Bioconductor: open software development for computational biology and bioinformatics

Oncogenic Kras drives invasion and maintains metastases in colorectal cancer

Boutin, A. T., Liao, W.-T., Wang, M., Hwang, S. S., Karpinets, T. V., Cheung, H., Chu, G. C., Jiang, S., Hu, J., Chang, K., et al. (2017) · Genes & Development · doi:10.1101/gad.293449.116 · Cited by 195

Childhood abuse is associated with methylation of multiple loci in adult DNA

Suderman, M., Borghol, N., Pappas, J. J., Pinto Pereira, S. M., Pembrey, M., Hertzman, C., Power, C., & Szyf, M. (2014) · BMC Medical Genomics · doi:10.1186/1755-8794-7-13 · Cited by 193

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D

Perocchi, F., Xu, Z., Clauder-Münster, S., & Steinmetz, L. M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm683 · Cited by 193

Small molecule activation of PKM2 in cancer cells induces serine auxotrophy

Kung, C., Hixon, J., Choe, S., Marks, K., Gross, S., Murphy, E., DeLaBarre, B., Cianchetta, G., Sethumadhavan, S., Wang, X., et al. (2012) · Chemistry & Biology · doi:10.1016/j.chembiol.2012.07.021 · Cited by 192

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

Epigenetic reprogramming of tumor cell–intrinsic STING function sculpts antigenicity and T cell recognition of melanoma

Falahat, R., Berglund, A., Putney, R. M., Perez-Villarroel, P., Aoyama, S., Pilon-Thomas, S., Barber, G. N., & Mulé, J. J. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013598118 · Cited by 190

Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo

Smith, J. J., Kenney, R. D., Gagne, D. J., Frushour, B. P., Ladd, W., Galonek, H. L., Israelian, K., Song, J., Razvadauskaite, G., Lynch, A. V., et al. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-31 · Cited by 186

Data Integration Challenges for Machine Learning in Precision Medicine

Martínez-García, M., & Hernández-Lemus, E. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2021.784455 · Cited by 185

Global proteomic assessment of the classical protein-tyrosine phosphatome and “Redoxome”

Karisch, R., Fernandez, M., Taylor, P., Virtanen, C., St-Germain, J. R., Jin, L. L., Harris, I. S., Mori, J., Mak, T. W., Senis, Y. A., et al. (2011) · Cell · doi:10.1016/j.cell.2011.07.020 · Cited by 179

High-Throughput 3D Screening Reveals Differences in Drug Sensitivities between Culture Models of JIMT1 Breast Cancer Cells

Hongisto, V., Jernström, S., Fey, V., Mpindi, J.-P., Kleivi Sahlberg, K., Kallioniemi, O., & Perälä, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077232 · Cited by 181

Two independent transcription initiation codes overlap on vertebrate core promoters

Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A. M., et al. (2014) · Nature · doi:10.1038/nature12974 · Cited by 180

PHGDH defines a metabolic subtype in lung adenocarcinomas with poor prognosis

Zhang, B., Zheng, A., Hydbring, P., Ambroise, G., Ouchida, A. T., Goiny, M., Vakifahmetoglu-Norberg, H., & Norberg, E. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.05.067 · Cited by 178

Mitochondrial proteome remodelling in pressure overload-induced heart failure: the role of mitochondrial oxidative stress

Dai, D.-F., Hsieh, E. J., Liu, Y., Chen, T., Beyer, R. P., Chin, M. T., MacCoss, M. J., & Rabinovitch, P. S. (2012) · Cardiovascular Research · doi:10.1093/cvr/cvr274 · Cited by 178

Strand-specific 5′-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity

Chen, P. Y., Weinmann, L., Gaidatzis, D., Pei, Y., Zavolan, M., Tuschl, T., & Meister, G. (2008) · RNA · doi:10.1261/rna.789808 · Cited by 176

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

Cole, M. B., Risso, D., Wagner, A., DeTomaso, D., Ngai, J., Purdom, E., Dudoit, S., & Yosef, N. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.010 · Cited by 173

Gene expression profiling of aging reveals activation of a p53-mediated transcriptional program

Edwards, M. G., Anderson, R. M., Yuan, M., Kendziorski, C. M., Weindruch, R., & Prolla, T. A. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-80 · Cited by 174

MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy

Patterson, E. E., Holloway, A. K., Weng, J., Fojo, T., & Kebebew, E. (2011) · Cancer · doi:10.1002/cncr.25724 · Cited by 171

Control of embryonic stem cell lineage commitment by core promoter factor, TAF3

Liu, Z., Scannell, D. R., Eisen, M. B., & Tjian, R. (2011) · Cell · doi:10.1016/j.cell.2011.08.005 · Cited by 167

Human Monocyte Subsets Are Transcriptionally and Functionally Altered in Aging in Response to Pattern Recognition Receptor Agonists

Metcalf, T. U., Wilkinson, P. A., Cameron, M. J., Ghneim, K., Chiang, C., Wertheimer, A. M., Hiscott, J. B., Nikolich-Zugich, J., & Haddad, E. K. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1700148 · Cited by 166

MicroRNA Expression Levels Are Altered in the Cerebrospinal Fluid of Patients with Young-Onset Alzheimer’s Disease

McKeever, P. M., Schneider, R., Taghdiri, F., Weichert, A., Multani, N., Brown, R. A., Boxer, A. L., Karydas, A., Miller, B., Robertson, J., et al. (2018) · Molecular Neurobiology · doi:10.1007/s12035-018-1032-x · Cited by 166

Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

Rizzardi, L. F., Hickey, P. F., Rodriguez DiBlasi, V., Tryggvadóttir, R., Callahan, C. M., Idrizi, A., Hansen, K. D., & Feinberg, A. P. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0297-8 · Cited by 146

Accelerated Recruitment of New Brain Development Genes into the Human Genome

Zhang, Y. E., Landback, P., Vibranovski, M. D., & Long, M. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001179 · Cited by 164

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

Richard, H., Schulz, M. H., Sultan, M., Nürnberger, A., Schrinner, S., Balzereit, D., Dagand, E., Rasche, A., Lehrach, H., Vingron, M., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq041 · Cited by 160

TNFα-senescence initiates a STAT-dependent positive feedback loop, leading to a sustained interferon signature, DNA damage, and cytokine secretion

Kandhaya-Pillai, R., Miro-Mur, F., Alijotas-Reig, J., Tchkonia, T., Kirkland, J. L., & Schwartz, S. (2017) · Aging · doi:10.18632/aging.101328 · Cited by 165

NALP3 inflammasome upregulation and CASP1 cleavage of the glucocorticoid receptor cause glucocorticoid resistance in leukemia cells

Paugh, S. W., Bonten, E. J., Savic, D., Ramsey, L. B., Thierfelder, W. E., Gurung, P., Malireddi, R. K. S., Actis, M., Mayasundari, A., Min, J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3283 · Cited by 164

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Tang, W., Zhou, M., Dorsey, T. H., Prieto, D. A., Wang, X. W., Ruppin, E., Veenstra, T. D., & Ambs, S. (2018) · Genome Medicine · doi:10.1186/s13073-018-0602-x · Cited by 162

Development and evaluation of a multiplexed mass spectrometry based assay for measuring candidate peptide biomarkers in Alzheimer's Disease Neuroimaging Initiative (ADNI) CSF

Spellman, D. S., Wildsmith, K. R., Honigberg, L. A., Tuefferd, M., Baker, D., Raghavan, N., Nairn, A. C., Croteau, P., Schirm, M., Allard, R., et al. (2015) · PROTEOMICS – Clinical Applications · doi:10.1002/prca.201400178 · Cited by 161

Network methods for describing sample relationships in genomic datasets: Application to Huntington’s disease

Oldham, M. C., Langfelder, P., & Horvath, S. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-63 · Cited by 154

Scl Represses Cardiomyogenesis in Prospective Hemogenic Endothelium and Endocardium

Van Handel, B., Montel-Hagen, A., Sasidharan, R., Nakano, H., Ferrari, R., Boogerd, C. J., Schredelseker, J., Wang, Y., Hunter, S., Org, T., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.026 · Cited by 154

Long-Term Pioglitazone Treatment Improves Learning and Attenuates Pathological Markers in a Mouse Model of Alzheimer's Disease

