Discovering Motifs in Ranked Lists of DNA Sequences

Gene Ontology: tool for the unification of biology

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Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

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Transcriptional Regulatory Networks in Saccharomyces cerevisiae

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Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells

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The Polycomb group protein EZH2 directly controls DNA methylation

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Transcriptional regulatory code of a eukaryotic genome

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GO::TermFinder–open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes

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Molecular classification of cutaneous malignant melanoma by gene expression profiling

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Genome-Wide Location and Function of DNA Binding Proteins

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Control of Pancreas and Liver Gene Expression by HNF Transcription Factors

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Molecular and genetic properties of tumors associated with local immune cytolytic activity

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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

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Host microbiota constantly control maturation and function of microglia in the CNS

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Microglia development follows a stepwise program to regulate brain homeostasis

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Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

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Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span

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The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight

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RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

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Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

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Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

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Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

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DC isoketal-modified proteins activate T cells and promote hypertension

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Abundant Pleiotropy in Human Complex Diseases and Traits

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Morphometric Similarity Networks Detect Microscale Cortical Organization and Predict Inter-Individual Cognitive Variation

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The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids

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A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

Singer, M., Wang, C., Cong, L., Marjanovic, N. D., Kowalczyk, M. S., Zhang, H., Nyman, J., Sakuishi, K., Kurtuluş, S., Gennert, D. G., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.052 · Cited by 422

A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging

Xiao, H., Jedrychowski, M. P., Schweppe, D. K., Huttlin, E. L., Yu, Q., Heppner, D. E., Li, J., Long, J., Mills, E. L., Szpyt, J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.012 · Cited by 412

Developmental programming of CpG island methylation profiles in the human genome

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The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epithelia

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Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

Benayoun, B. A., Pollina, E. A., Singh, P. P., Mahmoudi, S., Harel, I., Casey, K. M., Dulken, B. W., Kundaje, A., & Brunet, A. (2019) · Genome Research · doi:10.1101/gr.240093.118 · Cited by 360

A cellular and spatial map of the choroid plexus across brain ventricles and ages

Dani, N., Herbst, R. H., McCabe, C., Green, G. S., Kaiser, K., Head, J. P., Cui, J., Shipley, F. B., Jang, A., Dionne, D., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.003 · Cited by 388

Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity

Li, J., Casteels, T., Frogne, T., Ingvorsen, C., Honoré, C., Courtney, M. L., Huber, K., Schmitner, N., Kimmel, R. A., Romanov, R. A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.010 · Cited by 397

The genomic landscape of nasopharyngeal carcinoma

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Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8+ T Cell-Derived Interferon-γ

Liu, C., Chikina, M. D., Deshpande, R., Menk, A. V., Wang, T., Tabib, T., Brunazzi, E. A., Vignali, K. M., Sun, M., Stolz, D. B., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.06.017 · Cited by 347

The Fine-Scale and Complex Architecture of Human Copy-Number Variation

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Transcriptomic and cellular decoding of regional brain vulnerability to neurogenetic disorders

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DNA methylation profiles of human active and inactive X chromosomesPreprint

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miRNA-mRNA Integrated Analysis Reveals Roles for miRNAs in Primary Breast Tumors

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The Mitochondrial-Encoded Peptide MOTS-c Translocates to the Nucleus to Regulate Nuclear Gene Expression in Response to Metabolic Stress

Kim, K. H., Son, J. M., Benayoun, B. A., & Lee, C. D. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.06.008 · Cited by 318

Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding

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SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples

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pH-gated succinate secretion regulates muscle remodeling in response to exercise

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Detecting microRNA binding and siRNA off-target effects from expression data

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Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice

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Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner

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The transcriptional landscape of αβ T cell differentiation

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Blocking immunoinhibitory receptor LILRB2 reprograms tumor-associated myeloid cells and promotes antitumor immunity

Chen, H.-M., van der Touw, W., Wang, Y. S., Kang, K., Mai, S., Zhang, J., Alsina‐Beauchamp, D., Duty, J. A., Mungamuri, S. K., Zhang, B., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci97570 · Cited by 254

Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo

Finkbeiner, S. R., Hill, D. R., Altheim, C. H., Dedhia, P. H., Taylor, M. J., Tsai, Y.-H., Chin, A. M., Mahé, M. M., Watson, C. L., Freeman, J. J., et al. (2015) · Stem Cell Reports · doi:10.1016/j.stemcr.2015.04.010 · Cited by 260

ASCL1 reprograms mouse Müller glia into neurogenic retinal progenitors

Pollak, J., Wilken, M. S., Ueki, Y., Cox, K. E., Sullivan, J., Taylor, R. J., Levine, E. M., & Reh, T. A. (2013) · Development · doi:10.1242/dev.091355 · Cited by 253

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification

Nicetto, D., Donahue, G., Jain, T., Peng, T., Sidoli, S., Sheng, L., Montavon, T., Becker, J. S., Grindheim, J. M., Blahnik, K. R., et al. (2019) · Science · doi:10.1126/science.aau0583 · Cited by 240

A Vertebrate Polycomb Response Element Governs Segmentation of the Posterior Hindbrain

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Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model

Kasendra, M. J., Luc, R., Yin, J., Manatakis, D. V., Kulkarni, G., Lucchesi, C., Sliz, J. D., Apostolou, A. P., Sunuwar, L., Obrigewitch, J., et al. (2020) · eLife · doi:10.7554/elife.50135 · Cited by 234

Gene transcription profiles associated with inter-modular hubs and connection distance in human functional magnetic resonance imaging networks

Vértes, P. E., Rittman, T., Whitaker, K. J., Romero-García, R., Váša, F., Kitzbichler, M. G., Wagstyl, K., Fonagy, P., Dolan, R. J., Jones, P. B., et al. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0362 · Cited by 206

MoMo: discovery of statistically significant post-translational modification motifs

Cheng, A., Grant, C. E., Noble, W. S., & Bailey, T. L. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty1058 · Cited by 204

The Repertoire of Serous Ovarian Cancer Non-genetic Heterogeneity Revealed by Single-Cell Sequencing of Normal Fallopian Tube Epithelial Cells

Hu, Z., Artibani, M., Alsaadi, A., Wietek, N. C., Morotti, M., Shi, T., Zhong, Z., González, L. S., El-Sahhar, S., Carrami, E. M., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.01.003 · Cited by 195

VDAC2 enables BAX to mediate apoptosis and limit tumor development

Chin, H. S., Li, M. X., Tan, I. K. L., Ninnis, R. L., Reljic, B., Scicluna, K., Dagley, L. F., Sandow, J. J., Kelly, G. L., Samson, A. L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07309-4 · Cited by 196

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

Hernando-Herraez, I., Prado-Martinez, J., Garg, P., Fernández-Callejo, M., Heyn, H., Hvilsom, C., Navarro, A., Esteller, M., Sharp, A. J., & Marquès‐Bonet, T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003763 · Cited by 206

Computational epigenetics

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A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data

DeGiorgio, M., Lohmueller, K. E., & Nielsen, R. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004561 · Cited by 179

Genome-Wide DNA Methylation Profiling Reveals Epigenetic Changes in the Rat Nucleus Accumbens Associated With Cross-Generational Effects of Adolescent THC Exposure

Watson, C. T., Szutorisz, H., Garg, P., Martin, Q., Landry, J. A., Sharp, A. J., & Hurd, Y. L. (2015) · Neuropsychopharmacology · doi:10.1038/npp.2015.155 · Cited by 185

scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells

Tegowski, M., Flamand, M. N., & Meyer, K. D. (2022) · Molecular Cell · doi:10.1016/j.molcel.2021.12.038 · Cited by 185

Brain Endothelial- and Epithelial-Specific Interferon Receptor Chain 1 Drives Virus-Induced Sickness Behavior and Cognitive Impairment

