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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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THE UBIQUITIN SYSTEM

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Mitochondrial Evolution

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The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

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Phylogenomics and the reconstruction of the tree of life

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A kingdom-level phylogeny of eukaryotes based on combined protein data.

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Protein Tyrosine Kinase Structure and Function

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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

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The Age of Crosstalk: Phosphorylation, Ubiquitination, and Beyond

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Ubiquitin-binding domains — from structures to functions

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For Quite a Few Chromosomes More: The Origin of Eukaryotes…

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Reproductive competence: a recurrent logic module in eukaryotic development

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What Is a Scientific Theory?

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A data-intelligence-intensive bioinformatics copilot system for large-scale omics research and scientific insights

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Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation

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Transitions between the Arabidopsis-type and the human-type telomere sequence in green algae (clade Caudivolvoxa, Chlamydomonadales)

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A formal analysis of phylogenetic terminology: Towards a reconsideration of the current paradigm in systematics

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Origin of the Eukaryotic Cell

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Perspectives on Principles of Cellular Behavior from the Biophysics of Protists

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Current Perspectives on Uniparental Mitochondrial Inheritance in Cryptococcus neoformans

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An Evolutionary Perspective on the Plant Hormone Ethylene

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Understanding eukaryotic chromosome segregation from a comparative biology perspective

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Beyond Xeroderma Pigmentosum: DNA Damage and Repair in an Ecological Context. A Tribute to James E. Cleaver

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Cellular gauge symmetry and the Li organization principle: General considerations

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Complex Plastids and the Evolution of the Marine Phytoplankton

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A billion years of geological drama – Boring or brilliant?

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Deep conservation and co-option of programmed cell death facilitates evolution of alternative phenotypes at multiple biological levels

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The chromatin landscape of the euryarchaeon Haloferax volcanii

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Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth

Egel, R. (2011) · Springer eBooks · doi:10.1007/978-3-642-21625-1_12 · Cited by 8

Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication

Manzano-Morales, S., & Gabaldón, T. (2026) · Nature Communications · doi:10.1038/s41467-026-71534-5 · Cited by 7

The World of Proteases Across Microbes, Insects, and Medicinal Trees

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Pluralism or unity in biology: could microbes hold the secret to life?

Cleland, C. E. (2013) · Biology & Philosophy · doi:10.1007/s10539-013-9361-7 · Cited by 6

Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist

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A look beyond the QR code of SNARE proteins

Yadav, D., Hacisuleyman, A., Dergai, M., Khalifeh, D., Abriata, L. A., Peraro, M. D., & Fasshauer, D. (2024) · Protein Science · doi:10.1002/pro.5158 · Cited by 6

The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants

Roffler, S., Menardo, F., & Wicker, T. (2015) · Mobile DNA · doi:10.1186/s13100-015-0054-4 · Cited by 7

Mitochondria and the Origin of Eukaryotes

Lang, B. F. (2013) · Springer eBooks · doi:10.1007/978-3-7091-1303-5_1 · Cited by 6

Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family

Mier, P., Pérez‐Pulido, A. J., Reynaud, E. G., & Andrade-Navarro, M. A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169750 · Cited by 6

Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans

Dubie, J. J., Katju, V., & Bergthorsson, U. (2024) · Heredity · doi:10.1038/s41437-024-00704-2 · Cited by 6

Horizontal gene transfer as a possible evolutionary predecessor of sexual reproduction

Markov, A. V. (2014) · Paleontological Journal · doi:10.1134/s0031030114030149 · Cited by 5

A Linear-Time Algorithm for Reconciliation of Non-binary Gene Tree and Binary Species Tree

Zheng, Y., Wu, T., & Zhang, L. (2013) · Lecture notes in computer science · doi:10.1007/978-3-319-03780-6_17 · Cited by 5

Cloning, molecular characterization, and phylogeny of two evolutionary distinct glutamine synthetase isoforms in the green microalga Haematococcus pluvialis (Chlorophyceae)

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How Natural a Kind Is "Eukaryote?"Preprint

Doolittle, W. F. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a015974 · Cited by 6