Searcy, J. L., Phelps, J. T., Pancani, T., Kadish, I., Popovic, J., Anderson, K. L., Beckett, T. L., Murphy, M. P., Chen, K.-C., Blalock, E. M., et al. (2012) · Journal of Alzheimer's Disease · doi:10.3233/jad-2012-111661 · Cited by 154

Notch activation inhibits AML growth and survival: a potential therapeutic approach

Kannan, S., Sutphin, R. M., Hall, M. G., Golfman, L. S., Fang, W., Nolo, R. M., Akers, L. J., Hammitt, R. A., McMurray, J. S., Kornblau, S. M., et al. (2013) · Journal of Experimental Medicine · doi:10.1084/jem.20121527 · Cited by 152

Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana

Zou, C., Lehti-Shiu, M. D., Thomashow, M., & Shiu, S.-H. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000581 · Cited by 149

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics

Ramsey, S. A., Klemm, S. L., Zak, D. E., Kennedy, K. A., Thorsson, V., Li, B., Gilchrist, M., Gold, E. S., Johnson, C. D., Litvak, V., et al. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000021 · Cited by 147

Macrophages in human colorectal cancer are pro‐inflammatory and prime T cells towards an anti‐tumour type‐1 inflammatory response

Ong, S., Tan, Y., Beretta, O., Jiang, D., Yeap, W., Tai, J. J. Y., Wong, W., Yang, H., Schwarz, H., Lim, K., et al. (2012) · European Journal of Immunology · doi:10.1002/eji.201141825 · Cited by 145

CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data

Program, C. S.-C. B., Abdulla, S., Aevermann, B., Assis, P., Badajoz, S., Bell, S. M., Bezzi, E., Cakir, B., Chaffer, J., Chambers, S., et al. (2023) · doi:10.1101/2023.10.30.563174 · Cited by 142

Regulation of tumor angiogenesis and mesenchymal–endothelial transition by p38α through TGF-β and JNK signaling

Batlle, R., Andrés, E., Gonzalez, L., Llonch, E., Igea, A., Gutierrez-Prat, N., Berenguer-Llergo, A., & Nebreda, A. R. (2019) · Nature Communications · doi:10.1038/s41467-019-10946-y · Cited by 142

Transcriptional Control of Monocyte Gene Expression in Post-Traumatic Stress Disorder

O’Donovan, A., Sun, B., Cole, S., Rempel, H., Lenoci, M., Pulliam, L., & Neylan, T. (2011) · Disease Markers · doi:10.1155/2011/560572 · Cited by 141

Slc45a2 and V ‐ ATP ase are regulators of melanosomal p Hhomeostasis in zebrafish, providing a mechanism for human pigment evolution and disease

Dooley, C. M., Schwarz, H., Mueller, K. P., Mongera, A., Konantz, M., Neuhauss, S. C. F., Nüsslein‐Volhard, C., & Geisler, R. (2013) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12053 · Cited by 140

Functional differences between mesenchymal stem cell populations are reflected by their transcriptome

Jansen, B. J. H., Gilissen, C., Roelofs, H., Schaap-Oziemlak, A., Veltman, J. A., Raymakers, R. A. P., Jansen, J. H., Kögler, G., Figdor, C. G., Torensma, R., et al. (2010) · Stem Cells and Development · doi:10.1089/scd.2009.0288 · Cited by 139

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

Scheckel, C., Drapeau, E., Frias, M. A., Park, C. Y., Fak, J., Zucker-Scharff, I., Kou, Y., Haroutunian, V., Ma'ayan, A., Buxbaum, J. D., et al. (2016) · eLife · doi:10.7554/elife.10421 · Cited by 139

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

Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals

Montagner, A., Korecka, A., Polizzi, A., Lippi, Y., Blum, Y., Canlet, C., Tremblay-Franco, M., Gautier-Stein, A., Burcelin, R., Yen, Y.-C., et al. (2016) · Scientific Reports · doi:10.1038/srep20127 · Cited by 137

Variations in the progranulin gene affect global gene expression in frontotemporal lobar degeneration

Chen-Plotkin, A. S., Geser, F., Plotkin, J. B., Clark, C. M., Kwong, L. K., Yuan, W., Grossman, M., Van Deerlin, V. M., Trojanowski, J. Q., & Lee, V. M.-Y. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn023 · Cited by 135

The gut microbiota and mucosal homeostasis: Colonized at birth or at adulthood, does it matter?

El Aidy, S., Hooiveld, G., Tremaroli, V., Bäckhed, F., & Kleerebezem, M. (2013) · Gut Microbes · doi:10.4161/gmic.23362 · Cited by 131

Dlk1-Mediated Temporal Regulation of Notch Signaling Is Required for Differentiation of Alveolar Type II to Type I Cells during Repair

Finn, J., Sottoriva, K., Pajcini, K. V., Kitajewski, J. K., Chen, C., Zhang, W., Malik, A. B., & Liu, Y. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.02.046 · Cited by 133

Induction of Cardiac Angptl4 by Dietary Fatty Acids Is Mediated by Peroxisome Proliferator-Activated Receptor β/δ and Protects Against Fatty Acid–Induced Oxidative Stress

Georgiadi, A., Lichtenstein, L., Degenhardt, T., Boekschoten, M. V., van Bilsen, M., Desvergne, B., Müller, M., & Kersten, S. (2010) · Circulation Research · doi:10.1161/circresaha.110.217380 · Cited by 133

Short-term high fat-feeding results in morphological and metabolic adaptations in the skeletal muscle of C57BL/6J mice

de Wilde, J., Mohren, R., van den Berg, S., Boekschoten, M., Dijk, K. W.-V., de Groot, P., Müller, M., Mariman, E., & Smit, E. (2008) · Physiological Genomics · doi:10.1152/physiolgenomics.00219.2007 · Cited by 132

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

The aged retinal pigment epithelium/choroid: a potential substratum for the pathogenesis of age-related macular degeneration

Chen, H., Liu, B., Lukas, T. J., & Neufeld, A. H. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002339 · Cited by 129

A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

Li, C.-Y., Zhang, Y., Wang, Z., Zhang, Y., Cao, C., Zhang, P.-W., Lu, S.-J., Li, X.-M., Yu, Q., Zheng, X., et al. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000734 · Cited by 130

Nicotinamide mononucleotide requires SIRT3 to improve cardiac function and bioenergetics in a Friedreich’s ataxia cardiomyopathy model

Martin, A. S., Abraham, D. M., Hershberger, K. A., Bhatt, D. P., Mao, L., Cui, H., Liu, J., Liu, X., Muehlbauer, M. J., Grimsrud, P. A., et al. (2017) · JCI Insight · doi:10.1172/jci.insight.93885 · Cited by 128

A Specific ChREBP and PPARα Cross-Talk Is Required for the Glucose-Mediated FGF21 Response

Iroz, A., Montagner, A., Benhamed, F., Levavasseur, F., Polizzi, A., Anthony, E., Régnier, M., Fouché, E., Lukowicz, C., Cauzac, M., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.09.065 · Cited by 128

A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK

Campbell, J. D., McDonough, J. E., Zeskind, J. E., Hackett, T. L., Pechkovsky, D. V., Brandsma, C.-A., Suzuki, M., Gosselink, J. V., Liu, G., Alekseyev, Y. O., et al. (2012) · Genome Medicine · doi:10.1186/gm367 · Cited by 128

Human ESC-derived chimeric mouse models of Huntington's disease reveal cell-intrinsic defects in glial progenitor cell differentiation

Osipovitch, M., Asenjo Martinez, A., Mariani, J. N., Cornwell, A., Dhaliwal, S., Zou, L., Chandler-Militello, D., Wang, S., Li, X., Benraiss, S.-J., et al. (2019) · Cell Stem Cell · doi:10.1016/j.stem.2018.11.010 · Cited by 120

Features that define the best ChIP-seq peak calling algorithms

Thomas, R., Thomas, S., Holloway, A. K., & Pollard, K. S. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw035 · Cited by 112

Aryl Sulfonamides Degrade RBM39 and RBM23 by Recruitment to CRL4-DCAF15

Ting, T. C., Goralski, M., Klein, K., Wang, B., Kim, J., Xie, Y., & Nijhawan, D. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.09.079 · Cited by 123

