Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts

(2021) Lakshminarayan M. Iyer et al.   Viruses-Basel

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

(2020) Gurmeet Kaur et al.   eLife

Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum

(2020) Daniel E. Schäffer et al.   Frontiers in Genetics

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

(2020) A. Maxwell Burroughs et al.   JOURNAL OF BACTERIOLOGY

STING cyclic dinucleotide sensing originated in bacteria

(2020) Benjamin R. Morehouse et al.   NATURE

Cell death signalling in virus infection

(2020) Gergely Imre   CELLULAR SIGNALLING

Evolution of Mutator transposable elements across eukaryotic diversity

(2019) Mathilde Dupeyron et al.   Mobile DNA

Structural Basis of Response Regulator Function

(2019) Rong Gao et al.   Annual Review of Microbiology

Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation

(2019) Mo’men Abdelkareem et al.   MOLECULAR CELL

The Roles of Hippo Signaling Transducers Yap and Taz in Chromatin Remodeling

(2019) Ryan E. Hillmer et al.   Cells

Benchmarking fold detection by DaliLite v.5

(2019) Liisa Holm   BIOINFORMATICS

Evolution of Alternative Adaptive Immune Systems in Vertebrates

(2018) Thomas Boehm et al.   Annual Review of Immunology

TIR Domain Proteins Are an Ancient Family of NAD + -Consuming Enzymes

(2018) Kow Essuman et al.   CURRENT BIOLOGY

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

TRIM21 Promotes Innate Immune Response to RNA Viral Infection through Lys27-Linked Polyubiquitination of MAVS

(2018) Binbin Xue et al.   JOURNAL OF VIROLOGY

Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla

(2018) Michael J. Metzger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Arunkumar Krishnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemicals released by male sea cucumber mediate aggregation and spawning behaviours

(2018) Nathalie Marquet et al.   Scientific Reports

Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

(2018) Qin Yu et al.   MOLECULAR CELL

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

TIR-domain-containing adapter-inducing interferon-β (TRIF) forms filamentous structures, whose pro-apoptotic signalling is terminated by autophagy

(2017) Ian E. Gentle et al.   FEBS Journal

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

(2017) Lakshminarayan M. Iyer et al.   JOURNAL OF BACTERIOLOGY

Programmed cell death as one of the stages of streptomycete differentiation

(2017) S. N. Filippova et al.   MICROBIOLOGY

Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey

(2017) Li Wu et al.   NUCLEIC ACIDS RESEARCH

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

(2016) Maria Hauser et al.   BIOINFORMATICS

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

(2016) Dapeng Zhang et al.   NUCLEIC ACIDS RESEARCH

Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology

(2016) David T. Kysela et al.   PLOS BIOLOGY

RIG-I-like receptor-induced IRF3 mediated pathway of apoptosis (RIPA): a new antiviral pathway

(2016) Saurabh Chattopadhyay et al.   Protein & Cell

Toll/interleukin-1 receptor (TIR) domain-mediated cellular signaling pathways

(2015) Kannan Badri Narayanan et al.   APOPTOSIS

Horizontal Transmission of Clonal Cancer Cells Causes Leukemia in Soft-Shell Clams

(2015) Michael J. Metzger et al.   CELL

On the evolution of bacterial multicellularity

(2015) Nicholas A Lyons et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2015) A. Maxwell Burroughs et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hamilton's rule and the causes of social evolution

(2014) A. F. G. Bourke   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DNA Sequence Heterogeneity of Campylobacter jejuni CJIE4 Prophages and Expression of Prophage Genes

(2014) Clifford G. Clark et al.   PLoS One

Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts

(2014) Matthew D. Daugherty et al.   PLoS Genetics

The Meaning of Stromatolites

(2013) Tanja Bosak et al.   Annual Review of Earth and Planetary Sciences

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

(2013) Vivek Anantharaman et al.   Biology Direct

Prokaryotic Ancestry of Eukaryotic Protein Networks Mediating Innate Immunity and Apoptosis

(2013) Stanislaw Dunin-Horkawicz et al.   JOURNAL OF MOLECULAR BIOLOGY

Multiple Modes of Cell Death Discovered in a Prokaryotic (Cyanobacterial) Endosymbiont

(2013) Weiwen Zheng et al.   PLoS One

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

(2013) Alexander Maxwell Burroughs et al.   Wiley Interdisciplinary Reviews-RNA

Biochemical and functional characterization of the ROC domain of DAPK establishes a new paradigm of GTP regulation in ROCO proteins

(2012) Shani Bialik et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2012) Dapeng Zhang et al.   Biology Direct

Roles of NOD1 (NLRC1) and NOD2 (NLRC2) in innate immunity and inflammatory diseases

(2012) Ricardo G. Correa et al.   BIOSCIENCE REPORTS

The RIP1/RIP3 Necrosome Forms a Functional Amyloid Signaling Complex Required for Programmed Necrosis

(2012) Jixi Li et al.   CELL

SH3 domains come of age

(2012) Brian K. Kay   FEBS LETTERS

A novel big protein TPRBK possessing 25 units of TPR motif is essential for the progress of mitosis and cytokinesis

