A. Fomenkov

发表

Differential Recognition of Response Elements Determines Target Gene Specificity forp53 and p63

Keishi Yamashita, David Sidransky, S. Nomoto, 2005, Molecular and Cellular Biology.

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

Richard J. Roberts, Jonas Korlach, Tyson A. Clark, 2011, Nucleic acids research.

The COMBREX Project: Design, Methodology, and Initial Results

Michael Y. Galperin, S. Salzberg, R. Greiner, 2013, PLoS biology.

The Epigenomic Landscape of Prokaryotes

Dongwan D. Kang, Tyson A. Clark, Kelly M. Wetmore, 2016, PLoS genetics.

Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia

R. Roberts, A. Fomenkov, C. D. Johnston, 2017, PloS one.

The methylomes of six bacteria

Richard J. Roberts, Stephen W. Turner, Jonas Korlach, 2012, Nucleic acids research.

Structural and functional diversity among Type III restriction-modification systems that confer host DNA protection via methylation of the N4 atom of cytosine

Tyson A. Clark, J. Korlach, R. Roberts, 2021, PloS one.

AEC-Associated p63 Mutations Lead to Alternative Splicing/Protein Stabilization of p63 and Modulation of Notch Signaling

E. Ratovitski, A. Fomenkov, Yi-ping Huang, 2005, Cell cycle.

A protein architecture guided screen for modification dependent restriction endonucleases

Shuang-yong Xu, A. Fomenkov, H. Czapinska, 2019, Nucleic acids research.

Modification-Dependent Restriction Endonuclease-based sequencing method (EcoWI-seq) maps the genome-wide landscape of phosphorothioate modification at base resolution

L. Ettwiller, Shuang-yong Xu, A. Fomenkov, 2022, bioRxiv.

Cloning of NruI and Sbo13I restriction and modification sstems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases

C. Pedamallu, Shuang-yong Xu, A. Fomenkov, 2010, BMC Research Notes.

Isolation of temperature-sensitive mutants of the BamHI restriction endonuclease.

A. Fomenkov, S. Xu, 1995, Gene.

ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer

Guojun Wu, Zhongmin Guo, J. Califano, 2005, Cancer Research.

Np 63 A UpRegulates the Hsp 70 Gene in Human Cancer

Guojun Wu, Zhongmin Guo, J. Califano, 2005 .

Cloning of a gene from Thermus filiformis and characterization of the thermostable nuclease.

A. Fomenkov, S. Xu, 1995, Gene.

The 'endo-blue method' for direct cloning of restriction endonuclease genes in E. coli.

E. Raleigh, A. Fomenkov, S. Xu, 1994, Nucleic acids research.

DeltaNp63 induces beta-catenin nuclear accumulation and signaling.

S. Nomoto, J. Califano, B. Trink, 2002, Cancer cell.

CDC91L1 (PIG-U) is a newly discovered oncogene in human bladder cancer

L. Kiemeney, P. Meltzer, J. Trent, 2004, Nature Medicine.

Production and сharacterization of the exopolysaccharide from strain Paenibacillus polymyxa 2020

R. Roberts, A. Fomenkov, P. Toukach, 2021, PloS one.

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk

S. Tringe, B. Henrissat, R. Malmstrom, 2014, Proceedings of the National Academy of Sciences.

Expression of Human ACE2 N-terminal Domain, Part of the Receptor for SARS-CoV-2, in Fusion With Maltose-Binding Protein, E. coli Ribonuclease I and Human RNase A

Shuang-yong Xu, A. Fomenkov, Erbay Yigit, 2021, bioRxiv.

Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65

R. Roberts, Tamas Vincze, S. Degtyarev, 2017, Genome Announcements.

Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments

R. Roberts, B. Anton, A. Fomenkov, 2021, bioRxiv.

Altered Sumoylation of p63α Contributes to the Split-Hand/Foot Malformation Phenotype

Guojun Wu, Zhongmin Guo, B. Trink, 2004, Cell cycle.

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

R. Roberts, N. Geva-Zatorsky, J. Livny, 2020, Nucleic acids research.

High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution

L. Ettwiller, Shuang-yong Xu, A. Fomenkov, 2022, PLoS genetics.

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

R. Roberts, P. Davis, Shuang-yong Xu, 2011, Proceedings of the National Academy of Sciences.

ΔNp63 induces β-catenin nuclear accumulation and signaling

S. Nomoto, J. Califano, B. Trink, 2002 .

DeltaNp63alpha up-regulates the Hsp70 gene in human cancer.

Guojun Wu, Zhongmin Guo, J. Califano, 2005, Cancer research.

Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium

L. Bossi, R. Morgan, E. Raleigh, 2021, bioRxiv.

Protein Domain Guided Screen for Sequence Specific and Phosphorothioate-Dependent Restriction Endonucleases

Shuang-yong Xu, A. Fomenkov, H. Czapinska, 2020, Frontiers in Microbiology.

The non-specific adenine DNA methyltransferase M.EcoGII

R. Roberts, Xiaodong Cheng, R. Morgan, 2017, Nucleic acids research.

The non-specific adenine DNA methyltransferase M.EcoGII

Richard, R. Roberts, Xiaodong Cheng, 2017, Nucleic acids research.

