WebLogo: A Sequence Logo Generator: Figure 1

In vivo genome editing using Staphylococcus aureus Cas9

Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., et al. (2015) · Nature · doi:10.1038/nature14299 · Cited by 2,687

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

Abudayyeh, O. O., Gootenberg, J. S., Konermann, S., Joung, J., Slaymaker, I. M., Cox, D. B. T., Shmakov, S., Makarova, K. S., Semenova, E., Minakhin, L., et al. (2016) · Science · doi:10.1126/science.aaf5573 · Cited by 2,336

Quantifying similarity between motifs

Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L., & Noble, W. S. (2007) · Genome Biology · doi:10.1186/gb-2007-8-2-r24 · Cited by 2,058

Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation

Liu, S., Cai, X., Wu, J., Cong, Q., Chen, X., Li, T., Du, F., Ren, J., Wu, Y.-T., Grishin, N. V., et al. (2015) · Science · doi:10.1126/science.aaa2630 · Cited by 1,927

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

Hu, J. H., Miller, S. M., Geurts, M. H., Tang, W., Chen, L., Sun, N., Zeina, C. M., Gao, X., Rees, H. A., Lin, Z., et al. (2018) · Nature · doi:10.1038/nature26155 · Cited by 1,552

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1838 · Cited by 1,126

Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells

Chu, C. T., Ji, J., Dagda, R. K., Jiang, J. F., Tyurina, Y. Y., Kapralov, A. A., Tyurin, V. A., Yanamala, N., Shrivastava, I. H., Mohammadyani, D., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2837 · Cited by 1,083

5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader

Yang, X., Yang, Y., Sun, B.-F., Chen, Y.-S., Xu, J.-W., Lai, W.-Y., Li, A., Wang, X., Bhattarai, D. P., Xiao, W., et al. (2017) · Cell Research · doi:10.1038/cr.2017.55 · Cited by 1,062

Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways

Palmieri, M., Impey, S., Kang, H., di Ronza, A., Pelz, C., Sardiello, M., & Ballabio, A. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr306 · Cited by 1,022

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

Janky, R., Verfaillie, A., Imrichová, H., Van de Sande, B., Standaert, L., Christiaens, V., Hulselmans, G., Herten, K., Naval Sanchez, M., Potier, D., et al. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003731 · Cited by 900

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944

The Human Mitochondrial Transcriptome

Mercer, T. R., Neph, S., Dinger, M. E., Crawford, J., Smith, M. A., Shearwood, A.-M. J., Haugen, E., Bracken, C. P., Rackham, O., Stamatoyannopoulos, J. A., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.051 · Cited by 905

AMPK: An Energy-Sensing Pathway with Multiple Inputs and Outputs

Hardie, D. G., Schaffer, B. E., & Brunet, A. (2016) · Trends in Cell Biology · doi:10.1016/j.tcb.2015.10.013 · Cited by 859

Modulating Hox gene functions during animal body patterning

Pearson, J. C., Lemons, D., & McGinnis, W. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1726 · Cited by 879

Nascent transcript sequencing visualizes transcription at nucleotide resolution

Churchman, L. S., & Weissman, J. S. (2011) · Nature · doi:10.1038/nature09652 · Cited by 823

Large-scale phosphorylation analysis of mouse liver

Villén, J., Beausoleil, S. A., Gerber, S. A., & Gygi, S. P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609836104 · Cited by 730

RBPDB: a database of RNA-binding specificities

Cook, K. B., Kazan, H., Zuberi, K., Morris, Q., & Hughes, T. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1069 · Cited by 638

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R. M., & Sidow, A. (2008) · Nature Methods · doi:10.1038/nmeth.1246 · Cited by 695

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

Grünewald, J., Zhou, R., Garcia, S. P., Iyer, S., Lareau, C. A., Aryee, M. J., & Joung, J. K. (2019) · Nature · doi:10.1038/s41586-019-1161-z · Cited by 663

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

Yosef, I., Goren, M. G., & Qimron, U. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks216 · Cited by 655

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Smargon, A. A., Cox, D. B. T., Pyzocha, N. K., Zheng, K., Slaymaker, I. M., Gootenberg, J. S., Abudayyeh, O. A., Essletzbichler, P., Shmakov, S., Makarova, K. S., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.023 · Cited by 575

Global analysis of protein folding using massively parallel design, synthesis, and testing

Rocklin, G. J., Chidyausiku, T. M., Goreshnik, I., Ford, A., Houliston, S., Lemak, A., Carter, L., Ravichandran, R., Mulligan, V. K., Chevalier, A., et al. (2017) · Science · doi:10.1126/science.aan0693 · Cited by 501

The expanding universe of p53 targets

Menendez, D., Inga, A., & Resnick, M. A. (2009) · Nature Reviews Cancer · doi:10.1038/nrc2730 · Cited by 568

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

Dominguez, D., Freese, P., Alexis, M. S., Su, A., Hochman, M., Palden, T., Bazile, C., Lambert, N. J., Van Nostrand, E. L., Pratt, G. A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.001 · Cited by 562

Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome

Xie, W., Barr, C. L., Kim, A., Yue, F., Lee, A. Y., Eubanks, J., Dempster, E. L., & Ren, B. (2012) · Cell · doi:10.1016/j.cell.2011.12.035 · Cited by 543

Quantitative Phosphoproteomics Reveal mTORC1 Activates de Novo Pyrimidine Synthesis

Robitaille, A. M., Christen, S., Shimobayashi, M., Cornu, M., Fava, L. L., Moes, S., Prescianotto-Baschong, C., Sauer, U., Jenoe, P., & Hall, M. N. (2013) · Science · doi:10.1126/science.1228771 · Cited by 525

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

Angermueller, C., Lee, H. J., Reik, W., & Stegle, O. (2017) · Genome Biology · doi:10.1186/s13059-017-1189-z · Cited by 536

De novo design of potent and selective mimics of IL-2 and IL-15

Silva, D.-A., Yu, S., Ulge, U. Y., Spangler, J. B., Jude, K. M., Labão-Almeida, C., Ali, L. R., Quijano-Rubio, A., Ruterbusch, M., Leung, I., et al. (2019) · Nature · doi:10.1038/s41586-018-0830-7 · Cited by 531

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

Zhou, C., Sun, Y., Yan, R., Liu, Y., Zuo, E., Gu, C., Han, L., Wei, Y., Hu, X., Zeng, R., et al. (2019) · Nature · doi:10.1038/s41586-019-1314-0 · Cited by 482

Identification of Novel Mobilized Colistin Resistance Gene mcr-9 in a Multidrug-Resistant, Colistin-Susceptible Salmonella enterica Serotype Typhimurium Isolate

Carroll, L. M., Gaballa, A., Guldimann, C., Sullivan, G., Henderson, L. O., & Wiedmann, M. (2019) · mBio · doi:10.1128/mbio.00853-19 · Cited by 506

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

Noyes, M. B., Christensen, R. G., Wakabayashi, A., Stormo, G. D., Brodsky, M. H., & Wolfe, S. A. (2008) · Cell · doi:10.1016/j.cell.2008.05.023 · Cited by 452

Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors

Doman, J. L., Raguram, A., Newby, G. A., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0414-6 · Cited by 473

Alternative splicing as a source of phenotypic diversity

Wright, C. J., Smith, C. W. J., & Jiggins, C. D. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00514-4 · Cited by 454

The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers

Russler-Germain, D. A., Spencer, D. H., Young, M. A., Lamprecht, T. L., Miller, C. A., Fulton, R., Meyer, M. R., Erdmann-Gilmore, P., Townsend, R. R., Wilson, R. K., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.02.010 · Cited by 452

SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice

Palacino, J., Swalley, S. E., Song, C., Cheung, A. K., Shu, L., Zhang, X., Van Hoosear, M., Shin, Y., Chin, D. N., Keller, C. G., et al. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1837 · Cited by 432

Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease

Karvelis, T., Druteika, G., Bigelyte, G., Budre, K., Zedaveinyte, R., Silanskas, A., Kazlauskas, D., Venclovas, Č., & Siksnys, V. (2021) · Nature · doi:10.1038/s41586-021-04058-1 · Cited by 348

A new clustering of antibody CDR loop conformations

North, B., Lehmann, A., & Dunbrack, R. L. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.10.030 · Cited by 380

Selectivity determinants of GPCR–G-protein binding

Flock, T., Hauser, A. S., Lund, N., Gloriam, D. E., Balaji, S., & Babu, M. M. (2017) · Nature · doi:10.1038/nature22070 · Cited by 384

CoV-AbDab: the coronavirus antibody database

Raybould, M. I. J., Kovaltsuk, A., Marks, C., & Deane, C. M. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btaa739 · Cited by 383

Evaluation of methods for modeling transcription factor sequence specificity

DREAM5 Consortium, Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2486 · Cited by 381

Coordinated regulation of protein synthesis and degradation by mTORC1

Zhang, Y., Nicholatos, J., Dreier, J. R., Ricoult, S. J. H., Widenmaier, S. B., Hotamisligil, G. S., Kwiatkowski, D. J., & Manning, B. D. (2014) · Nature · doi:10.1038/nature13492 · Cited by 350

Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity

Nuñez, J. K., Lee, A. S. Y., Engelman, A., & Doudna, J. A. (2015) · Nature · doi:10.1038/nature14237 · Cited by 347

Hippo Signaling Regulates Microprocessor and Links Cell-Density-Dependent miRNA Biogenesis to Cancer

Mori, M., Triboulet, R., Mohseni, M., Schlegelmilch, K., Shrestha, K., Camargo, F. D., & Gregory, R. I. (2014) · Cell · doi:10.1016/j.cell.2013.12.043 · Cited by 335

Crystal structure of HIV-1 Tat complexed with human P-TEFb

Tahirov, T. H., Babayeva, N. D., Varzavand, K., Cooper, J. J., Sedore, S. C., & Price, D. H. (2010) · Nature · doi:10.1038/nature09131 · Cited by 314

IRGB10 Liberates Bacterial Ligands for Sensing by the AIM2 and Caspase-11-NLRP3 Inflammasomes

Man, S. M., Karki, R., Sasai, M., Place, D. E., Kesavardhana, S., Temirov, J., Frase, S., Zhu, Q., Malireddi, R. K. S., Kuriakose, T., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.012 · Cited by 312

STRUCTURE AND PHYSIOLOGIC FUNCTION OF THE LOW-DENSITY LIPOPROTEIN RECEPTOR

Jeon, H., & Blacklow, S. C. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.082803.133354 · Cited by 310

Landscape of tumor-infiltrating T cell repertoire of human cancers

Li, B., Li, T., Pignon, J.-C., Wang, B., Wang, J., Shukla, S. A., Dou, R., Chen, Q., Hodi, F. S., Choueiri, T. K., et al. (2016) · Nature Genetics · doi:10.1038/ng.3581 · Cited by 306

Dynamics of the skeletal muscle secretome during myoblast differentiation

Henningsen, J., Rigbolt, K. T. G., Blagoev, B., Pedersen, B. K., & Kratchmarova, I. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002113 · Cited by 303

The mechanism of retroviral integration from X-ray structures of its key intermediates

Maertens, G. N., Hare, S., & Cherepanov, P. (2010) · Nature · doi:10.1038/nature09517 · Cited by 296

High frequency of shared clonotypes in human B cell receptor repertoires

Soto, C., Bombardi, R. G., Branchizio, A., Kose, N., Matta, P., Sevy, A. M., Sinkovits, R. S., Gilchuk, P., Finn, J. A., & Crowe, J. E. (2019) · Nature · doi:10.1038/s41586-019-0934-8 · Cited by 294

Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail

Dong, J., Zost, S. J., Greaney, A. J., Starr, T. N., Dingens, A. S., Chen, E. C., Chen, R. E., Case, J. B., Sutton, R. E., Gilchuk, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00972-2 · Cited by 285

Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells

Li, M., He, Y., Dubois, W., Wu, X., Shi, J., & Huang, J. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.01.020 · Cited by 264

BRANCHED1 Promotes Axillary Bud Dormancy in Response to Shade in Arabidopsis

González-Grandío, E., Poza-Carrión, C., Sorzano, C. O. S., & Cubas, P. (2013) · The Plant Cell · doi:10.1105/tpc.112.108480 · Cited by 272

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

Lickwar, C. R., Mueller, F., Hanlon, S. E., McNally, J. G., & Lieb, J. D. (2012) · Nature · doi:10.1038/nature10985 · Cited by 241

Identification of an Acinetobacter baumannii Zinc Acquisition System that Facilitates Resistance to Calprotectin-mediated Zinc Sequestration

Hood, M. I., Mortensen, B. L., Moore, J. L., Zhang, Y., Kehl-Fie, T. E., Sugitani, N., Chazin, W. J., Caprioli, R. M., & Skaar, E. P. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1003068 · Cited by 255

Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo

De Renzis, S., Elemento, O., Tavazoie, S., & Wieschaus, E. F. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050117 · Cited by 265

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

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

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Sugimoto, Y., König, J., Hussain, S., Zupan, B., Curk, T., Frye, M., & Ule, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-r67 · Cited by 234

Comparative analysis of nanobody sequence and structure data

Mitchell, L. S., & Colwell, L. J. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25497 · Cited by 233

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs

Rosenberg, B. R., Hamilton, C. E., Mwangi, M. M., Dewell, S., & Papavasiliou, F. N. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1975 · Cited by 232

Structural Basis for Target-Directed MicroRNA Degradation

Sheu-Gruttadauria, J., Pawlica, P., Klum, S. M., Wang, S., Yario, T. A., Schirle Oakdale, N. T., Steitz, J. A., & MacRae, I. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.06.019 · Cited by 230

The evolution of combinatorial gene regulation in fungi

Tuch, B. B., Galgoczy, D. J., Hernday, A. D., Li, H., & Johnson, A. D. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060038 · Cited by 228

Quantifying the contribution of recessive coding variation to developmental disorders

Martin, H. C., Jones, W. D., McIntyre, R., Sanchez-Andrade, G., Sanderson, M., Stephenson, J. D., Jones, C. P., Handsaker, J., Gallone, G., Bruntraeger, M., et al. (2018) · Science · doi:10.1126/science.aar6731 · Cited by 201

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

Markenscoff-Papadimitriou, E., Allen, W. E., Colquitt, B. M., Goh, T., Murphy, K. K., Monahan, K., Mosley, C. P., Ahituv, N., & Lomvardas, S. (2014) · Cell · doi:10.1016/j.cell.2014.09.033 · Cited by 214

Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

Meydan, S., Marks, J., Klepacki, D., Sharma, V., Baranov, P. V., Firth, A. E., Margus, T., Kefi, A., Vázquez-Laslop, N., & Mankin, A. S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.017 · Cited by 184

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

Cenik, C., Cenik, E. S., Byeon, G. W., Grubert, F., Candille, S. I., Spacek, D., Alsallakh, B., Tilgner, H., Araya, C. L., Tang, H., et al. (2015) · Genome Research · doi:10.1101/gr.193342.115 · Cited by 208

Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

Cuperus, J. T., Groves, B., Kuchina, A., Rosenberg, A. B., Jojic, N., Fields, S., & Seelig, G. (2017) · Genome Research · doi:10.1101/gr.224964.117 · Cited by 205

