List of works by Michael Y. Galperin

'Conserved hypothetical' proteins: prioritization of targets for experimental study

scientific article

A Time to Scatter Genes and a Time to Gather Them

article

A bacterial coat that is not pure cotton.

scientific article published in January 2018

A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts

scientific article

A decade of research on the second messenger c-di-AMP

scientific article published on 30 May 2020

A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia

scientific article

A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family

scientific article

A specialized version of the HD hydrolase domain implicated in signal transduction

scientific article

A square archaeon, the smallest eukaryote and the largest bacteria

scientific article

A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases

scientific article (publication date: August 1998)

Acetyl-CoA synthetase from the amitochondriate eukaryote Giardia lamblia belongs to the newly recognized superfamily of acyl-CoA synthetases (Nucleoside diphosphate-forming).

scientific article published on February 2000

Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea

scientific article

Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea

scholarly article by M Galperin published in February 2000

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

scientific article

All bugs, big and small

scientific article

Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases

scientific article published in May 2003

An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands

scientific article published on 01 April 2003

An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi

scientific article

Analogous enzymes: independent inventions in enzyme evolution

scientific article

Analysis of Structure and Function of Putative Surface-Exposed Proteins Encoded in theStreptococcus pneumoniaeGenome: A Bioinformatics-Based Approach to Vaccine and Drug Design ⬇️

scientific article published on January 1, 2003

Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics

scientific article

Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions

scientific article published on 12 June 2015

Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance.

scientific article published on 20 August 2013

Bacterial signal transduction network in a genomic perspective

scientific article

Beyond complete genomes: from sequence to structure and function

scientific article

Bioinformatics for all!

scientific article published on 01 July 1999

C-di-GMP: the dawning of a novel bacterial signalling system

scientific article

C1/2 Energetics of the first bacteria as inferred from genome analysis

Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase

scientific article

Chemiluminescent Detection of Dextran Bound to Streptococcal Glucan-Binding Lectin

scientific article published on 01 February 1995

Co-evolution of primordial membranes and membrane proteins

scientific article published on 18 March 2009

Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea

scientific article

Comparative Genomics Approaches to Identifying Functionally Related Genes

article

Comparative analysis of lipid biosynthesis in archaea, bacteria and eukaryotes: What was the structure of the first membrane lipids?

Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems

scientific article published on 9 January 2015

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

scientific article

Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea

scientific article

Complete Genome Sequences of the Human Pathogen Paenibacillus thiaminolyticus Mbale and Type Strain P. thiaminolyticus NRRL B-4156

scientific article published on 09 April 2020

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

scientific article

Conserved core structure and active site residues in alkaline phosphatase superfamily enzymes

scientific article

Copper chaperones in bacteria: association with copper-transporting ATPases

scientific article published on 01 October 2000

Coregulation of beta-galactoside uptake and hydrolysis by the hyperthermophilic bacterium Thermotoga neapolitana ⬇️

scientific article published on March 1, 1997

Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism

scientific article

Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology

scientific article published on 18 November 2019

Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion

scientific article

Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms

scientific article published on 01 April 2020

Cyclic di-GMP: the first 25 years of a universal bacterial second messenger

scientific article

Dark matter in a deep-sea vent and in human mouth

scientific article

Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions

scientific article

Discovery of the Second Messenger Cyclic di-GMP.

scientific article published on January 2017

Divergence and convergence in enzyme evolution

scientific article

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

scientific article

Diversity of structure and function of response regulator output domains

scientific article

Editorial

Emergence of cytochrome bc complexes in the context of photosynthesis

scientific article

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

scientific article (publication date: 2008)

Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins

scientific article published on 15 October 2015

Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases

Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism

scientific article published on 11 December 2018

Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

scientific article

Evolutionary origins of membrane proteins

article

Evolutionary primacy of sodium bioenergetics

scientific article published on April 2008

Expanded microbial genome coverage and improved protein family annotation in the COG database

scientific article

Experimental verification of a sequence-based prediction: F(1)F(0)-type ATPase of Vibrio cholerae transports protons, not Na(+) ions

scientific article

Faculty of 1000 evaluation for Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP

From biofouling to bioremediation: the good, the bad and the vague

scientific article published in June 2004

From complete genome sequence to 'complete' understanding?

