TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696

The Diploid Genome Sequence of an Individual Human

Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778

Improving RNA-Seq expression estimates by correcting for fragment bias

Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L., & Pachter, L. (2011) · Genome Biology · doi:10.1186/gb-2011-12-3-r22 · Cited by 1,725

Personal omics profiling reveals dynamic molecular and medical phenotypes

Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y. K., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.009 · Cited by 1,291

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., He, X., Mieczkowski, P., Grimm, S. A., Perou, C. M., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq622 · Cited by 1,193

Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability

Pattabiraman, D. R., Bierie, B., Kober, K. I., Thiru, P., Krall, J. A., Zill, C., Reinhardt, F., Tam, W. L., & Weinberg, R. A. (2016) · Science · doi:10.1126/science.aad3680 · Cited by 332

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells

Walter, M., Teissandier, A., Pérez-Palacios, R., & Bourc'his, D. (2016) · eLife · doi:10.7554/elife.11418 · Cited by 303

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

Piwecka, M., Rajewsky, N., & Rybak-Wolf, A. (2023) · Nature Reviews Neurology · doi:10.1038/s41582-023-00809-y · Cited by 320

A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1

Li, W., Hang, S., Fang, Y., Bae, S., Zhang, Y., Zhang, M., Wang, G., McCurry, M. D., Bae, M., Paik, D., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.07.013 · Cited by 306

Proteogenomic Characterization of Human Early-Onset Gastric Cancer

Mun, D.-G., Bhin, J., Kim, S., Kim, H., Jung, J. H., Jung, Y., Jang, Y. E., Park, J. M., Kim, H., Jung, Y., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2018.12.003 · Cited by 294

A distributed network for social cognition enriched for oxytocin receptors

Mitre, M., Marlin, B. J., Schiavo, J. K., Morina, E., Norden, S. E., Hackett, T. A., Aoki, C. J., Chao, M. V., & Froemke, R. C. (2016) · The Journal of Neuroscience · doi:10.1523/jneurosci.2409-15.2016 · Cited by 305

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

Rouhani, F., Kumasaka, N., de Brito, M. C., Bradley, A., Vallier, L., & Gaffney, D. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004432 · Cited by 294

The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine

Saal, L. H., Vallon-Christersson, J., Häkkinen, J., Hegardt, C., Grabau, D., Winter, C., Brueffer, C., Tang, M.-H. E., Reuterswärd, C., Schulz, R., et al. (2015) · Genome Medicine · doi:10.1186/s13073-015-0131-9 · Cited by 255

p21 produces a bioactive secretome that places stressed cells under immunosurveillance

Sturmlechner, I., Zhang, C., Sine, C. C., van Deursen, E.-J., Jeganathan, K. B., Hamada, N., Grasic, J., Friedman, D., Stutchman, J. T., Can, I., et al. (2021) · Science · doi:10.1126/science.abb3420 · Cited by 295

Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo

Shirai, C. L., Ley, J. N., White, B. S., Kim, S., Tibbitts, J., Shao, J., Ndonwi, M., Wadugu, B., Duncavage, E. J., Okeyo-Owuor, T., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.04.008 · Cited by 287

Inhibition of mTOR induces a paused pluripotent state

Bulut-Karslioglu, A., Biechele, S., Jin, H., Macrae, T. A., Hejna, M., Gertsenstein, M., Song, J. S., & Ramalho-Santos, M. (2016) · Nature · doi:10.1038/nature20578 · Cited by 283

Codon-specific translation reprogramming promotes resistance to targeted therapy

Rapino, F., Delaunay, S., Rambow, F., Zhou, Z., Tharun, L., De Tullio, P., Sin, O., Shostak, K., Schmitz, S., Piepers, J., et al. (2018) · Nature · doi:10.1038/s41586-018-0243-7 · Cited by 271

CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas

Jiang, Y., Ortega-Molina, A., Geng, H., Ying, H.-Y., Hatzi, K., Parsa, S., McNally, D., Wang, L., Doane, A. S., Agirre, X., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0975 · Cited by 278

TGFβ inhibition restores a regenerative response in acute liver injury by suppressing paracrine senescence

