Clustal W and Clustal X version 2.0

ViennaRNA Package 2.0

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Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

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Accurate prediction of protein structures and interactions using a 3-track network

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Lysine acetylation targets protein complexes and co-regulates major cellular functions

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A new bioinformatics analysis tools framework at EMBL-EBI

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The Colletotrichum gloeosporioides species complex

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SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19

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Structures of Cas9 endonucleases reveal RNA-mediated conformational activation

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Comparative genomics reveals insights into avian genome evolution and adaptation

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Using the Acropora digitifera genome to understand coral responses to environmental change

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GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

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Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

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The ctenophore genome and the evolutionary origins of neural systems

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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

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Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

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Autophagy mediates degradation of nuclear lamina

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Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction

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Widespread macromolecular interaction perturbations in human genetic disorders

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Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

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Targeted genome editing in human repopulating haematopoietic stem cells

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Quantitative Phosphoproteomics Reveal mTORC1 Activates de Novo Pyrimidine Synthesis

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SIRT5 regulates both cytosolic and mitochondrial protein malonylation with glycolysis as a major target

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System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

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The Molecular Basis of CRL4DDB2/CSA Ubiquitin Ligase Architecture, Targeting, and Activation

Fischer, E. S., Scrima, A., Böhm, K., Matsumoto, S., Lingaraju, G. M., Faty, M., Yasuda, T., Cavadini, S., Wakasugi, M., Hanaoka, F., et al. (2011) · Cell · doi:10.1016/j.cell.2011.10.035 · Cited by 460

On a Cercopithifilaria sp. transmitted by Rhipicephalus sanguineus: a neglected, but widespread filarioid of dogs

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Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

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Molecular basis for manganese sequestration by calprotectin and roles in the innate immune response to invading bacterial pathogens

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Members of the human gut microbiota involved in recovery from Vibrio cholerae infection

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Rho guanine nucleotide exchange factors: regulators of Rho GTPase activity in development and disease

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Structural integration in hypoxia-inducible factors

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Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

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Learning the language of viral evolution and escape

Hie, B., Zhong, E. D., Berger, B., & Bryson, B. (2021) · Science · doi:10.1126/science.abd7331 · Cited by 361

Mammalian Per-Arnt-Sim Proteins in Environmental Adaptation

McIntosh, B. E., Hogenesch, J. B., & Bradfield, C. A. (2010) · Annual Review of Physiology · doi:10.1146/annurev-physiol-021909-135922 · Cited by 352

Coordinated regulation of protein synthesis and degradation by mTORC1

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Glial glycolysis is essential for neuronal survival in Drosophila

Volkenhoff, A., Weiler, A., Letzel, M., Stehling, M., Klämbt, C., & Schirmeier, S. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.006 · Cited by 339

Engineering an allosteric transcription factor to respond to new ligands

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Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors

Yoshimura, S.-I., Gerondopoulos, A., Linford, A., Rigden, D. J., & Barr, F. A. (2010) · Journal of Cell Biology · doi:10.1083/jcb.201008051 · Cited by 317

SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication

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Mutations in the nuclear bile acid receptor FXR cause progressive familial intrahepatic cholestasis

Gomez-Ospina, N., Potter, C. J., Xiao, R., Manickam, K., Kim, M.-S., Kim, K. H., Shneider, B. L., Picarsic, J. L., Jacobson, T. A., Zhang, J., et al. (2016) · Nature Communications · doi:10.1038/ncomms10713 · Cited by 300

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

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ATG12 Conjugation to ATG3 Regulates Mitochondrial Homeostasis and Cell Death

Radoshevich, L., Murrow, L., Chen, N., Fernandez, E., Roy, S., Fung, C., & Debnath, J. (2010) · Cell · doi:10.1016/j.cell.2010.07.018 · Cited by 290

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

Fong, N., Kim, H., Zhou, Y., Ji, X., Qiu, J., Saldi, T., Diener, K., Jones, K., Fu, X.-D., & Bentley, D. L. (2014) · Genes & Development · doi:10.1101/gad.252106.114 · Cited by 287

In silico method for modelling metabolism and gene product expression at genome scale

Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., Schrimpe-Rutledge, A. C., Smith, R. D., Adkins, J. N., Zengler, K., et al. (2012) · Nature Communications · doi:10.1038/ncomms1928 · Cited by 266

Ancient deuterostome origins of vertebrate brain signalling centres

Pani, A. M., Mullarkey, E. E., Aronowicz, J., Assimacopoulos, S., Grove, E. A., & Lowe, C. J. (2012) · Nature · doi:10.1038/nature10838 · Cited by 252

Fungal laccases

Rivera-Hoyos, C. M., Morales-Álvarez, E. D., Poutou-Piñales, R. A., Pedroza-Rodríguez, A. M., RodrÍguez-Vázquez, R., & Delgado-Boada, J. M. (2013) · Fungal Biology Reviews · doi:10.1016/j.fbr.2013.07.001 · Cited by 256

Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors

Angel, T. E., Chance, M. R., & Palczewski, K. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903545106 · Cited by 235

The Devil Lies in the Details: How Variations in Polysaccharide Fine-Structure Impact the Physiology and Evolution of Gut Microbes

Martens, E. C., Kelly, A. G., Tauzin, A. S., & Brumer, H. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.06.022 · Cited by 235

Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

Martínez-del Campo, A., Bodea, S., Hamer, H. A., Marks, J. A., Haiser, H. J., Turnbaugh, P. J., & Balskus, E. P. (2015) · mBio · doi:10.1128/mbio.00042-15 · Cited by 224

Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow’s Capacity To Harvest Energy from Its Feed

Sasson, G., Kruger Ben-Shabat, S., Seroussi, E., Doron-Faigenboim, A., Shterzer, N., Yaacoby, S., Berg Miller, M. E., White, B. A., Halperin, E., & Mizrahi, I. (2017) · mBio · doi:10.1128/mbio.00703-17 · Cited by 219

Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin

Dailey, H. A., Gerdes, S., Dailey, T. A., Burch, J. S., & Phillips, J. D. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416285112 · Cited by 196

The ATP-Binding Cassette Transporter ABCA4: Structural and Functional Properties and Role in Retinal Disease

Tsybovsky, Y., Molday, R. S., & Palczewski, K. (2010) · Advances in Experimental Medicine and Biology · doi:10.1007/978-1-4419-5635-4_8 · Cited by 200

Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

Miho, E., Yermanos, A., Weber, C. R., Berger, C. T., Reddy, S. T., & Greiff, V. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00224 · Cited by 189

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

Clausen, A. R., Lujan, S. A., Burkholder, A. B., Orebaugh, C. D., Williams, J. S., Clausen, M. F., Malc, E. P., Mieczkowski, P. A., Fargo, D. C., Smith, D. J., et al. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2957 · Cited by 188

High‐throughput SNP‐based authentication of human cell lines

Castro, F., Dirks, W. G., Fähnrich, S., Hotz‐Wagenblatt, A., Pawlita, M., & Schmitt, M. (2013) · International Journal of Cancer · doi:10.1002/ijc.27675 · Cited by 183

Resolving rates of mutation in the brain using single-neuron genomics

Evrony, G. D., Lee, E., Park, P. J., & Walsh, C. A. (2016) · eLife · doi:10.7554/elife.12966 · Cited by 163

Light-regulated collective contractility in a multicellular choanoflagellate

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Alarming incidence of hepatitis C virus re-infection after treatment of sexually acquired acute hepatitis C virus infection in HIV-infected MSM.

Lambers, F. A. E., Prins, M., Thomas, X., Molenkamp, R., Kwa, D., Brinkman, K., van der Meer, J. T. M., & Schinkel, J. (2011) · AIDS · doi:10.1097/qad.0b013e32834bac44 · Cited by 167

Emergence and evolution of the renin-angiotensin-aldosterone system

Fournier, D., Luft, F. C., Bader, M., Ganten, D., & Andrade-Navarro, M. A. (2012) · Journal of Molecular Medicine · doi:10.1007/s00109-012-0894-z · Cited by 165

A late methanogen origin for molybdenum-dependent nitrogenase

BOYD, E. S., ANBAR, A. D., MILLER, S., HAMILTON, T. L., LAVIN, M., & PETERS, J. W. (2011) · Geobiology · doi:10.1111/j.1472-4669.2011.00278.x · Cited by 161

Candida albicans Hap43 Is a Repressor Induced under Low-Iron Conditions and Is Essential for Iron-Responsive Transcriptional Regulation and Virulence

Hsu, P.-C., Yang, C.-Y., & Lan, C.-Y. (2011) · Eukaryotic Cell · doi:10.1128/ec.00158-10 · Cited by 157

Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome

Axelsson, E., Webster, M. T., Ratnakumar, A., The LUPA Consortium, Ponting, C. P., & Lindblad-Toh, K. (2012) · Genome Research · doi:10.1101/gr.124123.111 · Cited by 142

Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics

Klebba, P. E., Newton, S. M. C., Six, D. A., Kumar, A., Yang, T., Nairn, B. L., Munger, C., & Chakravorty, S. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01005 · Cited by 150

Functional Roles of Aggregation-Promoting-Like Factor in Stress Tolerance and Adherence of Lactobacillus acidophilus NCFM

Goh, Y. J., & Klaenhammer, T. R. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00030-10 · Cited by 149

Circadian and circalunar clock interactions in a marine annelid

Zantke, J., Ishikawa-Fujiwara, T., Arboleda, E., Lohs, C., Schipany, K., Hallay, N., Straw, A. D., Todo, T., & Tessmar-Raible, K. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.08.031 · Cited by 148

Ins and outs of AlphaFold2 transmembrane protein structure predictions

Hegedűs, T., Geisler, M., Lukács, G. L., & Farkas, B. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04112-1 · Cited by 127

FKS Mutations and Elevated Echinocandin MIC Values among Candida glabrata Isolates from U.S. Population-Based Surveillance

Zimbeck, A. J., Iqbal, N., Ahlquist, A. M., Farley, M. M., Harrison, L. H., Chiller, T., & Lockhart, S. R. (2010) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00836-10 · Cited by 136

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., Menzel, C., Liang, H., Yang, H., Zhao, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002327 · Cited by 130

Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals insights into metal co‐ordination

Sheikh, M. A., & Taylor, G. L. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06718.x · Cited by 126

Structure-Function Analysis of Diacylglycerol Acyltransferase Sequences from 70 Organisms

Cao, H. (2011) · BMC Research Notes · doi:10.1186/1756-0500-4-249 · Cited by 122

Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element

Jemt, E., Persson, Ö., Shi, Y., Mehmedovic, M., Uhler, J. P., Dávila López, M., Freyer, C., Gustafsson, C. M., Samuelsson, T., & Falkenberg, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv804 · Cited by 121

The yellow sea green tides were dominated by one species, Ulva (Enteromorpha) prolifera, from 2007 to 2011

Zhao, J., Jiang, P., Liu, Z., Wei, W., Lin, H., Li, F., Wang, J., & Qin, S. (2013) · Chinese Science Bulletin · doi:10.1007/s11434-012-5441-3 · Cited by 117

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

The drought response displayed by a DRE-binding protein from Triticum dicoccoides

Lucas, S., Durmaz, E., Akpınar, B. A., & Budak, H. (2011) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2011.01.016 · Cited by 110

Ribosomal oxygenases are structurally conserved from prokaryotes to humans

Chowdhury, R., Sekirnik, R., Brissett, N. C., Krojer, T., Ho, C.-H., Ng, S. S., Clifton, I. J., Ge, W., Kershaw, N. J., Fox, G. C., et al. (2014) · Nature · doi:10.1038/nature13263 · Cited by 105

Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

Davies, K. T. J., Cotton, J. A., Kirwan, J. D., Teeling, E. C., & Rossiter, S. J. (2012) · Heredity · doi:10.1038/hdy.2011.119 · Cited by 105

LOGICOIL—multi-state prediction of coiled-coil oligomeric state

Vincent, T. L., Green, P. J., & Woolfson, D. N. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts648 · Cited by 103

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

Bayha, K. M., Dawson, M. N., Collins, A. G., Barbeitos, M. S., & Haddock, S. H. D. (2010) · Integrative and Comparative Biology · doi:10.1093/icb/icq074 · Cited by 102

Sph3 Is a Glycoside Hydrolase Required for the Biosynthesis of Galactosaminogalactan in Aspergillus fumigatus

Bamford, N. C., Snarr, B. D., Gravelat, F. N., Little, D. J., Lee, M. J., Zacharias, C. A., Chabot, J. C., Geller, A. M., Baptista, S. D., Baker, P., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.679050 · Cited by 102

Species richness of jellyfishes (Scyphozoa: Discomedusae) in the Tropical Eastern Pacific: missed taxa, molecules, and morphology match in a biodiversity hotspot

Gómez Daglio, L., & Dawson, M. N. (2017) · Invertebrate Systematics · doi:10.1071/is16055 · Cited by 98

Structural insights into adeno-associated virus serotype 5

Govindasamy, L., DiMattia, M. A., Gurda, B. L., Halder, S., McKenna, R., Chiorini, J. A., Muzyczka, N., Zolotukhin, S., & Agbandje-McKenna, M. (2013) · Journal of Virology · doi:10.1128/jvi.00867-13 · Cited by 95

The evolution and structure prediction of coiled coils across all genomes.

Rackham, O. J. L., Madera, M., Armstrong, C. T., Vincent, T. L., Woolfson, D. N., & Gough, J. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.08.032 · Cited by 97

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

Calero, P., Volke, D. C., Lowe, P. T., Gotfredsen, C. H., O’Hagan, D., & Nikel, P. I. (2020) · Nature Communications · doi:10.1038/s41467-020-18813-x · Cited by 97

CREB-Dependent Regulation of GAD65 Transcription by BDNF/TrkB in Cortical Interneurons

Sánchez-Huertas, C., & Rico, B. (2011) · Cerebral Cortex · doi:10.1093/cercor/bhq150 · 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

ORGAN BOUNDARY1 defines a gene expressed at the junction between the shoot apical meristem and lateral organs

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Differential regulation of JAMM domain deubiquitinating enzyme activity within the RAP80 complex

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