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List of works by Aravind L Iyer

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis ⬇️

scientific article published on January 15, 2002

A TET homologue protein from Coprinopsis cinerea (CcTET) that biochemically converts 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine

scientific article published on 25 March 2014

A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea

scientific article published on 27 February 2004

A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

scientific article

A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins

scientific article

A hemolytic pigment of Group B Streptococcus allows bacterial penetration of human placenta

scientific article

A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications

scientific article

A multidomain adhesion protein family expressed in Plasmodium falciparum is essential for transmission to the mosquito

scientific article (publication date: 7 June 2004)

A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases

scientific article

A non-hemolytic Group B Streptococcus strain exhibits hypervirulence

scientific article published on 13 December 2017

A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain

scientific article

A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease

scientific article

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems ⬇️

scientific article

A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands

scientific article published on 24 January 2007

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

scientific article

A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey

scientific article

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes

scientific article (publication date: 1999)

ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons

scientific article (publication date: 12 November 2012)

AMIN domains have a predicted role in localization of diverse periplasmic protein complexes.

scientific article published on 21 August 2008

AT-hook motifs identified in a wide variety of DNA-binding proteins ⬇️

scientific article published on October 1, 1998

ATP hydrolysis by a domain related to translation factor GTPases drives polymerization of a static bacterial morphogenetic protein

scientific journal article

Adaptive evolution by optimizing expression levels in different environments

scientific article published on 13 December 2005

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

scientific article published on 12 December 2015

Adhesion molecules and other secreted host-interaction determinants in Apicomplexa: insights from comparative genomics

scientific article

Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins

scientific article

An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin

scientific article

An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent aggregation

scientific article

Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis

scientific article

Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation

scientific article

Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins

scientific article

Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria

scientific article

Apprehending multicellularity: regulatory networks, genomics, and evolution

scientific article

BEN: a novel domain in chromatin factors and DNA viral proteins

scientific article

Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms

scientific article

CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems

scientific article published on 30 April 2014

CHAPTER 11. The TET/JBP Family of Nucleic Acid Base-Modifying 2-Oxoglutarate and Iron-Dependent Dioxygenases

CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes

scientific article

Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors

scientific article

Centrins, cell cycle regulation proteins in human malaria parasite Plasmodium falciparum

scientific article (publication date: 14 November 2008)

Chitinases of the avian malaria parasite Plasmodium gallinaceum, a class of enzymes necessary for parasite invasion of the mosquito midgut.

scientific article published on April 2000

Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum

scientific article (publication date: 6 November 1998)

Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52

scientific article

Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins

scientific article

Clinical and molecular aspects of malaria fever

scientific article published on 26 July 2011

Cloning the human and mouse MMS19 genes and functional complementation of a yeast mms19 deletion mutant

scientific article

Common origin of four diverse families of large eukaryotic DNA viruses

scientific article

Comparative analysis of apicomplexa and genomic diversity in eukaryotes

scientific article published on September 2004

Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum

scientific article

Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling

scientific article published on 20 November 2015

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces

scientific article

Comparative genomics and evolution of proteins involved in RNA metabolism

scientific article

Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems

scientific article

Comparative genomics and structural biology of the molecular innovations of eukaryotes

scientific article published on 5 May 2006

Comparative genomics of protists: new insights into the evolution of eukaryotic signal transduction and gene regulation

scientific article

Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging

scientific article published on 5 October 2004

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

scientific article

Comparative genomics uncovers novel structural and functional features of the heterotrimeric GTPase signaling system

scientific article

Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex

scientific article

Comparison of the complete protein sets of worm and yeast: orthology and divergence

scientific article

Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?

scientific article

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast

scientific article published on 3 May 2006

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

scientific article

Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA.

scientific article

Conserved domains in DNA repair proteins and evolution of repair systems

scientific article

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

scientific article

DNA Methylation on N6-Adenine in C. elegans

scientific article

DNA-binding proteins and evolution of transcription regulation in the archaea

scientific article

DOMON: an ancient extracellular domain in dopamine beta-monooxygenase and other proteins.

scientific article

De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling

scientific article

Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily

scientific article

Differences in evolutionary pressure acting within highly conserved ortholog groups

scientific article

Differential action of natural selection on the N and C-terminal domains of 2'-5' oligoadenylate synthetases and the potential nuclease function of the C-terminal domain

scientific article

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

scientific article published on 23 May 2007

Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease

scientific article published in 2012

Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains

scientific article

Diversification and spectral tuning in marine proteorhodopsins

scientific article

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity

scientific article

Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase.

scientific article

Diversity and evolution of chromatin proteins encoded by DNA viruses

scientific article published on 28 October 2009

Domain architectures of the Scm3p protein provide insights into centromere function and evolution

scientific article

EFCAB7 and IQCE regulate hedgehog signaling by tethering the EVC-EVC2 complex to the base of primary cilia

scientific article

Editorial overview: Sequences and topology: Protein function - synthesizing information from sequence, structure and disorder

scientific article published on 8 July 2016

Editorial overview: Sequences and topology: sequences, structures, genomes and populations

scientific article

Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins

scientific article

Erratum: Corrigendum: Themis is a member of a new metazoan gene family and is required for the completion of thymocyte positive selection

article

Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation

scientific article published on 16 October 2006

Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system

scientific article

Eukaryotic transcription regulators derive from ancient enzymatic domains ⬇️

scientific article published on February 12, 1998

Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles

article

Evolution and classification of P-loop kinases and related proteins

scientific article published in October 2003

Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase

scientific article

Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects

scientific article

Evolution of Eukaryotic Chromatin Proteins and Transcription Factors

Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer

scientific article

Evolution of cell–cell signaling in animals: did late horizontal gene transfer from bacteria have a role?

scientific article

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems

scientific article

Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing

scientific article published on 11 May 2020

Evolutionary and Biochemical Aspects of Chemical Stress Resistance in Saccharomyces cerevisiae ⬇️

scientific article published on March 30, 2012

Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases

scientific article

Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective

scientific article

Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes

scientific article published on 18 April 2018

Evolutionary dynamics of prokaryotic transcriptional regulatory networks

scientific article published on 28 February 2006

Evolutionary genomics of nucleo-cytoplasmic large DNA viruses

scientific article

Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes

scientific article published on 7 July 2006

Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys

scientific article published on 19 March 2018

Expression, Purification, and Biological Characterization of Babesia microti Apical Membrane Antigen 1.

scientific article published on 20 July 2015

Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors

scientific article

Filling out the structural map of the NTF2-like superfamily

scientific article

Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system

scientific article (publication date: July 2011)

G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins

scientific article published on 01 September 1999

GREB1: An evolutionarily conserved protein with a glycosyltransferase domain links ERα glycosylation and stability to cancer

scientific article published on 17 March 2021

Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb.

scientific article

Gene flow and biological conflict systems in the origin and evolution of eukaryotes

scientific article

General trends in the evolution of prokaryotic transcriptional regulatory networks

scientific article published on January 2007

Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis

scientific article

Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1

scientific article

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

scientific article

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics

scientific article

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

scientific article published on 18 August 2009

Genomic donor cassette sharing during VLRA and VLRC assembly in jawless vertebrates

scientific article

Global transcriptional effects of PEG-IFN-alpha and ribavirin on peripheral blood cells obtained from patients with chronic hepatitis C.

scientific article published on 9 October 2006

HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes ⬇️

scientific article

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells

scientific article

High-confidence mapping of chemical compounds and protein complexes reveals novel aspects of chemical stress response in yeast

scientific article

Highly-regulated, diversifying NTP-based biological conflict systems with implications for emergence of multicellularity

scientific article published on 26 February 2020

Host biomarkers and biological pathways that are associated with the expression of experimental cerebral malaria in mice

scientific article published on 21 July 2008

Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily

scientific article

HutC/FarR-like bacterial transcription factors of the GntR family contain a small molecule-binding domain of the chorismate lyase fold

scientific article

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices

scientific article

Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions ⬇️

scientific article published on March 7, 2012

Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes

scientific article

Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels

scientific article

Identification of uncharacterized components of prokaryotic immune systems and their diverse eukaryotic reformulations

scientific article published on 31 August 2020

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

scientific article

Incarnation of classical pro- and eukaryotic mechanisms of mutagenesis in hypermutagenesis and immunity of vertebrates

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Insights from the architecture of the bacterial transcription apparatus

scientific article (publication date: September 2012)

Interplay between gene expression noise and regulatory network architecture

scientific article

Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli

scientific article

Intraproteomic networks: new forays into predicting interaction partners

scientific article

LUD, a new protein domain associated with lactate utilization

scientific article

Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes

scientific article

Lineage-specific loss and divergence of functionally linked genes in eukaryotes

scientific article

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

scientific article

MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems

scientific article

MORC2 signaling integrates phosphorylation-dependent, ATPase-coupled chromatin remodeling during the DNA damage response

scientific article

MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal-sulfur cluster biosynthesis proteins including Molybdenum cofactor sulfurases

scientific article (publication date: 22 January 2002)

Malaria parasite clag3 genes determine channel-mediated nutrient uptake by infected red blood cells

scientific article published in May 2011

MicroRNA targeting in mammalian genomes: genes and mechanisms

scientific article

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX.

scientific article published on 7 April 2013

Molecular Markers of Radiation Induced Attenuation in Intrahepatic Plasmodium falciparum Parasites

scientific article

Molecular cloning, expression, and structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing metalloenzyme

scientific article

Molecular correlates of experimental cerebral malaria detectable in whole blood

scientific article

Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites

scientific article published on 5 February 2007

Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.

scientific article

Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids

scientific article

Multiple transporters associated with malaria parasite responses to chloroquine and quinine

scientific article published on August 2003

MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases

scientific article

Myosin 1G is an abundant class I myosin in lymphocytes whose localization at the plasma membrane depends on its ancient divergent pleckstrin homology (PH) domain (Myo1PH).

scientific article

Natural history of eukaryotic DNA methylation systems

scientific article

Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation

scientific article

Natural history of the eukaryotic chromatin protein methylation system

scientific article

New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing

scientific article

No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho

scientific article published on 01 May 1999

Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems

scientific article

Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts

scientific article

Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability

scientific article

Novel eukaryotic enzymes modifying cell-surface biopolymers

scientific article

Novel predicted RNA-binding domains associated with the translation machinery

scientific article

Novel predicted peptidases with a potential role in the ubiquitin signaling pathway

scientific article

Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment

scientific article

O-GlcNAcylation destabilizes the active tetrameric PKM2 to promote the Warburg effect

scientific article published on 11 December 2017

OST-HTH: a novel predicted RNA-binding domain

scientific article

Opening Pandora's Box: making biological discoveries through computational data exploration

scientific article published on 20 November 2007

Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase

scientific article

Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members

scientific article

Origin of multicellular eukaryotes - insights from proteome comparisons.

scientific article

PSI-BLAST Tutorial

Pathogenic roles of CD14, galectin-3, and OX40 during experimental cerebral malaria in mice

scientific article

PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum

scientific article (publication date: 11 July 2013)

Phosphoesterase domains associated with DNA polymerases of diverse origins ⬇️

scientific article published on August 15, 1998

Plasmodium biology: genomic gleanings

scientific article

Plasmodium falciparum: characterization of a late asexual stage golgi protein containing both ankyrin and DHHC domains

scientific article (publication date: August 2005)

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

scientific article

Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements

scientific article

Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis

scientific article

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

scientific article

Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach

scientific article

Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains

scientific article

Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system

scientific article

Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide

scientific journal article

Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics

scientific article

Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit.

scientific article

Prune cAMP phosphodiesterase binds nm23-H1 and promotes cancer metastasis.

scientific article published in February 2004

Quod erat demonstrandum?The mystery of experimental validation of apparently erroneous computational analyses of protein sequences ⬇️

scientific article published on November 13, 2001

RNA damage in biological conflicts and the diversity of responding RNA repair systems

scientific article

Radiation-induced cellular and molecular alterations in asexual intraerythrocytic Plasmodium falciparum

scientific article

Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria

scientific article

Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions

scientific article

Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.

scientific article

Resilience of biochemical activity in protein domains in the face of structural divergence

scientific article

Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory interactions

scientific article

Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome

scientific article

Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1.

scientific article

SAP - a putative DNA-binding motif involved in chromosomal organization

scientific article (publication date: March 2000)

STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer

scientific article

START: a lipid-binding domain in StAR, HD-ZIP and signalling proteins

scientific article (publication date: April 1999)