Bird, T. G., Müller, M., Boulter, L., Vincent, D. F., Ridgway, R. A., Lopez-Guadamillas, E., Lu, W.-Y., Jamieson, T., Govaere, O., Campbell, A. D., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aan1230 · Cited by 261

High-Content Screening in hPSC-Neural Progenitors Identifies Drug Candidates that Inhibit Zika Virus Infection in Fetal-like Organoids and Adult Brain

Zhou, T., Tan, L., Cederquist, G. Y., Fan, Y., Hartley, B. J., Mukherjee, S., Tomishima, M., Brennand, K. J., Zhang, Q., Schwartz, R. E., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.06.017 · Cited by 263

BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure

Duan, Q., McMahon, S., Anand, P., Shah, H., Thomas, S., Salunga, H. T., Huang, Y., Zhang, R., Sahadevan, A., Lemieux, M. E., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aah5084 · Cited by 262

Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer

Woolston, A., Khan, K., Spain, G., Barber, L. J., Griffiths, B., Gonzalez-Exposito, R., Hornsteiner, L., Punta, M., Patil, Y., Newey, A., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.05.013 · Cited by 254

PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells

Georgilis, A., Klotz, S., Hanley, C. J., Herranz, N., Weirich, B., Morancho, B., Leote, A. C., D'Artista, L., Gallage, S., Seehawer, M., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.06.007 · Cited by 237

Social deficits in Shank3-deficient mouse models of autism are rescued by histone deacetylase (HDAC) inhibition

Qin, L., Ma, K., Wang, Z.-J., Hu, Z., Matas, E., Wei, J., & Yan, Z. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0110-8 · Cited by 240

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance

Hinohara, K., Wu, H.-J., Vigneau, S., McDonald, T. O., Igarashi, K. J., Yamamoto, K. N., Madsen, T., Fassl, A., Egri, S. B., Papanastasiou, M., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.10.014 · Cited by 255

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation

Kelmer Sacramento, E., Kirkpatrick, J. M., Mazzetto, M., Baumgart, M., Bartolome, A., Di Sanzo, S., Caterino, C., Sanguanini, M., Papaevgeniou, N., Lefaki, M., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209596 · Cited by 236

Bromodomain Protein BRD4 Is a Transcriptional Repressor of Autophagy and Lysosomal Function

Sakamaki, J.-I., Wilkinson, S., Hahn, M., Tasdemir, N., O’Prey, J., Clark, W., Hedley, A., Nixon, C., Long, J. S., New, M., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.027 · Cited by 249

Distributed hepatocytes expressing telomerase repopulate the liver in homeostasis and injury

Lin, S., Nascimento, E. M., Gajera, C. R., Chen, L., Neuhöfer, P., Garbuzov, A., Wang, S., & Artandi, S. E. (2018) · Nature · doi:10.1038/s41586-018-0004-7 · Cited by 241

PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation

Cruz-Molina, S., Respuela, P., Tebartz, C., Kolovos, P., Nikolic, M., Fueyo, R., van Ijcken, W. F. J., Grosveld, F., Frommolt, P., Bazzi, H., et al. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.02.004 · Cited by 240

Frequent loss of heterozygosity in CRISPR-Cas9–edited early human embryos

Alanis-Lobato, G., Zohren, J., McCarthy, A., Fogarty, N. M. E., Kubikova, N., Hardman, E., Greco, M., Wells, D., Turner, J. M. A., & Niakan, K. K. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004832117 · Cited by 234

Glioblastoma-targeted CD4+ CAR T cells mediate superior antitumor activity

Wang, D., Aguilar, B., Starr, R., Alizadeh, D., Brito, A., Sarkissian, A., Ostberg, J. R., Forman, S. J., & Brown, C. E. (2018) · JCI Insight · doi:10.1172/jci.insight.99048 · Cited by 233

A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription

Platanitis, E., Demiroz, D., Schneller, A., Fischer, K., Capelle, C., Hartl, M., Gossenreiter, T., Müller, M., Novatchkova, M., & Decker, T. (2019) · Nature Communications · doi:10.1038/s41467-019-10970-y · Cited by 233