RACK1 and Stratifin Target ΔNp63α for a Proteasome Degradation in Head and Neck Squamous Cell Carcinoma Cells upon DNA Damage

Zhongmin Guo, B. Trink, D. Sidransky, 2004 .

Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

T. C. Evans, Andrew C. Tolonen, R. Roberts, 2021, bioRxiv.

Plasmid replication-associated single-strand-specific methyltransferases

R. Roberts, E. Raleigh, A. Fomenkov, 2020, Nucleic acids research.

Characterization of Type II and III Restriction-Modification Systems from Bacillus cereus Strains ATCC 10987 and ATCC 14579

R. Morgan, Shuang-yong Xu, A. Aggarwal, 2011, Journal of bacteriology.

Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

L. Ettwiller, E. Raleigh, A. Fomenkov, 2021, bioRxiv.

Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI

Xiaodong Cheng, G. Wilson, Shuang-yong Xu, 2014, Scientific Reports.

EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determination

R. Roberts, B. Anton, E. Raleigh, 2017, PloS one.

Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12

R. Roberts, E. Mongodin, B. Anton, 2015, PloS one.

Complete Genome Sequence of ER 2796 , a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12

R. Roberts, E. Mongodin, B. Anton, 2015 .

p63α Mutations Lead to Aberrant Splicing of Keratinocyte Growth Factor Receptor in the Hay-Wells Syndrome*

B. Trink, D. Sidransky, Yiping Huang, 2003, Journal of Biological Chemistry.

p63-specific activation of the BPAG-1e promoter.

Y. Nagakawa, Guojun Wu, B. Trink, 2005, The Journal of investigative dermatology.

ATCC 14579 Bacillus cereus Strains ATCC 10987 and Restriction-Modification Systems from Characterization of Type II and III

R. Morgan, Shuang-yong Xu, A. Aggarwal, 2012 .

Targeting DNA 5mCpG sites with chimeric endonucleases.

Laurie Mazzola, Shuang-yong Xu, Shuang-yong Xu, 2008, Analytical biochemistry.

Characterization of BisI Homologs

R. Roberts, S. Degtyarev, Shuang-yong Xu, 2021, Frontiers in Microbiology.

Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring

R. Roberts, B. Anton, Tamas Vincze, 2016, Genome Announcements.

Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine

R. Roberts, Xiaodong Cheng, J. Bitinaite, 2015, Proceedings of the National Academy of Sciences.

Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex

R. Roberts, B. Anton, A. Fomenkov, 2021, Scientific Reports.

Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease

J. Bray, R. Roberts, B. Anton, 2020, Scientific Reports.

Complete Annotated Genome Sequence of the Salmonella enterica Serovar Typhimurium LT7 Strain STK003, Historically Used in Gene Transfer Studies

R. Morgan, E. Raleigh, A. Fomenkov, 2021, Microbiology Resource Announcements.

Complete Genome and Methylome Analysis of the Box-Shaped Halophilic Archaeon Haloarcula sinaiiensis ATCC 33800

R. Roberts, P. DasSarma, S. DasSarma, 2021, Microbiology resource announcements.

Complete Genome Sequences of Two Rhodobacter Strains

R. Roberts, B. Anton, A. Fomenkov, 2018, Microbiology Resource Announcements.

Expression of Human ACE2 N-terminal Domain, Part of the Receptor for SARS-CoV-2, in Fusion With Maltose-Binding Protein, E. coli Ribonuclease I and Human RNase A

Shuang-yong Xu, A. Fomenkov, Erbay Yigit, 2021, bioRxiv.

Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T

R. Roberts, Tamas Vincze, A. Fomenkov, 2015, Genome Announcements.

The XmnI restriction-modification system: cloning, expression, sequence organization and similarity between the R and M genes.

B. Slatko, A. Fomenkov, J. J. Lynch, 1996, Gene.

RACK1 and stratifin target DeltaNp63alpha for a proteasome degradation in head and neck squamous cell carcinoma cells upon DNA damage.

Zhongmin Guo, B. Trink, D. Sidransky, 2004, Cell cycle.

In vivo and in vitro complementation of the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system by the cloned C-terminal domain.

S. Roseman, A. Fomenkov, L. Brand, 1998, Proceedings of the National Academy of Sciences of the United States of America.

The third restriction–modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities

R. Roberts, B. Anton, R. Morgan, 2017, Nucleic acids research.

Complete Genome Sequence and Methylome Analysis of Sphaerotilus natans subsp. sulfidivorans D-507

R. Roberts, A. Fomenkov, G. Dubinina, 2019, Microbiology Resource Announcements.

Targeting DNA 5mCpG sites with chimeric endonucleases.

Shuang-yong Xu, A. Fomenkov, Beth Ann Cantin, 2008, Analytical biochemistry.

Nucleotide sequence of a small plasmid isolated from Acetobacter pasteurianus.

A. Fomenkov, S. Xu, J. Xiao, 1995, Gene.

Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å

R. Roberts, Xiaodong Cheng, G. Wilson, 2019, Nucleic acids research.

Complete genome assembly and methylome dissection of Methanococcus aeolicus PL15/Hp

R. Roberts, P. Weigele, A. Fomenkov, 2023, Frontiers in Microbiology.

Cloning of NruI and Sbo13I restriction and modification sstems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases

C. Pedamallu, Shuang-yong Xu, A. Fomenkov, 2010, BMC Research Notes.