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories

scientific article

SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes

scientific article

Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation

scientific article

Scores of RINGS but No PHDs in Ubiquitin Signaling ⬇️

scientific article published on March 1, 2003

Selection of the lamprey VLRC antigen receptor repertoire

scientific article

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea

scientific article

Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold

scientific article

Specific Expansion of Protein Families in the Radioresistant Bacterium Deinococcus Radiodurans

article

Structural basis of oligomerization in septin-like GTPase of immunity-associated protein 2 (GIMAP2)

scientific article

Structure and Evolution of Ubiquitin and Ubiquitin-Related Domains

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis

scientific article

Structure and evolution of transcriptional regulatory networks

scientific article

Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

scientific article

Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen

scientific article

Structure of the Plasmodium 6-cysteine s48/45 domain

scientific article

Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation

scientific article

Structure-function analysis of manganese exporter proteins across bacteria

scientific article published on 13 February 2018

TCRβ-expressing macrophages induced by a pathogenic murine malaria correlate with parasite burden and enhanced phagocytic activity

scientific article published in PLoS ONE

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

scientific article published on June 2013

THEMIS enhances TCR signaling and enables positive selection by selective inhibition of the phosphatase SHP-1.

scientific article

Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing

scientific article

The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism

scientific article

The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains

scientific article

The C. elegans Polycomb gene SOP-2 encodes an RNA binding protein

scientific article published in June 2004

The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases

scientific article

The DOMON domains are involved in heme and sugar recognition

scientific article

The GAF domain: an evolutionary link between diverse phototransducing proteins.

scientific article published in December 1997

The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications

scientific article

The HD domain defines a new superfamily of metal-dependent phosphohydrolases

scientific article

The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA.

scientific article

The Knickkopf DOMON domain is essential for cuticle differentiation in Drosophila melanogaster

scientific article

The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation

scientific article (publication date: May 2000)

The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways

scientific article published on 23 April 2019

The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins

scientific article

The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.

scientific article

The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities

scientific article

The Shwachman-Bodian-Diamond syndrome gene encodes an RNA-binding protein that localizes to the pseudopod of Dictyostelium amoebae during chemotaxis

article

The U box is a modified RING finger — a common domain in ubiquitination

scientific article published on 01 February 2000

The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation

scientific article

The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function

scientific article

The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates

scientific article

The bacterial replicative helicase DnaB evolved from a RecA duplication

scientific article (publication date: 2000)

The bridge-region of the Ku superfamily is an atypical zinc ribbon domain

scientific article

The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis

scientific article published on 13 August 2019

The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates

scientific article

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

scientific article

The conserved protein SZY-20 opposes the Plk4-related kinase ZYG-1 to limit centrosome size

scientific article

The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins

scholarly article by Aravind L Iyer published in July 1999

The emergence of catalytic and structural diversity within the beta-clip fold

scientific article

The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications

scientific article published on 15 May 2015

The many faces of the helix-turn-helix domain: transcription regulation and beyond

scientific article (publication date: April 2005)

The mechanism of force transmission at bacterial focal adhesion complexes.

scientific article

The natural history of ADP-ribosyltransferases and the ADP-ribosylation system

scientific article

The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons

scientific article (publication date: 2006)

The natural history of ubiquitin and ubiquitin-related domains

scientific article published on January 2012

The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains

scientific article

The role of lineage-specific gene family expansion in the evolution of eukaryotes

scientific article

The scaffolding protein synapse-associated protein 97 is required for enhanced signaling through isotype-switched IgG memory B cell receptors

scientific article

The signaling helix: a common functional theme in diverse signaling proteins

scientific article published on 5 September 2006

The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

scientific article

The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism ⬇️

scientific article published on September 8, 2003

The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networks

scientific article

The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element

scientific article

Themis is a member of a new metazoan gene family and is required for the completion of thymocyte positive selection

scientific article

Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins ⬇️

scientific article published on September 15, 1998

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

scientific article

Transcription factors, chromatin proteins and the diversification of Hemiptera

scientific article published on 27 July 2015

Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors

scientific article

Trends in protein evolution inferred from sequence and structure analysis.

scientific article

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila

scientific article

Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes

scientific article

UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes

scientific article

Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks

scientific article published on 27 April 2006

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

scientific article

Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination

scientific article

Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria

scientific article published on 27 February 2018

Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes

scientific article published on 9 April 2018

Whole exome sequencing identifies the TNNI3K gene as a cause of familial conduction system disease and congenital junctional ectopic tachycardia.

scientific article

YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics

scientific article

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