Analysis of the brain mural cell transcriptome

He, L., Vanlandewijck, M., Raschperger, E., Andaloussi Mäe, M., Jung, B., Lebouvier, T., Ando, K., Hofmann, J., Keller, A., & Betsholtz, C. (2016) · Scientific Reports · doi:10.1038/srep35108 · Cited by 233

Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis

Churko, J. M., Garg, P., Treutlein, B., Venkatasubramanian, M., Wu, H., Lee, J., Wessells, Q. N., Chen, S.-Y., Chen, W.-Y., Chetal, K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07333-4 · Cited by 207

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Imrichová, H., Hulselmans, G., Kalender Atak, Z., Potier, D., & Aerts, S. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv395 · Cited by 202

A Role for p53 in the Adaptation to Glutamine Starvation through the Expression of SLC1A3

Tajan, M., Hock, A. K., Blagih, J., Robertson, N. A., Labuschagne, C. F., Kruiswijk, F., Humpton, T. J., Adams, P. D., & Vousden, K. H. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.07.005 · Cited by 230

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

Mall, M., Kareta, M. S., Chanda, S., Ahlenius, H., Perotti, N., Zhou, B., Grieder, S. D., Ge, X., Drake, S., Euong Ang, C., et al. (2017) · Nature · doi:10.1038/nature21722 · Cited by 225

Smooth Muscle Enriched Long Noncoding RNA ( SMILR ) Regulates Cell Proliferation

Ballantyne, M. D., Pinel, K., Dakin, R., Vesey, A. T., Diver, L., Mackenzie, R., Garcia, R., Welsh, P., Sattar, N., Hamilton, G., et al. (2016) · Circulation · doi:10.1161/circulationaha.115.021019 · Cited by 223

Identification and Quantification of Proteoforms by Mass Spectrometry

Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., et al. (2019) · PROTEOMICS · doi:10.1002/pmic.201800361 · Cited by 209

Lats1/2 Sustain Intestinal Stem Cells and Wnt Activation through TEAD-Dependent and Independent Transcription

Li, Q., Sun, Y., Jarugumilli, G. K., Liu, S., Dang, K., Cotton, J. L., Xiol, J., Chan, P. Y., DeRan, M., Ma, L., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.03.002 · Cited by 180

Widespread Inducible Transcription Downstream of Human Genes

Vilborg, A., Passarelli, M. C., Yario, T. A., Tycowski, K. T., & Steitz, J. A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.06.016 · Cited by 206

The myokine decorin is regulated by contraction and involved in muscle hypertrophy

Kanzleiter, T., Rath, M., Görgens, S. W., Jensen, J., Tangen, D. S., Kolnes, A. J., Kolnes, K. J., Lee, S., Eckel, J., Schürmann, A., et al. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.06.123 · Cited by 209

Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance

Chen, K., Luan, X., Liu, Q., Wang, J., Chang, X., Snijders, A. M., Mao, J.-H., Secombe, J., Dan, Z., Chen, J.-H., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.02.003 · Cited by 208

Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel

Dey, N., Wagner, V. E., Blanton, L. V., Cheng, J., Fontana, L., Haque, R., Ahmed, T., & Gordon, J. I. (2015) · Cell · doi:10.1016/j.cell.2015.08.059 · Cited by 195

Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression

McCoy, R. C., Wakefield, J., & Akey, J. M. (2017) · Cell · doi:10.1016/j.cell.2017.01.038 · Cited by 200

Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease

Warren, C. R., O’Sullivan, J. F., Friesen, M., Becker, C. E., Zhang, X., Liu, P., Wakabayashi, Y., Morningstar, J. E., Shi, X., Choi, J., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.01.010 · Cited by 191

Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling

Herz, H.-M., Morgan, M., Gao, X., Jackson, J., Rickels, R., Swanson, S. K., Florens, L., Washburn, M. P., Eissenberg, J. C., & Shilatifard, A. (2014) · Science · doi:10.1126/science.1255104 · Cited by 199

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder

Wu, Y. E., Parikshak, N. N., Belgard, T. G., & Geschwind, D. H. (2016) · Nature Neuroscience · doi:10.1038/nn.4373 · Cited by 195

The Sense of Smell Impacts Metabolic Health and Obesity

Riera, C. E., Tsaousidou, E., Halloran, J., Follett, P., Hahn, O., Pereira, M. M. A., Ruud, L. E., Alber, J., Tharp, K., Anderson, C. M., et al. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.06.015 · Cited by 191

Multiparameter functional diversity of human C2H2 zinc finger proteins

Schmitges, F. W., Radovani, E., Najafabadi, H. S., Barazandeh, M., Campitelli, L. F., Yin, Y., Jolma, A., Zhong, G., Guo, H., Kanagalingam, T., et al. (2016) · Genome Research · doi:10.1101/gr.209643.116 · Cited by 193

Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression

Contrepois, K., Coudereau, C., Benayoun, B. A., Schuler, N., Roux, P.-F., Bischof, O., Courbeyrette, R., Carvalho, C., Thuret, J.-Y., Ma, Z., et al. (2017) · Nature Communications · doi:10.1038/ncomms14995 · Cited by 191

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

Love, M. I., Hogenesch, J. B., & Irizarry, R. A. (2016) · Nature Biotechnology · doi:10.1038/nbt.3682 · Cited by 186

Neuronal CRTC-1 governs systemic mitochondrial metabolism and lifespan via a catecholamine signal

Burkewitz, K., Morantte, I., Weir, H. J. M., Yeo, R., Zhang, Y., Huynh, F. K., Ilkayeva, O. R., Hirschey, M. D., Grant, A. R., & Mair, W. B. (2015) · Cell · doi:10.1016/j.cell.2015.02.004 · Cited by 186

Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses

Pulko, V., Davies, J. S., Martinez, C., Lanteri, M. C., Busch, M. P., Diamond, M. S., Knox, K., Bush, E. C., Sims, P. A., Sinari, S., et al. (2016) · Nature Immunology · doi:10.1038/ni.3483 · Cited by 175

Astrocyte senescence promotes glutamate toxicity in cortical neurons

Limbad, C., Oron, T. R., Alimirah, F., Davalos, A. R., Tracy, T. E., Gan, L., Desprez, P.-Y., & Campisi, J. (2020) · PLOS ONE · doi:10.1371/journal.pone.0227887 · Cited by 183

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

A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma

Yang, W., Feng, Y., Zhou, J., Cheung, O. K.-W., Cao, J., Wang, J., Tang, W., Tu, Y., Xu, L., Wu, F., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.aaz6804 · Cited by 172

Expression profiling of budding cells in colorectal cancer reveals an EMT-like phenotype and molecular subtype switching

De Smedt, L., Palmans, S., Andel, D., Govaere, O., Boeckx, B., Smeets, D., Galle, E., Wouters, J., Barras, D., Suffiotti, M., et al. (2017) · British Journal of Cancer · doi:10.1038/bjc.2016.382 · Cited by 163

Nutrient sensing modulates malaria parasite virulence

Mancio-Silva, L., Slavic, K., Grilo Ruivo, M. T., Grosso, A. R., Modrzynska, K. K., Vera, I. M., Sales-Dias, J., Gomes, A. R., MacPherson, C. R., Crozet, P., et al. (2017) · Nature · doi:10.1038/nature23009 · Cited by 169

Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice

Aoki, R., Onuki, M., Hattori, K., Ito, M., Yamada, T., Kamikado, K., Kim, Y.-G., Nakamoto, N., Kimura, I., Clarke, J. M., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01125-7 · Cited by 167

The acinar differentiation determinant PTF1A inhibits initiation of pancreatic ductal adenocarcinoma

Krah, N. M., De La O, J.-P., Swift, G. H., Hoang, C. Q., Willet, S. G., Chen Pan, F., Cash, G. M., Bronner, M. P., Wright, C. V., MacDonald, R. J., et al. (2015) · eLife · doi:10.7554/elife.07125 · Cited by 166

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes

Krueger, F., & Andrews, S. R. (2016) · F1000Research · doi:10.12688/f1000research.9037.2 · Cited by 163

The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s

Tunbak, H., Enriquez-Gasca, R., Tie, C. H. C., Gould, P. A., Mlcochova, P., Gupta, R. K., Fernandes, L., Holt, J., van der Veen, A. G., Giampazolias, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19170-5 · Cited by 162

Origins of De Novo Genes in Human and Chimpanzee

Ruiz-Orera, J., Hernandez-Rodriguez, J., Chiva, C., Sabidó, E., Kondova, I., Bontrop, R., Marqués-Bonet, T., & Albà, M. M. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005721 · Cited by 160

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Pan, W.-H., Sommer, F., Falk-Paulsen, M., Ulas, T., Best, L., Fazio, A., Kachroo, P., Luzius, A., Jentzsch, M., Rehman, A., et al. (2018) · Genome Medicine · doi:10.1186/s13073-018-0534-5 · Cited by 157

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

Jaffe, A. E., Shin, J., Collado-Torres, L., Leek, J. T., Tao, R., Li, C., Gao, Y., Jia, Y., Maher, B. J., Hyde, T. M., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3898 · Cited by 156

Transcriptomic Analysis of Vulvovaginal Candidiasis Identifies a Role for the NLRP3 Inflammasome

Bruno, V. M., Shetty, A. C., Yano, J., Fidel, P. L., Noverr, M. C., & Peters, B. M. (2015) · mBio · doi:10.1128/mbio.00182-15 · Cited by 155

Aging impairs both primary and secondary RIG-I signaling for interferon induction in human monocytes

Molony, R. D., Nguyen, J. T., Kong, Y., Montgomery, R. R., Shaw, A. C., & Iwasaki, A. (2017) · Science Signaling · doi:10.1126/scisignal.aan2392 · Cited by 154

The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2

Kovalski, J. R., Bhaduri, A., Zehnder, A. M., Neela, P. H., Che, Y., Wozniak, G. G., & Khavari, P. A. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.12.001 · Cited by 154

Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response

Uchimura, Y., Fuhrer, T., Li, H., Lawson, M. A., Zimmermann, M., Yilmaz, B., Zindel, J., Ronchi, F., Sorribas, M., Hapfelmeier, S., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.08.004 · Cited by 153

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso, A. R., Leite, A. P., Carvalho, S., Matos, M. R., Martins, F. B., Vítor, A. C., Desterro, J. M., Carmo-Fonseca, M., & de Almeida, S. F. (2015) · eLife · doi:10.7554/elife.09214 · Cited by 152

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification

Zhao, S., & Zhang, B. (2015) · BMC Genomics · doi:10.1186/s12864-015-1308-8 · Cited by 130

C9orf72 deficiency promotes microglial-mediated synaptic loss in aging and amyloid accumulation

Lall, D., Lorenzini, I., Mota, T. A., Bell, S., Mahan, T. E., Ulrich, J. D., Davtyan, H., Rexach, J. E., Muhammad, A. K. M. G., Shelest, O., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.05.020 · Cited by 147

Click chemistry enables preclinical evaluation of targeted epigenetic therapies

Tyler, D. S., Vappiani, J., Cañeque, T., Lam, E. Y. N., Ward, A., Gilan, O., Chan, Y.-C., Hienzsch, A., Rutkowska, A., Werner, T., et al. (2017) · Science · doi:10.1126/science.aal2066 · Cited by 146

Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development

Vallecillo-García, P., Orgeur, M., vom Hofe-Schneider, S., Stumm, J., Kappert, V., Ibrahim, D. M., Börno, S. T., Hayashi, S., Relaix, F., Hildebrandt, K., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01120-3 · Cited by 126

Combined Mutation of Apc, Kras , and Tgfbr2 Effectively Drives Metastasis of Intestinal Cancer

Sakai, E., Nakayama, M., Oshima, H., Kouyama, Y., Niida, A., Fujii, S., Ochiai, A., Nakayama, K. I., Mimori, K., Suzuki, Y., et al. (2018) · Cancer Research · doi:10.1158/0008-5472.can-17-3303 · Cited by 133

Insights into the biogenesis and potential functions of exonic circular RNA

Ragan, C., Goodall, G. J., Shirokikh, N. E., & Preiss, T. (2019) · Scientific Reports · doi:10.1038/s41598-018-37037-0 · Cited by 137

qSVA framework for RNA quality correction in differential expression analysis

Jaffe, A. E., Tao, R., Norris, A. L., Kealhofer, M., Nellore, A., Shin, J. H., Kim, D., Jia, Y., Hyde, T. M., Kleinman, J. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617384114 · Cited by 114

Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia

Swarup, V., Hinz, F. I., Rexach, J. E., Noguchi, K.-I., Toyoshiba, H., Oda, A., Hirai, K., Sarkar, A., Seyfried, N. T., Cheng, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-018-0223-3 · Cited by 136

An organ boundary‐enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation

Tian, C., Zhang, X., He, J., Yu, H., Wang, Y., Shi, B., Han, Y., Wang, G., Feng, X., Zhang, C., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145470 · Cited by 133

Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris

Muñoz, J. F., Welsh, R. M., Shea, T., Batra, D., Gade, L., Howard, D., Rowe, L. A., Meis, J. F., Litvintseva, A. P., & Cuomo, C. A. (2021) · Genetics · doi:10.1093/genetics/iyab029 · Cited by 125

Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma

Babaian, A., Romanish, M. T., Gagnier, L., Kuo, L. Y., Karimi, M. M., Steidl, C., & Mager, D. L. (2016) · Oncogene · doi:10.1038/onc.2015.308 · Cited by 121

Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy

Liang, K., Smith, E. R., Aoi, Y., Stoltz, K. L., Katagi, H., Woodfin, A. R., Rendleman, E. J., Marshall, S. A., Murray, D. C., Wang, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.027 · Cited by 124

Role of Hydrophobins in Aspergillus fumigatus

Valsecchi, I., Dupres, V., Stephen-Victor, E., Guijarro, J., Gibbons, J., Beau, R., Bayry, J., Coppee, J.-Y., Lafont, F., Latgé, J.-P., et al. (2017) · Journal of Fungi · doi:10.3390/jof4010002 · Cited by 123

Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors

Gonzalez, C., Sims, J. S., Hornstein, N., Mela, A., Garcia, F., Lei, L., Gass, D. A., Amendolara, B., Bruce, J. N., Canoll, P., et al. (2014) · Journal of Neuroscience · doi:10.1523/jneurosci.0084-14.2014 · Cited by 116

Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients

Prudencio, M., Gonzales, P. K., Cook, C. N., Gendron, T. F., Daughrity, L. M., Song, Y., Ebbert, M. T. W., van Blitterswijk, M., Zhang, Y.-J., Jansen-West, K., et al. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx233 · Cited by 122

A comprehensive study of the genetic impact of rare variants in SORL1 in European early-onset Alzheimer’s disease

Verheijen, J., Van den Bossche, T., van der Zee, J., Engelborghs, S., Sanchez-Valle, R., Lladó, A., Graff, C., Thonberg, H., Pastor, P., Ortega-Cubero, S., et al. (2016) · Acta Neuropathologica · doi:10.1007/s00401-016-1566-9 · Cited by 112

3′ UTR lengthening as a novel mechanism in regulating cellular senescence.

Chen, M., Lyu, G., Han, M., Nie, H., Shen, T., Chen, W., Niu, Y., Song, Y., Li, X., Li, H., et al. (2018) · Genome Research · doi:10.1101/gr.224451.117 · Cited by 111

Dorsal tegmental dopamine neurons gate associative learning of fear

Groessl, F., Munsch, T., Meis, S., Griessner, J., Kaczanowska, J., Pliota, P., Kargl, D., Badurek, S., Kraitsy, K., Rassoulpour, A., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0174-5 · Cited by 118

Age and Alzheimer’s disease gene expression profiles reversed by the glutamate modulator riluzole

Pereira, A. C., Gray, J. D., Kogan, J. F., Davidson, R. L., Rubin, T. G., Okamoto, M., Morrison, J. H., & McEwen, B. S. (2017) · Molecular Psychiatry · doi:10.1038/mp.2016.33 · Cited by 116

YAP Tyrosine Phosphorylation and Nuclear Localization in Cholangiocarcinoma Cells Are Regulated by LCK and Independent of LATS Activity

Sugihara, T., Werneburg, N. W., Hernandez, M. C., Yang, L., Kabashima, A., Hirsova, P., Yohanathan, L., Sosa, C., Truty, M. J., Vasmatzis, G., et al. (2018) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-18-0158 · Cited by 110

Role of the Astroglial Glutamate Exchanger xCT in Ventral Hippocampus in Resilience to Stress

Nasca, C., Bigio, B., Zelli, D., de Angelis, P., Lau, T., Okamoto, M., Soya, H., Ni, J., Brichta, L., Greengard, P., et al. (2017) · Neuron · doi:10.1016/j.neuron.2017.09.020 · Cited by 113

The ERBB network facilitates KRAS-driven lung tumorigenesis

Kruspig, B., Monteverde, T., Neidler, S., Hock, A., Kerr, E., Nixon, C., Clark, W., Hedley, A., Laing, S., Coffelt, S. B., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aao2565 · Cited by 111

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data

Hayer, K. E., Pizarro, A., Lahens, N. F., Hogenesch, J. B., & Grant, G. R. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv488 · Cited by 93

Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms

Franke, K. R., & Crowgey, E. L. (2020) · Genomics & Informatics · doi:10.5808/gi.2020.18.1.e10 · Cited by 95

Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics

Sagner, A., Gaber, Z. B., Delile, J., Kong, J. H., Rousso, D. L., Pearson, C. A., Weicksel, S. E., Melchionda, M., Mousavy Gharavy, S. N., Briscoe, J., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2003127 · Cited by 96

Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage

Younger, S. T., Kenzelmann-Broz, D., Jung, H., Attardi, L. D., & Rinn, J. L. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv284 · Cited by 99

Re‐annotation, improved large‐scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

Cormier, A., Avia, K., Sterck, L., Derrien, T., Wucher, V., Andres, G., Monsoor, M., Godfroy, O., Lipinska, A., Perrineau, M., et al. (2017) · New Phytologist · doi:10.1111/nph.14321 · Cited by 103

A reanalysis of mouse ENCODE comparative gene expression data

Gilad, Y., & Mizrahi-Man, O. (2015) · F1000Research · doi:10.12688/f1000research.6536.1 · Cited by 100

Genomic responses to selection for tame/aggressive behaviors in the silver fox ( Vulpes vulpes )

Wang, X., Pipes, L., Trut, L. N., Herbeck, Y., Vladimirova, A. V., Gulevich, R. G., Kharlamova, A. V., Johnson, J. L., Acland, G. M., Kukekova, A. V., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800889115 · Cited by 100

RNA‐seq Data: Challenges in and Recommendations for Experimental Design and Analysis

Williams, A. G., Thomas, S., Wyman, S. K., & Holloway, A. K. (2014) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1113s83 · Cited by 93

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

Zhu, X., Ching, T., Pan, X., Weissman, S. M., & Garmire, L. (2017) · PeerJ · doi:10.7717/peerj.2888 · Cited by 86

Inverse data-driven modeling and multiomics analysis reveals Phgdh as a metabolic checkpoint of macrophage polarization and proliferation

Wilson, J. L., Nägele, T., Linke, M., Demel, F., Fritsch, S. D., Mayr, H. K., Cai, Z., Katholnig, K., Sun, X., Fragner, L., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.011 · Cited by 97

Heterogeneity of human prostate carcinoma-associated fibroblasts implicates a role for subpopulations in myeloid cell recruitment

Vickman, R. E., Broman, M. M., Lanman, N. A., Franco, O. E., Sudyanti, P. A. G., Ni, Y., Ji, Y., Helfand, B. T., Petkewicz, J., Paterakos, M. C., et al. (2020) · The Prostate · doi:10.1002/pros.23929 · Cited by 88

Massive reshaping of genome-nuclear lamina interactions during oncogene-induced senescence.

Lenain, C., de Graaf, C. A., Pagie, L., Visser, N. L., de Haas, M., de Vries, S. S., Peric-Hupkes, D., van Steensel, B., & Peeper, D. S. (2017) · Genome Research · doi:10.1101/gr.225763.117 · Cited by 89