GRcalculator: an online tool for calculating and mining dose–response data

Clark, N. A., Hafner, M., Kouril, M., Williams, E. H., Muhlich, J. L., Pilarczyk, M., Niepel, M., Sorger, P. K., & Medvedovic, M. (2017) · BMC Cancer · doi:10.1186/s12885-017-3689-3 · Cited by 121

Human thyroid tumor cell lines derived from different tumor types present a common dedifferentiated phenotype

van Staveren, W. C. G., Solís, D. W., Delys, L., Duprez, L., Andry, G., Franc, B., Thomas, G., Libert, F., Dumont, J. E., Detours, V., et al. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-4026 · Cited by 123

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability

Zatreanu, D., Han, Z., Mitter, R., Tumini, E., Williams, H., Gregersen, L., Dirac-Svejstrup, A. B., Roma, S., Stewart, A., Aguilera, A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.037 · Cited by 124

Transcriptional cofactors display specificity for distinct types of core promoters

Haberle, V., Arnold, C. D., Pagani, M., Rath, M., Schernhuber, K., & Stark, A. (2019) · Nature · doi:10.1038/s41586-019-1210-7 · Cited by 123

MicroRNA-132 Is Enriched in Developing Axons, Locally Regulates Rasa1 mRNA, and Promotes Axon Extension

Hancock, M. L., Preitner, N., Quan, J., & Flanagan, J. G. (2014) · The Journal of Neuroscience · doi:10.1523/jneurosci.3371-13.2014 · Cited by 123

Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons

Reid, D. A., Reed, P. J., Schlachetzki, J. C. M., Nitulescu, I. I., Chou, G., Tsui, E. C., Jones, J. R., Chandran, S., Lu, A. T., McClain, C. A., et al. (2021) · Science · doi:10.1126/science.abb9032 · Cited by 121

Single‐cell based high‐throughput sequencing of full‐length immunoglobulin heavy and light chain genes

Busse, C. E., Czogiel, I., Braun, P., Arndt, P. F., & Wardemann, H. (2014) · European Journal of Immunology · doi:10.1002/eji.201343917 · Cited by 121

Functional coordination of alternative splicing in the mammalian central nervous system

Fagnani, M., Barash, Y., Ip, J. Y., Misquitta, C., Pan, Q., Saltzman, A. L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., et al. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r108 · Cited by 120

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

Close, P., East, P., Dirac-Svejstrup, A. B., Hartmann, H., Heron, M., Maslen, S., Chariot, A., Söding, J., Skehel, M., & Svejstrup, J. Q. (2012) · Nature · doi:10.1038/nature10925 · Cited by 119

Identification of neurodegenerative factors using translatome–regulatory network analysis

Brichta, L., Shin, W., Jackson-Lewis, V., Blesa, J., Yap, E.-L., Walker, Z., Zhang, J., Roussarie, J.-P., Alvarez, M. J., Califano, A., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4070 · Cited by 118

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

Peixoto, L., Risso, D., Poplawski, S. G., Wimmer, M. E., Speed, T. P., Wood, M. A., & Abel, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv736 · Cited by 105

GDE2 Promotes Neurogenesis by Glycosylphosphatidylinositol-Anchor Cleavage of RECK

Park, S., Lee, C., Sabharwal, P., Zhang, M., Meyers, C. L. F., & Sockanathan, S. (2013) · Science · doi:10.1126/science.1231921 · Cited by 118

TSPYL5 suppresses p53 levels and function by physical interaction with USP7.

Epping, M. T., Meijer, L. A. T., Krijgsman, O., Bos, J. L., Pandolfi, P. P., & Bernards, R. (2011) · Nature Cell Biology · doi:10.1038/ncb2142 · Cited by 117

MiR-204 is responsible for inherited retinal dystrophy associated with ocular coloboma

Conte, I., Hadfield, K. D., Barbato, S., Carrella, S., Pizzo, M., Bhat, R. S., Carissimo, A., Karali, M., Porter, L. F., Urquhart, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401464112 · Cited by 115

The active human gut microbiota differs from the total microbiota

Peris-Bondia, F., Latorre, A., Artacho, A., Moya, A., & D'Auria, G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022448 · Cited by 113

Midbrain dopamine neurons in Parkinson׳s disease exhibit a dysregulated miRNA and target-gene network

Briggs, C. E., Wang, Y., Kong, B., Woo, T.-U. W., Iyer, L. K., & Sonntag, K. C. (2015) · Brain Research · doi:10.1016/j.brainres.2015.05.021 · Cited by 113

Identification of a Gene Regulatory Network Necessary for the Initiation of Oligodendrocyte Differentiation

Swiss, V. A., Nguyen, T., Dugas, J., Ibrahim, A., Barres, B., Androulakis, I. P., & Casaccia, P. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018088 · Cited by 112

Altered regulation of the PINK1 locus: a link between type 2 diabetes and neurodegeneration?

Scheele, C., Nielsen, A. R., Walden, T. B., Sewell, D. A., Fischer, C. P., Brogan, R. J., Petrovic, N., Larsson, O., Tesch, P. A., Wennmalm, K., et al. (2007) · The FASEB Journal · doi:10.1096/fj.07-8520com · Cited by 110

Pharmacogenomic and Pharmacoproteomic Studies of Cetuximab in Metastatic Colorectal Cancer: Biomarker Analysis of a Phase I Dose-Escalation Study

Tabernero, J., Cervantes, A., Rivera, F., Martinelli, E., Rojo, F., von Heydebreck, A., Macarulla, T., Rodriguez-Braun, E., Eugenia Vega-Villegas, M., Senger, S., et al. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.22.6043 · Cited by 110

Optimizing transformations for automated, high throughput analysis of flow cytometry data

Finak, G., Perez, J.-M., Weng, A., & Gottardo, R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-546 · Cited by 99

CD40L expression permits CD8+ T cells to execute immunologic helper functions

Frentsch, M., Stark, R., Matzmohr, N., Meier, S., Durlanik, S., Schulz, A. R., Stervbo, U., Jürchott, K., Gebhardt, F., Heine, G., et al. (2013) · Blood · doi:10.1182/blood-2013-02-483586 · Cited by 100

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

Zacher, B., Michel, M., Schwalb, B., Cramer, P., Tresch, A., & Gagneur, J. (2017) · PLOS ONE · doi:10.1371/journal.pone.0169249 · Cited by 91

KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans

Gacek-Matthews, A., Berger, H., Sasaki, T., Wittstein, K., Gruber, C., Lewis, Z. A., & Strauss, J. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006222 · Cited by 105

Thyroid hormone signalling genes are regulated by photoperiod in the hypothalamus of F344 rats

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Inosine Alters Gene Expression and Axonal Projections in Neurons Contralateral to a Cortical Infarct and Improves Skilled Use of the Impaired Limb

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Healthy aging and muscle function are positively associated with NAD+ abundance in humans

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BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response

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Systematic Identification of the HSP90 Regulated Proteome

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Losartan Blocks Osteosarcoma-Elicited Monocyte Recruitment, and Combined With the Kinase Inhibitor Toceranib, Exerts Significant Clinical Benefit in Canine Metastatic Osteosarcoma

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Generation of Mouse and Human Organoid-Forming Intestinal Progenitor Cells by Direct Lineage Reprogramming

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Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors

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Blunted hypertrophic response in aged skeletal muscle is associated with decreased ribosome biogenesis

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Challenges and recommendations to improve the installability and archival stability of omics computational tools

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Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers

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Angptl4 serves as an endogenous inhibitor of intestinal lipid digestion

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Combined mRNA microarray and proteomic analysis of eutopic endometrium of women with and without endometriosis

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Global analyses of mRNA translational control during early Drosophila embryogenesis

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Suppressed monocyte gene expression profile in men versus women with PTSD

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Multiple SET Methyltransferases Are Required to Maintain Normal Heterochromatin Domains in the Genome of Drosophila melanogaster

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A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers

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Association of Childhood Chronic Physical Aggression with a DNA Methylation Signature in Adult Human T Cells

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CIP2A signature reveals the MYC dependency of CIP2A-regulated phenotypes and its clinical association with breast cancer subtypes

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Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

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