Identification of AMPK Phosphorylation Sites Reveals a Network of Proteins Involved in Cell Invasion and Facilitates Large-Scale Substrate Prediction

Schaffer, B. E., Levin, R. S., Hertz, N. T., Maures, T. J., Schoof, M. L., Hollstein, P. E., Benayoun, B. A., Banko, M. R., Shaw, R. J., Shokat, K. M., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.09.009 · Cited by 184

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

Swart, E. C., Serra, V., Petroni, G., & Nowacki, M. (2016) · Cell · doi:10.1016/j.cell.2016.06.020 · Cited by 167

An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models

Reis, A. C., & Salis, H. M. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00394 · Cited by 166

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

Menschaert, G., Van Criekinge, W., Notelaers, T., Koch, A., Crappé, J., Gevaert, K., & Van Damme, P. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.027540 · Cited by 173

AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface

Homma, F., Huang, J., & van der Hoorn, R. A. L. (2023) · Nature Communications · doi:10.1038/s41467-023-41721-9 · Cited by 176

Compact RNA editors with small Cas13 proteins

Kannan, S., Altae-Tran, H., Jin, X., Madigan, V. J., Oshiro, R., Makarova, K. S., Koonin, E. V., & Zhang, F. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01030-2 · Cited by 176

Antifungal drug resistance evoked via RNAi-dependent epimutations

Calo, S., Shertz-Wall, C., Lee, S. C., Bastidas, R. J., Nicolás, F. E., Granek, J. A., Mieczkowski, P., Torres-Martínez, S., Ruiz-Vázquez, R. M., Cardenas, M. E., et al. (2014) · Nature · doi:10.1038/nature13575 · Cited by 175

Rationally designed APOBEC3B cytosine base editors with improved specificity

Jin, S., Fei, H., Zhu, Z., Luo, Y., Liu, J., Gao, S., Zhang, F., Chen, Y.-H., Wang, Y., & Gao, C. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.07.005 · Cited by 159

A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life

Haas, C. E., Rodionov, D. A., Kropat, J., Malasarn, D., Merchant, S. S., & de Crécy-Lagard, V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-470 · Cited by 159

DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity

Li, G., Iyer, B., Prasath, V. B. S., Ni, Y., & Salomonis, N. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab160 · Cited by 168

An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia

Berney, M., Greening, C., Conrad, R., Jacobs, W. R., & Cook, G. M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1407034111 · Cited by 142

The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection

Sultana, T., van Essen, D., Siol, O., Bailly-Bechet, M., Philippe, C., Zine El Aabidine, A., Pioger, L., Nigumann, P., Saccani, S., Andrau, J.-C., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.036 · Cited by 154

Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids

Lucas, L. N., Barrett, K., Kerby, R. L., Zhang, Q., Cattaneo, L. E., Stevenson, D., Rey, F. E., & Amador-Noguez, D. (2021) · mSystems · doi:10.1128/msystems.00805-21 · Cited by 168

Evolutionary primacy of sodium bioenergetics

Mulkidjanian, A. Y., Galperin, M. Y., Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2008) · Biology Direct · doi:10.1186/1745-6150-3-13 · Cited by 163

5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes

Mellén, M., Ayata, P., & Heintz, N. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708044114 · Cited by 151

Mass spectrometry for nutritional peptidomics: how to analyze food bioactives and their health effects.

Panchaud, A., Affolter, M., & Kussmann, M. (2012) · Journal of Proteomics · doi:10.1016/j.jprot.2011.12.022 · Cited by 159

Coevolution of ABC Transporters and Two-Component Regulatory Systems as Resistance Modules against Antimicrobial Peptides in Firmicutes Bacteria

Dintner, S., Staroń, A., Berchtold, E., Petri, T., Mascher, T., & Gebhard, S. (2011) · Journal of Bacteriology · doi:10.1128/jb.05175-11 · Cited by 156

Reconstitution and visualization of HIV-1 capsid-dependent replication and integration in vitro

Christensen, D. E., Ganser-Pornillos, B. K., Johnson, J. S., Pornillos, O., & Sundquist, W. I. (2020) · Science · doi:10.1126/science.abc8420 · Cited by 150

Non-photosynthetic predators are sister to red algae

Gawryluk, R. M. R., Tikhonenkov, D. V., Hehenberger, E., Husnik, F., Mylnikov, A. P., & Keeling, P. J. (2019) · Nature · doi:10.1038/s41586-019-1398-6 · Cited by 148

Global profiling of SRP interaction with nascent polypeptides.

Schibich, D., Gloge, F., Pöhner, I., Björkholm, P., Wade, R. C., von Heijne, G., Bukau, B., & Kramer, G. (2016) · Nature · doi:10.1038/nature19070 · Cited by 146

ZnuA and zinc homeostasis in Pseudomonas aeruginosa

Pederick, V. G., Eijkelkamp, B. A., Begg, S. L., Ween, M. P., McAllister, L. J., Paton, J. C., & McDevitt, C. A. (2015) · Scientific Reports · doi:10.1038/srep13139 · Cited by 138

Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics

Lemay, D. G., & Hwang, D. H. (2006) · Journal of Lipid Research · doi:10.1194/jlr.m500504-jlr200 · Cited by 143

Interpretation of deep learning in genomics and epigenomics

Talukder, A., Barham, C., Li, X., & Hu, H. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa177 · Cited by 142

Identification of Arx transcriptional targets in the developing basal forebrain

Fulp, C. T., Cho, G., Marsh, E. D., Nasrallah, I. M., Labosky, P. A., & Golden, J. A. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn271 · Cited by 138

Structural basis for retroviral integration into nucleosomes

Maskell, D. P., Renault, L., Serrao, E., Lesbats, P., Matadeen, R., Hare, S., Lindemann, D., Engelman, A. N., Costa, A., & Cherepanov, P. (2015) · Nature · doi:10.1038/nature14495 · Cited by 138

Quality control of transcription start site selection by nonsense-mediated-mRNA decay

Malabat, C., Feuerbach, F., Ma, L., Saveanu, C., & Jacquier, A. (2015) · eLife · doi:10.7554/elife.06722 · Cited by 134

Evolutionary origin and diversification of epidermal barrier proteins in amniotes

Strasser, B., Mlitz, V., Hermann, M., Rice, R. H., Eigenheer, R. A., Alibardi, L., Tschachler, E., & Eckhart, L. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu251 · Cited by 135

Functional and structural characterization of the integrase from the prototype foamy virus

Valkov, E., Gupta, S. S., Hare, S., Helander, A., Roversi, P., McClure, M., & Cherepanov, P. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn938 · Cited by 130

Molecular basis of accessible plasma membrane cholesterol recognition by the GRAM domain of GRAMD1b

Ercan, B., Naito, T., Koh, D. H. Z., Dharmawan, D., & Saheki, Y. (2021) · The EMBO Journal · doi:10.15252/embj.2020106524 · Cited by 132

Glucocorticoids and the innate immune system: crosstalk with the toll-like receptor signaling network

Chinenov, Y., & Rogatsky, I. (2007) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2007.04.014 · Cited by 133

A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan

Jones, B. C., Wood, J. G., Chang, C., Tam, A. D., Franklin, M. J., Siegel, E. R., & Helfand, S. L. (2016) · Nature Communications · doi:10.1038/ncomms13856 · Cited by 130

Candida glabrata environmental stress response involves Saccharomyces cerevisiae Msn2/4 orthologous transcription factors

Roetzer, A., Gregori, C., Jennings, A. M., Quintin, J., Ferrandon, D., Butler, G., Kuchler, K., Ammerer, G., & Schüller, C. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06301.x · Cited by 124