scientific article

Functional analysis of conserved polar residues in Vc-NhaD, Na+/H+ antiporter of Vibrio cholerae

scientific article published on 26 September 2005

Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes

scientific article

G protein-coupled receptors of class A harness the energy of membrane potential to increase their sensitivity and selectivity

scientific article published on 23 August 2019

GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria.

scientific article

Genome Diversity of Spore-Forming Firmicutes

scientific article

Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1)

scientific article

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

scientific article

Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

scientific article

Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae.

scientific article

Genomes back-to-back: when sequencing race is a good thing

scientific article

Genomes of model organisms: know thy tools

scientific article

Genomes to aid in bioremediation of dry cleaning solvents, mothballs and more

scientific article

Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes

scientific article

Genomics against flatulence

scientific article (publication date: August 2007)

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations

scientific article

Globins synthesize the second messenger bis-(3'-5')-cyclic diguanosine monophosphate in bacteria

scientific article

House cleaning, a part of good housekeeping

scientific article

How many signal peptides are there in bacteria?

scientific article published on April 2013

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

scientific article

Identification of sensory and signal-transducing domains in two-component signaling systems

scientific article

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium

scientific article published in January 2004

Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases

scientific article

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

scientific article

Interplay of heritage and habitat in the distribution of bacterial signal transduction systems

scientific article

Inventing the dynamo machine: the evolution of the F-type and V-type ATPases

scientific article published in November 2007

Life is not defined just in base pairs

scientific article

Linear chromosomes in bacteria: no straight edge advantage?

scientific article

Looking at big brothers for clues

scientific article

MASE1 and MASE2: two novel integral membrane sensory domains

scientific article

MHYT, a new integral membrane sensor domain

scientific article

MHYT, a new integral membrane sensor domain

article

Metagenomics: from acid mine to shining sea.

scientific article

Microbial genome analysis: the COG approach

scientific article

Microbial genomics as pursuit of happiness

scientific article published on March 2009

Microbial systems biology: bottom up and top down

scientific article published in 2009

Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly

scientific article published on 27 May 2015

More cool news from marine bacteria

scientific article

Multiple glucan-binding proteins of Streptococcus sobrinus

scientific article

Mycobacterial genomes for all tastes: from BCG to biodegradation of naphtalene and pyrene

scientific article

New feel for new phyla

scientific article (publication date: August 2008)

New metrics for comparative genomics

scientific article (publication date: October 2006)

New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins

scientific article

Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution

scientific article published on 30 April 2010

Novel domains of the prokaryotic two-component signal transduction systems

article

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.

scientific article

Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain

scientific article

OMICS-Related Research in Latin America

scholarly article by Daniel J. Rigden published in June 2005

OMICS-Related Research in South America

scholarly article by Michael Y. Galperin published in March 2005

On the abundance of zinc in the evolutionarily old protein domains ⬇️

scientific article published on August 6, 2010

On the bottom of the deep blue sea.

scientific article

On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth

scientific article (publication date: 24 August 2009)

Open questions on the origin of life at anoxic geothermal fields

scientific article published on October 2012

Origin of first cells at terrestrial, anoxic geothermal fields

scientific article

Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants

scientific article published on 01 September 2020

Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems

scientific article published on 20 December 2017

Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes

scientific article

Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen

scientific article

Phylogenomic reconstruction of archaeal fatty acid metabolism

scientific article

Physico-chemical and evolutionary constraints for the formation and selection of first biopolymers: towards the consensus paradigm of the abiogenic origin of life

scientific article published on September 2007

PilZ domain is part of the bacterial c-di-GMP binding protein

scientific article

Planctomycetes and eukaryotes: a case of analogy not homology

scientific article (publication date: November 2011)