‘Parabiotic Evolution’: From Stochasticity in Geochemical and Subsequent Processes to Genes, Genomes and Modular CellsPreprint

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Co-translational assembly promotes functional diversification of paralogous proteinsPreprint

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Tellurium as a valuable tool for studying the prokaryotic origins of mitochondria

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Minimization of extracellular space as a driving force in prokaryote association and the origin of eukaryotes

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Evolutionary analysis of Slc11 mechanism of proton-coupled metal-ion transmembrane import

Cellier, M. F., & Inrs-Institut Armand-Frappier, 5. (2016) · AIMS Biophysics · doi:10.3934/biophy.2016.2.286 · Cited by 4

The Evolution of the Earth and Its Atmosphere

Poderoso, J. J. (2016) · Springer eBooks · doi:10.1007/978-3-319-45865-6_2 · Cited by 4

Eukaryotic origins and the Proterozoic Earth system: A link between global scale glaciations and eukaryogenesis?

Boyle, R. (2017) · Earth-Science Reviews · doi:10.1016/j.earscirev.2017.09.001 · Cited by 4

Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells

Bateman, A. (2020) · Biology Direct · doi:10.1186/s13062-020-00260-9 · Cited by 4

On the Origin and Early Evolution of Translation in Eukaryotes

Hernández, G., Osnaya, V. G., García, A., & Velasco, M. X. (2016) · Springer eBooks · doi:10.1007/978-3-319-39468-8_5 · Cited by 4

The chromatin landscape of the histone-possessingBacteriovoraxbacteriaPreprint

Marinov, G. K., Doughty, B. R., Kundaje, A. B., & Greenleaf, W. J. (2024) · Genome Research · doi:10.1101/gr.279418.124 · Cited by 5

Structural and evolutionary analyses of the mitochondrial genome of Spuriopimpinella brachycarpa

Han, J. H., Xu, W., Yu, H., Han, Y., & Zhu, M. (2024) · Frontiers in Plant Science · doi:10.3389/fpls.2024.1492723 · Cited by 3

An Up-To-Date Review of Piglet Isosporosis

Boulaki, V., Vlachakis, D., Sotiraki, S., & Κοσσίδα, Σ. (2018) · IGI Global eBooks · doi:10.4018/978-1-5225-5640-4.ch006 · Cited by 3

Thermotogales origin scenario of eukaryogenesis

Kuwabara, T., & Igarashi, K. (2020) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2020.110192 · Cited by 3

Intraneuronal Computation

Navarro, J., del Moral, R., & Marijuán, P. C. (2016) · Wiley eBooks · doi:10.1002/9781118316757.ch4 · Cited by 3

Comparative genomics: A modern-day approach for understanding the blue print of life

Bhatt, G., Bhattarai, S., Negi, P., Thapa, V., Nandy, S., & Joshi, S. (2025) · International Journal of Zoology and Applied Biosciences · doi:10.55126/ijzab.2025.v10.i01.003 · Cited by 2

Beyond Genomes: Functional Signatures Reveal Evolutionary Patterns Across the Tree of Life

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The genome of Pleurosigma provides insights into the evolutionary adaptations of pelagic diatoms

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Gene migration of giardiasis in Iran; a microevolutionary scale for reflecting transmission patterns of Giardia lamblia assemblages in symptomatic patients

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Analysis of Mitochondrial Hsp70 Homolog Amino Acid Sequences of Amitochondriate Organisms Using Apriori and Decision Tree

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The role of archaea in the origin of eukaryotes

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Evidence for evolutionary relationship between archaeplastidal and cyanobacterial phytochromes based on their chromophore pockets

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On the emergence of eukaryotes and other enigmas

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A decade and genome of change

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Molecular Phylogeny Reconstruction

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The cell nucleus as a barrier against horizontal gene transfer in microbial endosymbioses

Zachar, I., Máté, J., & Oszoli, I. (2026) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2025.0096 · Cited by 1

Changes in Genomes and Karyotypes during Speciation and Progressive Evolution of Plants

Rodionov, A. V. (2025) · Russian Journal of Genetics · doi:10.1134/s1022795425701030 · Cited by 1

Phylogenetic ancestry of Metamonada proteins points to a common origin of mitochondria in all eukaryotes

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Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria

Sagy, O., Ron Shamir, A., & Rechavi, O. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00275 · Cited by 1

Polyphyly of chloroplast carriers: where do plants are located on the “tree of life”?

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In Silico Conformation of the Drug Colchicine into Tubulin Models and Acute Phytotoxic Activity on Cucumis sativus Radicles

Peña-Morán, O. A., Jiménez-Pérez, J., Cerón‐Romero, L., & Rodríguez‐Aguilar, M. (2022) · Plants · doi:10.3390/plants11141805 · Cited by 1

An Up-To-Date Review of Piglet Isosporosis

Boulaki, V., Vlachakis, D., Sotiraki, S., & Κοσσίδα, Σ. (2013) · International Journal of Systems Biology and Biomedical Technologies · doi:10.4018/ijsbbt.2013100104 · Cited by 1

Origin and early evolution of the nuclear envelope

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Searching for Extraterrestrial Life Without a Definition or Universal Theory of Life

Cleland, C. E. (2019) · Cambridge University Press eBooks · doi:10.1017/9781139046893.009 · Cited by 1

High Pressure and High-Pressure Environments

Macdonald, A. (2021) · Springer eBooks · doi:10.1007/978-3-030-67587-5_1 · Cited by 1

Challenges for a Universal Theory of Life

Cleland, C. E. (2019) · Cambridge University Press eBooks · doi:10.1017/9781139046893.006 · Cited by 1

Eukaryotes

Ligrone, R. (2019) · Springer eBooks · doi:10.1007/978-3-030-16057-9_6 · Cited by 1

Mitochondrial Origins

Gabaldón, T. (2011) · Springer eBooks · doi:10.1007/978-3-642-22380-8_1 · Cited by 1

A Tool for Non-binary Tree Reconciliation

Zheng, Y., & Zhang, L. (2013) · Lecture notes in computer science · doi:10.1007/978-3-642-38036-5_8 · Cited by 1

Challenging Eukaryogenesis: The Story of the Eukaryotic AncestorPreprint

Vidaurri, M. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2008.06608 · Cited by 1

The landscape of the histone-organized chromatin of Bdellovibrionota bacteriaPreprint

Marinov, G. K., Doughty, B. R., Kundaje, A. B., & Greenleaf, W. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.30.564843 · Cited by 1

Phylogénomique des structures multiprotéiques eucaryotes impliquées dans le cycle cellulaire et contribution à la phylogénie des eucaryotes.

Eme, L. (2011) · theses.fr (ABES) · doi:10.70675/f6a87363z8acaz4487z93e0z57bc870cf584 · Cited by 1

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamicsPreprint

Włodzimierz, P., Pérez-Román, E., Isa, J. G., Hong, M., Zhang, M., Oliveira, L., Jenike, K. M., Burns, R., Sierra, P., Heuberger, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.17.752431 · Cited by 1

Phylogenetics and Evolution of Virulence in the Kingdom Fungi

Garcia-Solache, M. A., & Casadevall, A. (2012) · Wiley eBooks · doi:10.1002/9781118308165.ch4

Genomics and Phylogeny of Cytoskeletal Proteins: Tools and Analyses

Hammesfahr, B. (2013) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-3704

The evolutionary history of meiotic genes

Pightling, A. (2011) · doi:10.17077/etd.6xg42cj3

Comparative Cell Biology in Diplomonads

Einarsson, E. (2015) · KTH Publication Database DiVA (KTH Royal Institute of Technology)

Insights & Perspectives Planctomycetes and eukaryotes: A case of analogy not homology

Scotia, N., & McInerney, J. O. (2011)

ENVIRONMENTAL SENSITIVITY OF MITOCHONDRIAL GENE EXPRESSION IN FISH

Bremer, K. (2013) · QSpace (Queen's University Library)

Evolution of Mitochondria in Eukaryotes versus Mitochondria “Maturing” from the Stage of Stem Cells to Committed Progenitors and Mature Cells

Ivanović, Z., & Vlaski‐Lafarge, M. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800540-8.00009-0

Prokaryotic Contributions Towards Eukaryotic Powerhouse

Kalia, V. C. (2015) · Springer eBooks · doi:10.1007/978-81-322-2595-9_21

The MicroRNA Repertoire of Symbiodinium, the Dinoflagellate Symbiont of Reef-Building Corals

Baumgarten, S. (2013) · King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) · doi:10.25781/kaust-a79nq

Bacteria and Eukaryotes Evolution

Ciancio, A. (2016) · Springer eBooks · doi:10.1007/978-94-024-0884-3_2

Mitochondrial clock: moderating evolution of early eukaryotes in light of the Proterozoic oceans

Dasgupta, S. (2016) · Biologia · doi:10.1515/biolog-2016-0117

In Search of Gauge Theories for Living Cells: a Topological Exploration on the Deep Structure of Biological ComplexityPreprint

Tozzi, A., Navarro, J., Peters, J. F., & Marijuán, P. C. (2016) · viXra

Structural and functional advances in the evolutionary studies of cells and viruses

Nasir, A. (2015) · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)

Functional characterisation of plant-specific mitochondrial outer membrane proteins in Arabidopsis thaliana

Kubiszewski-Jakubiak, S. (2015) · UWA Profiles and Research Repository (UWA)

The Mitochondrial Genome, Genomic Shifting, and Genomic Conflict

Brown, G. G. (2017) · Wiley eBooks · doi:10.1002/9781118647110.ch6

The impact of the mitochondrial bottleneck on mtDNA disease risk and embryogenesis

Otten, A. B. C. (2016) · Research Publications (Maastricht University) · doi:10.26481/dis.20161115ao

A Thesis on Life, the Universe and Almost Everything

Stevenson, D. S. (2017) · Astronomers' universe · doi:10.1007/978-3-319-52911-0_9

Organellar Genome Evolution in Red Algal Parasites: Differences in Adelpho- and Alloparasites

Salomaki, E. D. (2017) · Digital Commons - URI (University of Rhode Island) · doi:10.23860/diss-salomaki-eric-2017

Short Branch Attraction, the Fundamental Bipartition in Cellular Life, and Eukaryogenesis

Dick, & Amanda, A. (2016)

Allorecognition and Innate Immunity in the Dictyostelid Social Amoebae

Kuspa, A. (2018) · Springer eBooks · doi:10.1007/978-3-319-76768-0_2

The Origin and Early Evolution of Life

Stevenson, D. S. (2019) · Springer eBooks · doi:10.1007/978-3-030-25550-3_6

The Niche, Its Hypervolume and the Entropy of Existence

Stevenson, D. S. (2019) · Springer eBooks · doi:10.1007/978-3-030-25550-3_7

a Circulating cell free mitochondrial DNA copy number variation in neurodegenerative disease

Lowes, H. (2018)

Gene Mutation and Epigenetic Modification Origin in Glioma Initiation: Are the GDNF and SOX1 Overexpression the Causes of Its Initiation?Preprint

Kanwore, K., Guo, X., Ayanlaja, A. A., Kambey, P. A., Adekunle, A. O., & Gao, D. (2020) · Preprints.org · doi:10.20944/preprints202005.0388.v1

Origin and Early Evolution of the Eukaryotic Cell

Gabaldón, T. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090817-062213 · Cited by 121

The unlikely cell: origins and diversification of eukaryotes

Ligrone, R. (2022) · Università degli Studi di Napoli Federico II · doi:10.6093/2724-4393/9380 · Cited by 1

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

Koonin, E. V. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0333 · Cited by 145

Evolution: A gene-rich mitochondrial genome sheds light on the last eukaryotic common ancestor

Leger, M. M., & Gawryluk, R. M. R. (2024) · Current Biology · doi:10.1016/j.cub.2024.06.067 · Cited by 2

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López-García, P., & Moreira, D. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2015.09.005 · Cited by 135