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Identifying drug targets in tissues and whole blood with thermal-shift profiling

Perrin, J., Werner, T., Kurzawa, N., Rutkowska, A., Childs, D. D., Kalxdorf, M., Poeckel, D., Stonehouse, E., Strohmer, K., Heller, B., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0388-4 · Cited by 178

Stability and aggregation of ranked gene lists

Boulesteix, A., & Slawski, M. (2009) · Briefings Bioinform. · doi:10.1093/bib/bbp034 · Cited by 192

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

Gutiérrez‐Arcelus, M., Teslovich, N. C., Mola, A. R., Polidoro, R. B., Nathan, A., Kim, H., Hannes, S. K., Slowikowski, K., Watts, G. F. M., Korsunsky, I., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08604-4 · Cited by 168

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination

Braten, O., Livneh, I., Ziv, T., Admon, A., Kehat, I., Caspi, L. H., Gonen, H., Bercovich, B., Godzik, A., Jahandideh, S. S., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1608644113 · Cited by 173

Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity

Payen, V. L., Lavergne, A., Alevra Sarika, N., Colonval, M., Karim, L., Deckers, M., Najimi, M., Coppieters, W., Charloteaux, B., Sokal, E. M., et al. (2021) · JHEP Reports · doi:10.1016/j.jhepr.2021.100278 · Cited by 160

Cancer cells enter dormancy after cannibalizing mesenchymal stem/stromal cells (MSCs)

Bartosh, T. J., Ullah, M., Zeitouni, S., Beaver, J., & Prockop, D. J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612290113 · Cited by 169

PASTAA: identifying transcription factors associated with sets of co-regulated genes

Roider, H. G., Manke, T., O'Keeffe, S., Vingron, M., & Haas, S. A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btn627 · Cited by 154

Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis

Lee, B., Bhinge, A., & Iyer, V. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1313 · Cited by 157

Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression

Marttila, S., Kananen, L., Häyrynen, S., Jylhävä, J., Nevalainen, T., Hervonen, A., Jylhä, M. K., Nykter, M., & Hurme, M. (2015) · BMC Genomics · doi:10.1186/s12864-015-1381-z · Cited by 154

Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation

Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel, S. D., Kolm, N., Breden, F. J., Viçoso, B., & Mank, J. E. (2017) · Nature Communications · doi:10.1038/ncomms14251 · Cited by 148

Four glial cells regulate ER stress resistance and longevity via neuropeptide signaling in C. elegans

Frakes, A. E., Metcalf, M. G., Tronnes, S. U., Bar‐Ziv, R., Durieux, J., Gildea, H. K., Kandahari, N., Monshietehadi, S., & Dillin, A. G. (2020) · Science · doi:10.1126/science.aaz6896 · Cited by 146

Identification of Driver and Passenger DNA Methylation in Cancer by Epigenomic Analysis

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kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

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Coordinated Metabolic Transitions During Drosophila Embryogenesis and the Onset of Aerobic Glycolysis

Tennessen, J. M., Bertagnolli, N. M., Evans, J. M., Sieber, M., Cox, J. E., & Thummel, C. S. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.010652 · Cited by 141

Transcriptome Profiling of the Murine Testis during the First Wave of Spermatogenesis

Laiho, A., Kotaja, N., Gyenesei, A., & Sironen, A. I. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061558 · Cited by 138

Curcumin mediates oxaliplatin-acquired resistance reversion in colorectal cancer cell lines through modulation of CXC-Chemokine/NF-κB signalling pathway

de Porras, V. R., Bystrup, S., Martínez‐Cardús, A., Pluvinet, R., Sumoy, L., Howells, L. M., James, M. I., Iwuji, C., Manzano, J. L., Layos, L., et al. (2016) · Scientific Reports · doi:10.1038/srep24675 · Cited by 136

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DAZL Limits Pluripotency, Differentiation, and Apoptosis in Developing Primordial Germ Cells

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