Prokaryotic genomes: the emerging paradigm of genome-based microbiology

scientific article

Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkiapurinilytica comb. nov. a

scientific article published on August 2017

Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea

scientific article published on 5 December 2017

Protecting sausages with bacteria instead of salt

scientific article

Protein Domains Involved in Intracellular Signal Transduction

Purification, cloning, and expression of an apyrase from the bed bug Cimex lectularius. A new type of nucleotide-binding enzyme

scientific article

Salt in the wound: a possible role of Na+ gradient in chlamydial infection

scientific article

Sampling of microbial diversity by complete genomes

scientific article

Searching for drug targets in microbial genomes

scientific article

Sensory Transduction Network of E. coli

scholarly article published 2009

Sentra: a database of signal transduction proteins for comparative genome analysis

scientific article published on 29 November 2006

Sequence - Evolution - Function: Computational Approaches in Comparative Genomics

scientific article published on 7 December 2010

Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae

scientific article

Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution

scientific article published on 17 June 2008

Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors

scientific article published in August 2002

Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics

scientific article published on 24 February 2009

Social bacteria and asocial eukaryotes

scientific article

Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons

scientific article

Some bacteria degrade explosives, others prefer boiling methanol

scientific article

Sorting out the mix in microbial genomics

scientific article

Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.

scientific article

Stand-Alone EAL Domain Proteins Form a Distinct Subclass of EAL Proteins Involved in Regulation of Cell Motility and Biofilm Formation in Enterobacteria.

scientific article published on 26 June 2017

Structural Conservation and Diversity of PilZ-Related Domains

scientific article published on 29 January 2020

Structural Insight into the Mechanism of c-di-GMP Hydrolysis by EAL Domain Phosphodiesterases

scientific article

Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium

scientific article published on 12 July 2018

Structural classification of bacterial response regulators: diversity of output domains and domain combinations

scientific article

Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?

scientific article published on 01 July 2003

Subspecies-specific haemagglutination patterns of fimbriated Bacillus thuringiensis spores

scientific article published on December 1991

Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light

scientific article

Sustained sensing as an emerging principle in second messenger signaling systems

scientific article

Systematic Identification of Cyclic-di-GMP Binding Proteins in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with Type II Secretion Systems

scientific article

Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli

scientific article

Systems biology: sprint or marathon?

Telling bacteria: do not LytTR.

scientific article published in May 2008

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources

scientific article

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

scientific article

The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection ⬇️

scientific article

The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection

scientific article

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

scientific article

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection

scientific article

The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

scientific article

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

scientific article published in January 2017

The COMBREX project: design, methodology, and initial results

scientific article

The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution

scientific article published in October 2004

The Molecular Biology Database Collection: 2004 update

scientific article

The Molecular Biology Database Collection: 2005 update

scientific article

The Molecular Biology Database Collection: 2006 update

scientific article

The Molecular Biology Database Collection: 2007 update

scientific article

The Molecular Biology Database Collection: 2008 update

scientific article

The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules

scientific article published in July 2004

The bugs that came in from the cold

scientific article published in 2004

The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold

scientific article

The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases

scientific article

The cyanobacterial genome core and the origin of photosynthesis

scholarly article

The dawn of synthetic genomics

scientific article

The fuzzy border between a cell and an organelle

scientific article

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

scientific article

The glucose transport system of the hyperthermophilic anaerobic bacterium Thermotoga neapolitana ⬇️

scientific article published on August 1, 1996

The minimal genome keeps growing

scientific article published in 2006

The past and present of sodium energetics: may the sodium-motive force be with you

scientific article published on 27 April 2008

The quest for biofuels fuels genome sequencing

scientific article

The role of energy in the emergence of biology from chemistry

scientific article published on October 2012

The secret of being cool

scientific article

The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase

scientific article

The vibrio that sheds light

scientific article

To finish or not to finish?

scientific article published in 2005

Towards Automated Prediction of Protein Function from Microbial Genomic Sequences

article published in 1999

Towards BioDBcore: a community-defined information specification for biological databases

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article (publication date: 2011)

Two forms of phosphomannomutase in gammaproteobacteria: The overlooked membrane-bound form of AlgC is required for twitching motility of Lysobacter enzymogenes

scientific article published on 23 May 2019

Using archaeal genomics to fight global warming and clostridia to fight cancer

scientific article

Using metabolic pathway databases for functional annotation

scientific article published on 01 August 1998

Using the COG database to improve gene recognition in complete genomes

scientific article

Utilization of energy stored in the form of Na+ and K+ ion gradients by bacterial cells.

scientific article published on August 1983

Ways to control harmful biofilms: prevention, inhibition, and eradication

scientific article published on 28 December 2020

What bacteria want

scientific article published on 25 October 2018

Who's your neighbor? New computational approaches for functional genomics

scientific article

delta mu H+ is required for flagellar growth in Escherichia coli

scientific article published on 01 July 1982

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