Lista de obras - Krzysztof Ginalski - Dominio Público Uruguay

A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization

artículo científico publicado en 2020

A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

artículo científico publicado en 2009

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis

artículo científico publicado en 2015

A comprehensive update of the sequence and structure classification of kinases

artículo científico publicado en 2005

A heterozygous mutation in GOT1 is associated with familial macro-aspartate aminotransferase

artículo científico

Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners

artículo científico publicado en 2003

Application of 3D-Jury, GRDB, and Verify3D in fold recognition

artículo científico publicado en 2003

AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update

artículo científico publicado en 2007

BOF: a novel family of bacterial OB-fold proteins

artículo científico publicado en 2004

BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases

artículo científico publicado en 2004

Bacillus subtilis YkuK protein is distantly related to RNase H.

artículo científico publicado en 2005

Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding

artículo científico publicado en 2007

Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity toward CTP and increased tendency for cytidine incorporation at the 3'-terminal positions of synthesized tails

artículo científico publicado en 2017

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity

artículo científico publicado en 2004

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification

artículo científico publicado en 2012

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

artículo científico publicado en 2010

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

article published in 2018

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer

article

Comparative modeling for protein structure prediction

artículo científico publicado en 2006

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures

scholarly article by Thomas Clouaire published in September 2018

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human

artículo científico publicado en 2009

Comprehensive classification of the PIN domain-like superfamily

artículo científico publicado en 2017

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome

artículo científico publicado en 2011

Correction to: Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

artículo científico publicado en 2019

Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

article

Cut-and-paste transposons in fungi with diverse lifestyles

artículo científico publicado en 2017

DCC proteins: a novel family of thiol-disulfide oxidoreductases

artículo científico publicado en 2004

DIRS and Ngaro Retrotransposons in Fungi

artículo científico publicado en 2013

DUF1613 is a novel family of eucaryotic AdoMet-dependent methyltransferases

artículo científico publicado en 2006

Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing

artículo científico publicado en 2018

Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440

artículo científico publicado en 2008

Detailed mechanism of squalene epoxidase inhibition by terbinafine

artículo científico publicado en 2011

Detecting distant homology with Meta-BASIC.

artículo científico publicado en 2004

Detection of reliable and unexpected protein fold predictions using 3D-Jury

artículo científico publicado en 2003

Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III.

artículo científico publicado en 2002

Diverse cap-binding properties of Drosophila eIF4E isoforms

artículo científico publicado en 2016

ECEPE proteins: a novel family of eukaryotic cysteine proteinases

artículo científico publicado en 2004

Efficacy of 2-halogen substituted D-glucose analogs in blocking glycolysis and killing "hypoxic tumor cells".

artículo científico publicado en 2006

Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily

artículo científico publicado en 2006

Exome scale map of genetic alterations promoting metastasis in colorectal cancer

artículo científico publicado en 2018

Extending the aerolysin family: from bacteria to vertebrates

artículo científico publicado en 2011

FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases

artículo científico publicado en 2016

Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding

artículo científico publicado en 2014

Fungal lifestyle reflected in serine protease repertoire

artículo científico publicado en 2017

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.

artículo científico publicado en 2017

Glyoxylate reductase as versatile enzymatic system for pharmaceutical and medical use

HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein

artículo científico publicado en 2008

Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses

artículo científico publicado en 2003

HarmonyDOCK: the structural analysis of poses in protein-ligand docking

artículo científico publicado en 2010

Histone H1 Variants in Arabidopsis Are Subject to Numerous Post-Translational Modifications, Both Conserved and Previously Unknown in Histones, Suggesting Complex Functions of H1 in Plants

artículo científico publicado en 2016

Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease

artículo científico publicado en 2006

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

artículo científico publicado en 2011

Hypermethylation of TRIM59 and KLF14 Influences Cell Death Signaling in Familial Alzheimer's Disease.

artículo científico publicado en 2018

Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels

artículo científico publicado en 2013

Identification of novel restriction endonuclease-like fold families among hypothetical proteins

artículo científico publicado en 2005

In silico prediction of SARS protease inhibitors by virtual high throughput screening

artículo científico publicado en 2007

MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading

artículo científico publicado en 2019

Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication

artículo científico publicado en 2020

Mitochondrial release factor in yeast: interplay of functional domains

artículo científico publicado en 2008

Modelling of potentially promising SARS protease inhibitors

Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes

artículo científico publicado en 2004

Novel SARS unique AdoMet-dependent methyltransferase

artículo científico publicado en 2006

Novel transmembrane lipases of alpha/beta hydrolase fold

artículo científico publicado en 2011

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

artículo científico publicado en 2013

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

artículo científico publicado en 2003

Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease.

artículo científico publicado en 2018

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

artículo científico publicado en 2006

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain.

artículo científico publicado en 2017

Poly-Saturated Dolichols from Filamentous Fungi Modulate Activity of Dolichol-Dependent Glycosyltransferase and Physical Properties of Membranes

scientific article published on 21 June 2019

Practical lessons from protein structure prediction

artículo científico publicado en 2005

Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution

artículo científico publicado en 2018

Predicting proteome dynamics using gene expression data

artículo científico publicado en 2018

Prediction of signal peptides in protein sequences by neural networks.

artículo científico publicado en 2008

Probabilistic approach to predicting substrate specificity of methyltransferases

artículo científico publicado en 2014

Protein domain of unknown function DUF1023 is an alpha/beta hydrolase

artículo científico publicado en 2005

Protein structure prediction for the male-specific region of the human Y chromosome.

artículo científico publicado en 2004

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment

scientific article published on 01 January 2003

Raptor protein contains a caspase-like domain

artículo científico publicado en 2004

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches

artículo científico publicado en 2007

Reply to Behrman: “N-Formylmaleamic acid: An intermediate in nicotinic acid metabolism”.

artículo científico publicado en 2008

SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family

scientific journal article

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

artículo científico publicado en 2012

Sequence-structure mapping errors in the PDB: OB-fold domains

artículo científico publicado en 2004

Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade

artículo científico publicado en 2005

Snf2 proteins in plants: gene silencing and beyond

artículo científico publicado en 2008

Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress.

artículo científico publicado en 2017

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform

artículo científico publicado en 2015

Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies

artículo científico publicado en 2018

Systematic classification of the His-Me finger superfamily

artículo científico publicado en 2017

TOS1 is circularly permuted 1,3-beta-glucanase

artículo científico publicado en 2010

Target specific compound identification using a support vector machine.

artículo científico publicado en 2007

The C2H2 zinc finger transcription factors are likely targets for Ni(II) toxicity

artículo científico publicado en 2011

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification ⬇️

artículo científico publicado en 2014

The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast

artículo científico publicado en 2014

The interactome: Predicting the protein-protein interactions in cells

artículo científico publicado en 2009

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

artículo científico publicado en 2009

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

artículo científico publicado en 2020

Towards Engineering Novel PE-Based Immunotoxins by Targeting Them to the Nucleus

artículo científico publicado en 2016

Transposable elements contribute to fungal genes and impact fungal lifestyle

article

Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases

artículo científico publicado en 2007

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

artículo científico publicado en 2016

Virtual high throughput screening using combined random forest and flexible docking

artículo científico publicado en 2009

VoteDock: consensus docking method for prediction of protein-ligand interactions

artículo científico publicado en 2010

i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks

artículo científico publicado en 2018

qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing

artículo científico publicado en 2019

Lista de obras de Krzysztof Ginalski

A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization

A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis

A comprehensive update of the sequence and structure classification of kinases

A heterozygous mutation in GOT1 is associated with familial macro-aspartate aminotransferase

Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners

Application of 3D-Jury, GRDB, and Verify3D in fold recognition

AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update

BOF: a novel family of bacterial OB-fold proteins

BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases

Bacillus subtilis YkuK protein is distantly related to RNase H.

Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding

Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity toward CTP and increased tendency for cytidine incorporation at the 3'-terminal positions of synthesized tails

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer

Comparative modeling for protein structure prediction

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human

Comprehensive classification of the PIN domain-like superfamily

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome

Correction to: Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

Cut-and-paste transposons in fungi with diverse lifestyles

DCC proteins: a novel family of thiol-disulfide oxidoreductases

DIRS and Ngaro Retrotransposons in Fungi

DUF1613 is a novel family of eucaryotic AdoMet-dependent methyltransferases

Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing

Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440

Detailed mechanism of squalene epoxidase inhibition by terbinafine

Detecting distant homology with Meta-BASIC.

Detection of reliable and unexpected protein fold predictions using 3D-Jury

Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III.

Diverse cap-binding properties of Drosophila eIF4E isoforms

ECEPE proteins: a novel family of eukaryotic cysteine proteinases

Efficacy of 2-halogen substituted D-glucose analogs in blocking glycolysis and killing "hypoxic tumor cells".

Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily

Exome scale map of genetic alterations promoting metastasis in colorectal cancer

Extending the aerolysin family: from bacteria to vertebrates

FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases

Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding

Fungal lifestyle reflected in serine protease repertoire

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.

Glyoxylate reductase as versatile enzymatic system for pharmaceutical and medical use

HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein

Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses

HarmonyDOCK: the structural analysis of poses in protein-ligand docking

Histone H1 Variants in Arabidopsis Are Subject to Numerous Post-Translational Modifications, Both Conserved and Previously Unknown in Histones, Suggesting Complex Functions of H1 in Plants

Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

Hypermethylation of TRIM59 and KLF14 Influences Cell Death Signaling in Familial Alzheimer's Disease.

Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels

Identification of novel restriction endonuclease-like fold families among hypothetical proteins

In silico prediction of SARS protease inhibitors by virtual high throughput screening

MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading

Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication

Mitochondrial release factor in yeast: interplay of functional domains

Modelling of potentially promising SARS protease inhibitors

Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes

Novel SARS unique AdoMet-dependent methyltransferase

Novel transmembrane lipases of alpha/beta hydrolase fold

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease.

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain.

Poly-Saturated Dolichols from Filamentous Fungi Modulate Activity of Dolichol-Dependent Glycosyltransferase and Physical Properties of Membranes

Practical lessons from protein structure prediction

Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution

Predicting proteome dynamics using gene expression data

Prediction of signal peptides in protein sequences by neural networks.

Probabilistic approach to predicting substrate specificity of methyltransferases

Protein domain of unknown function DUF1023 is an alpha/beta hydrolase

Protein structure prediction for the male-specific region of the human Y chromosome.

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment

Raptor protein contains a caspase-like domain

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches