The Pfam Protein Families Database

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

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480

Predicting coiled coils from protein sequences.

Lupas, A., Van Dyke, M., & Stock, J. (1991) · Science · doi:10.1126/science.252.5009.1162 · Cited by 3,953

TreeFam: 2008 update

Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L. J. M., Guo, Y., Heriche, J.-K., Hu, Y., Kristiansen, K., Li, R., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1005 · Cited by 332

Learning generative models for protein fold families

Balakrishnan, S., Kamisetty, H., Carbonell, J. G., Lee, S., & Langmead, C. J. (2011) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22934 · Cited by 316

Human Transcription Factors Contain a High Fraction of Intrinsically Disordered Regions Essential for Transcriptional Regulation

Minezaki, Y., Homma, K., Kinjo, A. R., & Nishikawa, K. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.04.016 · Cited by 297

A Post-Synaptic Scaffold at the Origin of the Animal Kingdom

Sakarya, O., Armstrong, K. A., Adamska, M., Adamski, M., Wang, I.-F., Tidor, B., Degnan, B. M., Oakley, T. H., & Kosik, K. S. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000506 · Cited by 291

IsdG and IsdI, Heme-degrading Enzymes in the Cytoplasm of Staphylococcus aureus

Skaar, E. P., Gaspar, A. H., & Schneewind, O. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m307952200 · Cited by 282

A novel class of modular transporters for vitamins in prokaryotes

Rodionov, D. A., Hebbeln, P., Eudes, A., ter Beek, J., Rodionova, I. A., Erkens, G. B., Slotboom, D. J., Gelfand, M. S., Osterman, A. L., Hanson, A. D., et al. (2009) · Journal of Bacteriology · doi:10.1128/jb.01208-08 · Cited by 279

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

Gobler, C. J., Berry, D. L., Dyhrman, S. T., Wilhelm, S. W., Salamov, A., Lobanov, A. V., Zhang, Y., Collier, J. L., Wurch, L. L., Kustka, A. B., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016106108 · Cited by 285

APPRIS: annotation of principal and alternative splice isoforms

Rodriguez, J. M., Maietta, P., Ezkurdia, I., Pietrelli, A., Wesselink, J.-J., Lopez, G., Valencia, A., & Tress, M. L. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1058 · Cited by 232

Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors

Kemmeren, P., Sameith, K., van de Pasch, L. A. L., Benschop, J. J., Lenstra, T. L., Margaritis, T., O’Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C. W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.054 · Cited by 277

MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes

Bujalka, H., Koenning, M., Jackson, S., Perreau, V. M., Pope, B., Hay, C. M., Mitew, S., Hill, A. F., Lu, Q. R., Wegner, M., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001625 · Cited by 271

Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail–Like Structures

Shikuma, N. J., Pilhofer, M., Weiss, G. L., Hadfield, M. G., Jensen, G. J., & Newman, D. K. (2014) · Science · doi:10.1126/science.1246794 · Cited by 267

A Role for Insect Galectins in Parasite Survival

Kamhawi, S., Ramalho-Ortigao, M., Pham, V. M., Kumar, S., Lawyer, P. G., Turco, S. J., Barillas-Mury, C., Sacks, D. L., & Valenzuela, J. G. (2004) · Cell · doi:10.1016/j.cell.2004.10.009 · Cited by 266

Structure of the bacterial ribosome at 2 Å resolution

Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H. (2020) · eLife · doi:10.7554/elife.60482 · Cited by 263

Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock

Rubin, E. B., Shemesh, Y., Cohen, M., Elgavish, S., Robertson, H. M., & Bloch, G. (2006) · Genome Research · doi:10.1101/gr.5094806 · Cited by 257

A Basic Leucine Zipper Transcription Factor, AabZIP1, Connects Abscisic Acid Signaling with Artemisinin Biosynthesis in Artemisia annua

Zhang, F., Fu, X., Lv, Z., Lu, X., Shen, Q., Zhang, L., Zhu, M., Wang, G., Sun, X., Liao, Z., et al. (2015) · Molecular Plant · doi:10.1016/j.molp.2014.12.004 · Cited by 248

Independent evolution of striated muscles in cnidarians and bilaterians

Steinmetz, P. R. H., Kraus, J. E. M., Larroux, C., Hammel, J. U., Amon-Hassenzahl, A., Houliston, E., Wörheide, G., Nickel, M., Degnan, B. M., & Technau, U. (2012) · Nature · doi:10.1038/nature11180 · Cited by 252

Insights into corn genes derived from large-scale cDNA sequencing

Alexandrov, N. N., Brover, V. V., Freidin, S., Troukhan, M. E., Tatarinova, T. V., Zhang, H., Swaller, T. J., Lu, Y.-P., Bouck, J., Flavell, R. B., et al. (2009) · Plant Molecular Biology · doi:10.1007/s11103-008-9415-4 · Cited by 248

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

Zhang, D., Iyer, L. M., He, F., & Aravind, L. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00283 · Cited by 244

A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus

Livingston, B. T., Killian, C. E., Wilt, F., Cameron, A., Landrum, M. J., Ermolaeva, O., Sapojnikov, V., Maglott, D. R., Buchanan, A. M., & Ettensohn, C. A. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.07.047 · Cited by 243

Hamiltonella defensa , genome evolution of protective bacterial endosymbiont from pathogenic ancestors

Degnan, P. H., Yu, Y., Sisneros, N., Wing, R. A., & Moran, N. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900194106 · Cited by 241

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

Boldt, K., van Reeuwijk, J., Lu, Q., Koutroumpas, K., Nguyen, T.-M. T., Texier, Y., van Beersum, S. E. C., Horn, N., Willer, J. R., Mans, D. A., et al. (2016) · Nature Communications · doi:10.1038/ncomms11491 · Cited by 240

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

Song, Y., Botvinnik, O. B., Lovci, M. T., Kakaradov, B., Liu, P., Xu, J. L., & Yeo, G. W. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.003 · Cited by 204

Take five — Type VII secretion systems of Mycobacteria

Houben, E. N. G., Korotkov, K. V., & Bitter, W. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2013.11.003 · Cited by 223

Gene family innovation, conservation and loss on the animal stem lineage

(2018) · doi:10.7554/elife.34226 · Cited by 226

A novel sensor of NADH/NAD+ redox poise in Streptomyces coelicolor A3(2)

Brekasis, D., & Paget, M. S. B. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg453 · Cited by 224

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Huerta-Cepas, J., Capella-Gutiérrez, S., Pryszcz, L. P., Marcet-Houben, M., & Gabaldón, T. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1177 · Cited by 217

Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes

Grarup, N., Moltke, I., Andersen, M. K., Dalby, M., Vitting-Seerup, K., Kern, T., Mahendran, Y., Jørsboe, E., Larsen, C. V. L., Dahl-Petersen, I. K., et al. (2018) · Nature Genetics · doi:10.1038/s41588-017-0022-7 · Cited by 216

Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts

Lee, J.-H., Gao, C., Peng, G., Greer, C., Ren, S., Wang, Y., & Xiao, X. (2011) · Circulation Research · doi:10.1161/circresaha.111.249433 · Cited by 209

A Comparative Genome Analysis Identifies Distinct Sorting Pathways in Gram-Positive Bacteria

Comfort, D., & Clubb, R. T. (2004) · Infection and Immunity · doi:10.1128/iai.72.5.2710-2722.2004 · Cited by 203

The Origin of GPCRs: Identification of Mammalian like Rhodopsin, Adhesion, Glutamate and Frizzled GPCRs in Fungi

Krishnan, A., Almén, M. S., Fredriksson, R., & Schiöth, H. B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029817 · Cited by 204

LET-413 is a basolateral protein required for the assembly of adherens junctions in Caenorhabditis elegans

Legouis, R., Gansmuller, A., Sookhareea, S., Bosher, J. M., Baillie, D. L., & Labouesse, M. (2000) · Nature Cell Biology · doi:10.1038/35017046 · Cited by 189

Structure of a Lipid Droplet Protein

Hickenbottom, S. J., Kimmel, A. R., Londos, C., & Hurley, J. H. (2004) · Structure · doi:10.1016/j.str.2004.04.021 · Cited by 193

Conservation of core gene expression in vertebrate tissues

Chan, E. T., Quon, G. T., Chua, G., Babak, T., Trochesset, M., Zirngibl, R. A., Aubin, J., Ratcliffe, M. J., Wilde, A., Brudno, M., et al. (2009) · Journal of Biology · doi:10.1186/jbiol130 · Cited by 190

Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus : insights into the origin and evolution of storage carbohydrates in Eukaryotes

Michel, G., Tonon, T., Scornet, D., Cock, J. M., & Kloareg, B. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03345.x · Cited by 188

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps

Huang, H., Jedynak, B. M., & Bader, J. S. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030214 · Cited by 182

A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily

van Bloois, E., Torres Pazmiño, D. E., Winter, R. T., & Fraaije, M. W. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-009-2369-x · Cited by 180

Nectin-like proteins mediate axon–Schwann cell interactions along the internode and are essential for myelination

Maurel, P., Einheber, S., Galinska, J., Thaker, P., Lam, I., Rubin, M. B., Scherer, S. S., Murakami, Y., Gutmann, D. H., & Salzer, J. L. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200705132 · Cited by 177

BLR-1 and BLR-2, key regulatory elements of photoconidiation and mycelial growth in Trichoderma atroviride

Casas-Flores, S., Rios-Momberg, M., Bibbins, M., Ponce-Noyola, P., & Herrera-Estrella, A. (2004) · Microbiology · doi:10.1099/mic.0.27346-0 · Cited by 172

Structural Basis for Endosomal Targeting by the Bro1 Domain

Kim, J., Sitaraman, S., Hierro, A., Beach, B. M., Odorizzi, G., & Hurley, J. H. (2005) · Developmental Cell · doi:10.1016/j.devcel.2005.04.001 · Cited by 174

Zizimin1, a novel Cdc42 activator, reveals a new GEF domain for Rho proteins

Meller, N., Irani-Tehrani, M., Kiosses, W. B., Del Pozo, M. A., & Schwartz, M. A. (2002) · Nature Cell Biology · doi:10.1038/ncb835 · Cited by 171

Isolation and Expression of a Malassezia globosa Lipase Gene, LIP1

DeAngelis, Y. M., Saunders, C. W., Johnstone, K. R., Reeder, N. L., Coleman, C. G., Kaczvinsky, J. R., Gale, C., Walter, R., Mekel, M., Lacey, M. P., et al. (2007) · Journal of Investigative Dermatology · doi:10.1038/sj.jid.5700844 · Cited by 164

Helminth Allergens, Parasite-Specific IgE, and Its Protective Role in Human Immunity

Fitzsimmons, C. M., Falcone, F. H., & Dunne, D. W. (2014) · Frontiers in Immunology · doi:10.3389/fimmu.2014.00061 · Cited by 157

Clostridium butyricum Strains and Dysbiosis Linked to Necrotizing Enterocolitis in Preterm Neonates

Cassir, N., Benamar, S., Khalil, J. B., Croce, O., Saint-Faust, M., Jacquot, A., Million, M., Azza, S., Armstrong, N., Henry, M., et al. (2015) · Clinical Infectious Diseases · doi:10.1093/cid/civ468 · Cited by 151

Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato (Solanum lycopersicum)

Cao, J., & Li, X. (2015) · Planta · doi:10.1007/s00425-014-2215-y · Cited by 131

Comparative Genomics of Trace Elements: Emerging Dynamic View of Trace Element Utilization and Function

Zhang, Y., & Gladyshev, V. N. (2009) · Chemical Reviews · doi:10.1021/cr800557s · Cited by 143

Exploring structural diversity across the protein universe with The Encyclopedia of Domains

Lau, A. M., Bordin, N., Kandathil, S. M., Sillitoe, I., Waman, V. P., Wells, J., Orengo, C. A., & Jones, D. T. (2024) · Science · doi:10.1126/science.adq4946 · Cited by 140

Functional Overlap and Regulatory Links Shape Genetic Interactions between Signaling Pathways

van Wageningen, S., Kemmeren, P., Lijnzaad, P., Margaritis, T., Benschop, J. J., de Castro, I. J., van Leenen, D., Groot Koerkamp, M. J. A., Ko, C. W., Miles, A. J., et al. (2010) · Cell · doi:10.1016/j.cell.2010.11.021 · Cited by 133

NEAT: a domain duplicated in genes near the components of a putative Fe3+siderophore transporter from Gram-positive pathogenic bacteria

Andrade, M. A., Ciccarelli, F. D., Perez-Iratxeta, C., & Bork, P. (2002) · Genome Biology · doi:10.1186/gb-2002-3-9-research0047 · Cited by 135

Relapsed Classic E-Cadherin ( CDH1 )–Mutated Invasive Lobular Breast Cancer Shows a High Frequency of HER2 ( ERBB2 ) Gene Mutations

Ross, J. S., Wang, K., Sheehan, C. E., Boguniewicz, A. B., Otto, G., Downing, S. R., Sun, J., He, J., Curran, J. A., Ali, S., et al. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-0295 · Cited by 135

The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns

Moummou, H., Kallberg, Y., Tonfack, L. B., Persson, B., & van der Rest, B. (2012) · BMC Plant Biology · doi:10.1186/1471-2229-12-219 · Cited by 134

KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes

Presnell, J. S., Schnitzler, C. E., & Browne, W. E. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv141 · Cited by 119

An Unbiased Approach to Identifying Tau Kinases That Phosphorylate Tau at Sites Associated with Alzheimer Disease

Cavallini, A., Brewerton, S., Bell, A., Sargent, S., Glover, S., Hardy, C., Moore, R., Calley, J., Ramachandran, D., Poidinger, M., et al. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.463984 · Cited by 133

The Early Response to Acid Shock in Lactobacillus reuteri Involves the ClpL Chaperone and a Putative Cell Wall-Altering Esterase

Wall, T., Båth, K., Britton, R. A., Jonsson, H., Versalovic, J., & Roos, S. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01502-06 · Cited by 131

Metrics for the Human Proteome Project 2013–2014 and Strategies for Finding Missing Proteins

Lane, L., Bairoch, A., Beavis, R. C., Deutsch, E. W., Gaudet, P., Lundberg, E., & Omenn, G. S. (2014) · Journal of Proteome Research · doi:10.1021/pr401144x · Cited by 129

Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)

Ranea, J. A. G., Sillero, A., Thornton, J. M., & Orengo, C. A. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0289-7 · Cited by 122

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo

Mann, I. K., Chatterjee, R., Zhao, J., He, X., Weirauch, M. T., Hughes, T. R., & Vinson, C. (2013) · Genome Research · doi:10.1101/gr.146654.112 · Cited by 126

Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins

Li, S., Smith, K. D., Davis, J. H., Gordon, P. B., Breaker, R. R., & Strobel, S. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310439110 · Cited by 122

Bioinformatics opportunities for identification and study of medicinal plants

Sharma, V., & Sarkar, I. N. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs021 · Cited by 121

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

Barquist, L., Langridge, G. C., Turner, D. J., Phan, M.-D., Turner, A. K., Bateman, A., Parkhill, J., Wain, J., & Gardner, P. P. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt148 · Cited by 121

Redundancy in electronic health record corpora: analysis, impact on text mining performance and mitigation strategies

Cohen, R., Elhadad, M., & Elhadad, N. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-10 · Cited by 121

Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

Li, Y., & Wei, K. (2020) · BMC Plant Biology · doi:10.1186/s12870-020-2288-7 · Cited by 119

A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes

Nakjang, S., Ndeh, D. A., Wipat, A., Bolam, D. N., & Hirt, R. P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030287 · Cited by 116

Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume

Du, D., Zhang, Q., Cheng, T., Pan, H., Yang, W., & Sun, L. (2013) · Molecular Biology Reports · doi:10.1007/s11033-012-2250-3 · Cited by 111

Phylogenetic distribution of translational GTPases in bacteria

Margus, T., Remm, M., & Tenson, T. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-15 · Cited by 115

Quantifying the mechanisms of domain gain in animal proteins

Buljan, M., Frankish, A., & Bateman, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-7-r74 · Cited by 112

Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans

Copley, R. R., Aloy, P., Russell, R. B., & Telford, M. J. (2004) · Evolution & Development · doi:10.1111/j.1525-142x.2004.04021.x · Cited by 108

Origin of animal epithelia: insights from the sponge genome

Fahey, B., & Degnan, B. M. (2010) · Evolution & Development · doi:10.1111/j.1525-142x.2010.00445.x · Cited by 109

Asymmetric cross‐regulation between the nitrate‐responsive NarX–NarL and NarQ–NarP two‐component regulatory systems from Escherichia coli K‐12

Noriega, C. E., Lin, H., Chen, L., Williams, S. B., & Stewart, V. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06987.x · Cited by 108

Toxicological evaluation of proteins introduced into food crops

Hammond, B., Kough, J., Herouet-Guicheney, C., Jez, J. M., & on behalf of the ILSI International Food Biotechnology Committee Task Force on the Use of Mammalian Toxicology Studies in the Safety Assessment of GM Foods (2013) · Critical Reviews in Toxicology · doi:10.3109/10408444.2013.842956 · Cited by 110

Integrating biological data – the Distributed Annotation System

Jenkinson, A. M., Albrecht, M., Birney, E., Blankenburg, H., Down, T., Finn, R. D., Hermjakob, H., Hubbard, T. J., Jimenez, R. C., Jones, P., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-s8-s3 · Cited by 100

Peptidoglycan Remodeling and Conversion of an Inner Membrane into an Outer Membrane during Sporulation

Tocheva, E. I., Matson, E. G., Morris, D. M., Moussavi, F., Leadbetter, J. R., & Jensen, G. J. (2011) · Cell · doi:10.1016/j.cell.2011.07.029 · Cited by 103

Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production

Hao, P., Zheng, H., Yu, Y., Ding, G., Gu, W., Chen, S., Yu, Z., Ren, S., Oda, M., Konno, T., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0015964 · Cited by 100

RUN domains: a new family of domains involved in Ras-like GTPase signaling

Callebaut, I., Jean, de Gunzburg, Goud, B., & Mornon, J.-P. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01730-8 · Cited by 96

A refined genome‐scale reconstruction of Chlamydomonas metabolism provides a platform for systems‐level analyses

Imam, S., Schäuble, S., Valenzuela, J., López García de Lomana, A., Carter, W., Price, N. D., & Baliga, N. S. (2015) · The Plant Journal · doi:10.1111/tpj.13059 · Cited by 96

Differential evolution of voltage-gated sodium channels in tetrapods and teleost fishes

Widmark, J., Sundstrom, G., Ocampo Daza, D., & Larhammar, D. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq257 · Cited by 88

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function

Ezkurdia, I., del Pozo, A., Frankish, A., Rodriguez, J. M., Harrow, J., Ashman, K., Valencia, A., & Tress, M. L. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss100 · Cited by 89

ATP synthase evolution on a cross-braced dated tree of life

Mahendrarajah, T. A., Moody, E. R. R., Schrempf, D., Szánthó, L. L., Dombrowski, N., Davín, A. A., Pisani, D., Donoghue, P. C. J., Szöllősi, G. J., Williams, T. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42924-w · Cited by 86

Evolutionary analysis of the most polymorphic gene family in falciparum malaria

Otto, T. D., Assefa, S. A., Böhme, U., Sanders, M. J., Kwiatkowski, D. P., Pf3k consortium, Berriman, M., & Newbold, C. (2019) · Wellcome Open Research · doi:10.12688/wellcomeopenres.15590.1 · Cited by 90

Functionally Enigmatic Genes: A Case Study of the Brain Ignorome

Pandey, A. K., Lu, L., Wang, X., Homayouni, R., & Williams, R. W. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088889 · Cited by 90

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Unkefer, C. J., Sayre, R. T., Magnuson, J. K., Anderson, D. B., Baxter, I., Blaby, I. K., Brown, J. K., Carleton, M., Cattolico, R. A., Dale, T., et al. (2017) · Algal Research · doi:10.1016/j.algal.2016.06.002 · Cited by 90

Allelic Heterogeneity in the COH1 Gene Explains Clinical Variabilityin Cohen Syndrome

Hennies, H. C., Rauch, A., Seifert, W., Schumi, C., Moser, E., Al-Taji, E., Tariverdian, G., Chrzanowska, K. H., Krajewska-Walasek, M., Rajab, A., et al. (2004) · The American Journal of Human Genetics · doi:10.1086/422219 · Cited by 90

The STARD9/Kif16a Kinesin Associates with Mitotic Microtubules and Regulates Spindle Pole Assembly

Torres, J. Z., Summers, M. K., Peterson, D., Brauer, M. J., Lee, J., Senese, S., Gholkar, A. A., Lo, Y.-C., Lei, X., Jung, K., et al. (2011) · Cell · doi:10.1016/j.cell.2011.11.020 · Cited by 80

The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective

Coppi, M. V. (2005) · Microbiology · doi:10.1099/mic.0.27535-0 · Cited by 81

Reduced expression of a protein homologous to glycogenin leads to reduction of starch content in Arabidopsis leaves

Chatterjee, M., Berbezy, P., Vyas, D., Coates, S., & Barsby, T. (2005) · Plant Science · doi:10.1016/j.plantsci.2004.09.015 · Cited by 79

LFR1 ferric iron reductase of Leishmania amazonensis is essential for the generation of infective parasite forms

Flannery, A. R., Huynh, C., Mittra, B., Mortara, R. A., & Andrews, N. W. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.229674 · Cited by 74

The Genome of Spironucleus salmonicida Highlights a Fish Pathogen Adapted to Fluctuating Environments

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