, Michael, Kim, RyangGuk, Shimura, Tsutomu, Pommier, Yves, Aladjem, Mirit I.

“…The Mus81 endonuclease resolves recombination intermediates and mediates cellular responses to exogenous replicative stress. Here, we show that Mus81 also…”
Get full text

Genome-wide depletion of replication initiation events in highly transcribed regions by Martin, Melvenia M, Ryan, Michael, Kim, RyangGuk, Zakas, Anna L, Fu, Haiqing, Lin, Chii Mei, Reinhold, William C, Davis, Sean R, Bilke, Sven, Liu, Hongfang, Doroshow, James H, Reimers, Mark A, Valenzuela, Manuel S, Pommier, Yves, Meltzer, Paul S, Aladjem, Mirit I

“…This report investigates the mechanisms by which mammalian cells coordinate DNA replication with transcription and chromatin assembly. In yeast, DNA…”
Get full text

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures by Niknafs, Noushin, Kim, Dewey, Kim, RyangGuk, Diekhans, Mark, Ryan, Michael, Stenson, Peter D., Cooper, David N., Karchin, Rachel

“…Mutation position imaging toolbox (MuPIT) interactive is a browser-based application for single-nucleotide variants (SNVs), which automatically maps the…”
Get full text

A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells by Zhang, Ya, Huang, Liang, Fu, Haiqing, Smith, Owen K., Lin, Chii Mei, Utani, Koichi, Rao, Mishal, Reinhold, William C., Redon, Christophe E., Ryan, Michael, Kim, RyangGuk, You, Yang, Hanna, Harlington, Boisclair, Yves, Long, Qiaoming, Aladjem, Mirit I.

“…Mammalian chromosome replication starts from distinct sites; however, the principles governing initiation site selection are unclear because proteins essential…”
Get full text

TFinDit: transcription factor-DNA interaction data depository by Turner, Daniel, Kim, RyangGuk, Guo, Jun-tao

“…One of the crucial steps in regulation of gene expression is the binding of transcription factor(s) to specific DNA sequences. Knowledge of the binding…”
Get full text

PDA: an automatic and comprehensive analysis program for protein-DNA complex structures by Kim, RyangGuk, Guo, Jun-tao

“…Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation. Although…”
Get full text

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts by RYAN, Michael C, CLELAND, James, KIM, Ryangguk, WING CHUNG WONG, WEINSTEIN, John N

“…SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice…”
Get full text

ColoWeb: a resource for analysis of colocalization of genomic features by Kim, RyangGuk, Smith, Owen K, Wong, Wing Chung, Ryan, Alex M, Ryan, Michael C, Aladjem, Mirit I

“…Next-generation sequencing techniques such as ChIP-seq allow researchers to investigate the genomic position of nuclear components and events. These…”
Get full text

Systematic analysis of short internal indels and their impact on protein folding by Kim, RyangGuk, Guo, Jun-tao

“…Protein sequence insertions/deletions (indels) can be introduced during evolution or through alternative splicing (AS). Alternative splicing is an important…”
Get full text

Correction: Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle by Fu, Haiqing, Maunakea, Alika K., Martin, Melvenia M., Huang, Liang, Zhang, Ya, Ryan, Michael, Kim, RyangGuk, Lin, Chii Meil, Zhao, Keji, Aladjem, Mirit I.

Get full text

Correction: Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle by Haiqing Fu, Alika K. Maunakea, Melvenia M. Martin, Liang Huang, Ya Zhang, Michael Ryan, RyangGuk Kim, Chii Meil Lin, Keji Zhao, Mirit I. Aladjem

Get full text

Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle: e1003542 by Fu, Haiqing, Maunakea, Alika K, Martin, Melvenia M, Huang, Liang, Zhang, Ya, Ryan, Michael, Kim, RyangGuk, Lin, Chii Meil, Zhao, Keji, Aladjem, Mirit I

“…Mammalian DNA replication starts at distinct chromosomal sites in a tissue-specific pattern coordinated with transcription, but previous studies have not yet…”
Get full text

Benchmarks for flexible and rigid transcription factor-DNA docking by Kim, RyangGuk, Corona, Rosario I, Hong, Bo, Guo, Jun-tao

“…Structural insight from transcription factor-DNA (TF-DNA) complexes is of paramount importance to our understanding of the affinity and specificity of TF-DNA…”
Get full text

Just-DNA-Seq, open-source personal genomics platform: longevity science for everyone by Anton, Kulaga, Olga, Borysova, Alexey, Karmazin, Maria, Koval, Nikolay, Usanov, Alina, Fedorova, Sergey, Evfratov, Malvina, Pushkareva, Kim, Ryangguk, Robi, Tacutu

“…Genomic data has become increasingly accessible to the general public with the advent of companies offering whole genome sequencing at a relatively low cost…”
Get full text

Fragment library-based representation system for protein conformation by Kim, RyangGuk, Choi, Cha-Yong

“…The representation system for protein conformation has a crucial effect on the speed of various protein-related simulations, including ab initio protein…”
Get more information