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List of works by Krzysztof Ginalski

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

scientific article published on 27 November 2020

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

scientific article

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

scientific article (publication date: November 2015)

A comprehensive update of the sequence and structure classification of kinases

scientific article

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

scientific article published on 14 July 2017

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

scientific article published in September 2003

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

scientific article published on January 2003

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

scientific article published on 8 November 2007

BOF: a novel family of bacterial OB-fold proteins

scientific article

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

scientific article

Bacillus subtilis YkuK protein is distantly related to RNase H.

scientific article published in October 2005

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

scientific article

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

scientific article

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

scholarly article

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

scientific article

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

scientific article published in September 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

scientific article

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

scientific article

Comprehensive classification of the PIN domain-like superfamily

scientific article

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome

scientific article

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

scientific article published on 16 July 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

scientific article

DCC proteins: a novel family of thiol-disulfide oxidoreductases

scientific article published in July 2004

DIRS and Ngaro Retrotransposons in Fungi

scientific article

DUF1613 is a novel family of eucaryotic AdoMet-dependent methyltransferases.

scientific article

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

scientific article published on 12 January 2018

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

scientific article

Detailed mechanism of squalene epoxidase inhibition by terbinafine

scientific article published on 13 January 2011

Detecting distant homology with Meta-BASIC.

scientific article published on July 2004

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

scientific article

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

scientific article

Diverse cap-binding properties of Drosophila eIF4E isoforms

scientific article published on 29 June 2016

ECEPE proteins: a novel family of eukaryotic cysteine proteinases

scientific article published in October 2004

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

scientific article published on 23 March 2006

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

scientific article published on 15 December 2006

Exome scale map of genetic alterations promoting metastasis in colorectal cancer

scientific article published on 19 September 2018

Extending the aerolysin family: from bacteria to vertebrates

scientific article

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

scientific article

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

scientific article published on 18 November 2014

Fungal lifestyle reflected in serine protease repertoire

scientific article

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

scientific article published on 6 March 2017

Glyoxylate reductase as versatile enzymatic system for pharmaceutical and medical use

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

scientific article

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

scientific article published in April 2003

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

scientific article published on 20 November 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

scientific article published on 28 January 2016

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

scientific article published in March 2006

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

scientific article

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

scientific article published on 4 April 2018

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

scientific article

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

scientific article

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

scientific article published in April 2007

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

scientific article published on 20 November 2019

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

scientific article published on 04 March 2020

Mitochondrial release factor in yeast: interplay of functional domains

scientific article published on 26 January 2008

Modelling of potentially promising SARS protease inhibitors

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

scientific article

Novel SARS unique AdoMet-dependent methyltransferase.

scientific article published on 16 October 2006

Novel transmembrane lipases of alpha/beta hydrolase fold

scientific article published on 17 February 2011

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

scientific article published on 17 March 2013

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

scientific article

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

scientific article published in January 2018

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 15 March 2018

Predicting proteome dynamics using gene expression data

scientific article published in Scientific Reports

Prediction of signal peptides in protein sequences by neural networks.

scientific article published on 26 May 2008

Probabilistic approach to predicting substrate specificity of methyltransferases

scientific article

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

scientific article published in April 2005

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

scientific article

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

scientific article published in October 2004

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

scientific article

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

scholarly article

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

scientific article

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

scientific article published on 7 May 2004

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

scientific article published on December 2005

Snf2 proteins in plants: gene silencing and beyond

scientific article published on 09 September 2008

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

scientific article

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

scientific article published on 10 April 2015

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

scientific article

Systematic classification of the His-Me finger superfamily

scientific article published on 10 October 2017

TOS1 is circularly permuted 1,3-beta-glucanase.

scientific article

Target specific compound identification using a support vector machine.

scientific article

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

scientific article published on 25 August 2011

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

scientific article published on 23 January 2014

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

scientific article

The interactome: Predicting the protein-protein interactions in cells

scientific article published on 6 October 2008

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

scientific article

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

scientific article published on 07 August 2020

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

scientific article

Transposable elements contribute to fungal genes and impact fungal lifestyle

article

Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases.

scientific article

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

scientific article

Virtual high throughput screening using combined random forest and flexible docking

scientific article

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

scientific article

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

scientific article published on 31 October 2018

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

scientific article published on 24 May 2019

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