(2012) Tomohiro Izumiyama et al.   GENE

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

(2012) Kamil Steczkiewicz et al.   NUCLEIC ACIDS RESEARCH

PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites

(2012) Jiangning Song et al.   PLoS One

Identification and Characterization of FAM124B as a Novel Component of a CHD7 and CHD8 Containing Complex

(2012) Tserendulam Batsukh et al.   PLoS One

Towards an integrated network of coral immune mechanisms

(2012) C. V. Palmer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Structure and function of the SPRY/B30.2 domain proteins involved in innate immunity

(2012) Akshay A. D'Cruz et al.   PROTEIN SCIENCE

Structure of the Essential Diversity-Generating Retroelement Protein bAvd and Its Functionally Important Interaction with Reverse Transcriptase

(2012) Maher Alayyoubi et al.   STRUCTURE

Metabolic Stress in Autophagy and Cell Death Pathways

(2012) B. J. Altman et al.   Cold Spring Harbor Perspectives in Biology

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

(2012) L. Aravind et al.   Frontiers in Cellular and Infection Microbiology

The origin of multicellularity in cyanobacteria

(2011) Bettina E Schirrmeister et al.   BMC EVOLUTIONARY BIOLOGY

Structural Basis for the Activation of Innate Immune Pattern-Recognition Receptor RIG-I by Viral RNA

(2011) Eva Kowalinski et al.   CELL

Programmed Cell Death in Animal Development and Disease

(2011) Yaron Fuchs et al.   CELL

The PIDDosome, DNA-damage-induced apoptosis and beyond

(2011) S Janssens et al.   CELL DEATH AND DIFFERENTIATION

The natural history of ubiquitin and ubiquitin-related domains

(2011) Alexander Maxwell Burroughs   Frontiers in Bioscience-Landmark

Orphan Macrodomain Protein (Human C6orf130) Is anO-Acyl-ADP-ribose Deacylase

(2011) Francis C. Peterson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural and mechanistic comparisons of the metal-binding members of the vicinal oxygen chelate (VOC) superfamily

(2011) Panqing He et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

DDX60, a DEXD/H Box Helicase, Is a Novel Antiviral Factor Promoting RIG-I-Like Receptor-Mediated Signaling

(2011) M. Miyashita et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2011) A. Maxwell Burroughs et al.   Molecular BioSystems

The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase

(2011) Dea Slade et al.   NATURE

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

(2011) Dapeng Zhang et al.   NUCLEIC ACIDS RESEARCH

CARD8 and NLRP1 Undergo Autoproteolytic Processing through a ZU5-Like Domain

(2011) Andrea D'Osualdo et al.   PLoS One

OST-HTH: a novel predicted RNA-binding domain

(2010) Vivek Anantharaman et al.   Biology Direct

The inflammasomes: mechanisms of activation and function

(2010) Eicke Latz   CURRENT OPINION IN IMMUNOLOGY

Alternative cell death mechanisms in development and beyond

(2010) J. Yuan et al.   GENES & DEVELOPMENT

The Oligoadenylate Synthetase Family: An Ancient Protein Family with Multiple Antiviral Activities

(2010) Helle Kristiansen et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein

(2010) Shunsuke Tagami et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Polyubiquitin conjugation to NEMO by triparite motif protein 23 (TRIM23) is critical in antiviral defense

(2010) K.-i. Arimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The metzincins - Topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a super family of zinc-peptidases

(2010) Walter Stöcker et al.   PROTEIN SCIENCE

Protein kinases: evolution of dynamic regulatory proteins

(2010) Susan S. Taylor et al.   TRENDS IN BIOCHEMICAL SCIENCES

Different ways to die: cell death modes of the unicellular chlorophyte Dunaliella viridis exposed to various environmental stresses are mediated by the caspase-like activity DEVDase

(2009) C. Jimenez et al.   JOURNAL OF EXPERIMENTAL BOTANY

Population structure, growth and distribution of Lingula anatina (Brachiopoda) in Queensland, Australia

(2009) R. A. Kenchington et al.   JOURNAL OF ZOOLOGY

Origin and evolution of the adaptive immune system: genetic events and selective pressures

(2009) Martin F. Flajnik et al.   NATURE REVIEWS GENETICS

A tumor suppressive coactivator complex of p53 containing ASC-2 and histone H3-lysine-4 methyltransferase MLL3 or its paralogue MLL4

(2009) J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Origins of Multicellularity and the Early History of the Genetic Toolkit For Animal Development

(2008) Antonis Rokas   Annual Review of Genetics

Death Effector Domain-Containing Proteins

(2008) M. Gudur Valmiki et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity

(2008) S. Huang et al.   GENOME RESEARCH

Structural and Enzymatic Analysis of MshA fromCorynebacterium glutamicum

(2008) Matthew W. Vetting et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

(2008) Timo Lassmann et al.   NUCLEIC ACIDS RESEARCH

Glycosyltransferases: Structures, Functions, and Mechanisms

(2007) L.L. Lairson et al.   Annual Review of Biochemistry

Evolution of the β-propeller fold

(2007) Indronil Chaudhuri et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS