The rearing environment persistently modulates mouse phenotypes from the molecular to the behavioural level

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works

Fast gapped-read alignment with Bowtie 2

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259 · see citing works

fastp: an ultra-fast all-in-one FASTQ preprocessor

(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works

vegan: Community Ecology Package

Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099 · see citing works

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works

An obesity-associated gut microbiome with increased capacity for energy harvest

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · see citing works

An Ordination of the Upland Forest Communities of Southern Wisconsin

Bray, J. R., & Curtis, J. T. (1957) · Ecological Monographs · doi:10.2307/1942268 · Cited by 11,736 · see citing works

Why Most Published Research Findings Are False

Ioannidis, J. P. A. (2005) · PLoS Medicine · doi:10.1371/journal.pmed.0020124 · Cited by 10,505 · see citing works

Human gut microbes associated with obesity

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · see citing works

Power failure: why small sample size undermines the reliability of neuroscience

Button, K. S., Ioannidis, J. P. A., Mokrysz, C., Nosek, B. A., Flint, J., Robinson, E. S. J., & Munafò, M. R. (2013) · Nature Reviews Neuroscience · doi:10.1038/nrn3475 · Cited by 7,641 · see citing works

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · see citing works

Effects of stress throughout the lifespan on the brain, behaviour and cognition

Lupien, S. J., McEwen, B. S., Gunnar, M. R., & Heim, C. (2009) · Nature Reviews Neuroscience · doi:10.1038/nrn2639 · Cited by 6,256 · see citing works

1,500 scientists lift the lid on reproducibility

Baker, M. (2016) · Nature · doi:10.1038/533452a · Cited by 4,209 · cited 1× · see citing works

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Durinck, S., Spellman, P. T., Birney, E., & Huber, W. K. (2009) · Nature Protocols · doi:10.1038/nprot.2009.97 · Cited by 4,081 · see citing works

A manifesto for reproducible science

Munafò, M. R., Nosek, B. A., Bishop, D. V. M., Button, K. S., Chambers, C. D., Percie du Sert, N., Simonsohn, U., Wagenmakers, E.-J., Ware, J. J., & Ioannidis, J. P. A. (2017) · Nature Human Behaviour · doi:10.1038/s41562-016-0021 · Cited by 3,397 · see citing works

Are the Dorsal and Ventral Hippocampus Functionally Distinct Structures?

Fanselow, M. S., & Dong, H.-W. (2010) · Neuron · doi:10.1016/j.neuron.2009.11.031 · Cited by 3,358 · see citing works

ATAC-seq: a method for assaying chromatin accessibility genome-wide

Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2129s109 · Cited by 3,289 · see citing works

Normal gut microbiota modulates brain development and behavior

Heijtz, R. D., Wang, S., Anuar, F., Qian, Y., Björkholm, B., Samuelsson, A., Hibberd, M. L., Forssberg, H., & Pettersson, S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1010529108 · Cited by 3,228 · cited 1× · see citing works

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Liao, Y., Smyth, G. K., & Shi, W. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt214 · Cited by 3,064 · see citing works

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

Alexa, A., Rahnenführer, J., & Lengauer, T. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl140 · Cited by 2,194 · see citing works

Brain development in rodents and humans: identifying benchmarks of maturation and vulnerability to injury across species

Semple, B. D., Blomgren, K., Gimlin, K., Ferriero, D. M., & Noble-Haeusslein, L. J. (2013) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2013.04.001 · Cited by 2,132 · see citing works

Believe it or not: how much can we rely on published data on potential drug targets?

Prinz, F., Schlange, T., & Asadullah, K. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3439-c1 · Cited by 1,888 · see citing works

Genetics of Mouse Behavior: Interactions with Laboratory Environment

Crabbe, J. C., Wahlsten, D., & Dudek, B. C. (1999) · Science · doi:10.1126/science.284.5420.1670 · Cited by 1,666 · see citing works

PDZ domain proteins of synapses

Kim, E., & Sheng, M. (2004) · Nature reviews. Neuroscience · doi:10.1038/nrn1517 · Cited by 1,565 · see citing works

The neuro-symphony of stress

Joëls, M., & Baram, T. Z. (2009) · Nature Reviews Neuroscience · doi:10.1038/nrn2632 · Cited by 1,521 · see citing works

Adult neurogenesis and functional plasticity in neuronal circuits

Lledo, P., Alonso, M., & Grubb, M. S. (2006) · Nature reviews. Neuroscience · doi:10.1038/nrn1867 · Cited by 1,365 · see citing works

A two-dimensional neuropsychology of defense: fear/anxiety and defensive distance

McNaughton, N., & Corr, P. J. (2004) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2004.03.005 · Cited by 1,308 · see citing works

What does research reproducibility mean?

Goodman, S. N., Fanelli, D., & Ioannidis, J. P. A. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aaf5027 · Cited by 1,293 · see citing works

Brain on stress: how the social environment gets under the skin

McEwen, B. S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121254109 · Cited by 1,200 · see citing works

Control of brain development, function, and behavior by the microbiome

Sampson, T. R., & Mazmanian, S. K. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.011 · Cited by 1,093 · see citing works

The economics of reproducibility in preclinical research

Freedman, L. P., Cockburn, I. M., & Simcoe, T. S. (2015) · PLOS Biology · doi:10.1371/journal.pbio.1002165 · Cited by 1,055 · see citing works

Reproducibility in Science: Improving the Standard for Basic and Preclinical Research

Begley, C. G., & Ioannidis, J. P. A. (2015) · Circulation Research · doi:10.1161/circresaha.114.303819 · Cited by 1,035 · see citing works

Gut microbiota depletion from early adolescence in mice: implications for brain and behaviour

Desbonnet, L., Clarke, G., Traplin, A., O’Sullivan, O., Crispie, F., Moloney, R. D., Cotter, P. D., Dinan, T. G., & Cryan, J. F. (2015) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2015.04.004 · Cited by 760 · see citing works

Mouse genetics: concepts and applications

(1995) · Choice Reviews Online · doi:10.5860/choice.33-2135 · Cited by 757 · see citing works

Microbial genes, brain & behaviour – epigenetic regulation of the gut–brain axis

Stilling, R. M., Dinan, T. G., & Cryan, J. F. (2014) · Genes, Brain and Behavior · doi:10.1111/gbb.12109 · Cited by 637 · see citing works

Measurement error and the replication crisis

Loken, E., & Gelman, A. (2017) · Science · doi:10.1126/science.aal3618 · Cited by 628 · see citing works

Anxiety, depression, and the microbiome: A role for gut peptides

Lach, G., Schellekens, H., Dinan, T. G., & Cryan, J. F. (2018) · Neurotherapeutics · doi:10.1007/s13311-017-0585-0 · Cited by 573 · see citing works

Sex differences in the hypothalamic–pituitary–adrenal axis’ response to stress: an important role for gonadal hormones

Heck, A., & Handa, R. J. (2018) · Neuropsychopharmacology · doi:10.1038/s41386-018-0167-9 · Cited by 532 · see citing works

Meta-research: Evaluation and Improvement of Research Methods and Practices

Ioannidis, J. P. A., Fanelli, D., Dunne, D. D., & Goodman, S. N. (2015) · PLOS Biology · doi:10.1371/journal.pbio.1002264 · Cited by 495 · see citing works

Publication and other reporting biases in cognitive sciences: detection, prevalence, and prevention

Ioannidis, J. P. A., Munafò, M. R., Fusar-Poli, P., Nosek, B. A., & David, S. P. (2014) · Trends in Cognitive Sciences · doi:10.1016/j.tics.2014.02.010 · Cited by 471 · see citing works

Microbiota-derived metabolites as drivers of gut–brain communication

Ahmed, H., Leyrolle, Q., Koistinen, V., Kärkkäinen, O., Layé, S., Delzenne, N., & Hanhineva, K. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2102878 · Cited by 462 · see citing works

Environmental standardization: cure or cause of poor reproducibility in animal experiments?

Richter, S. H., Garner, J. P., & Würbel, H. (2009) · Nature Methods · doi:10.1038/nmeth.1312 · Cited by 425 · see citing works

Synapse-specific and developmentally regulated targeting of AMPA receptors by a family of MAGUK scaffolding proteins.

Elias, G. M., Funke, L., Stein, V., Grant, S., Bredt, D., & Nicoll, R. (2006) · Neuron · doi:10.1016/j.neuron.2006.09.012 · Cited by 413 · see citing works

Reproducibility of animal research in light of biological variation

Voelkl, B., Altman, N., Forsman, A., Forstmeier, W., Gurevitch, J., Jarić, I., Karp, N. A., Kas, M. J., Schielzeth, H., de Casteele, T. V., et al. (2020) · Nature reviews. Neuroscience · doi:10.1038/s41583-020-0313-3 · Cited by 391 · see citing works

Stress and the adolescent brain

ROMEO, R. D., & McEWEN, B. S. (2006) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1376.022 · Cited by 379 · see citing works

Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design

Laukens, D., Brinkman, B. M. N., Raes, J., Vos, M. D., & Vandenabeele, P. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv036 · Cited by 378 · see citing works

Physiological role of a novel neuropeptide, apelin, and its receptor in the rat brain

Goazigo, A. R.-L., Mota, N. D., Škultétyová, I., Lenkei, Z., Messari, S. E., Gallatz, K., Corvol, P. L., Palkovits, M., & Llorens‐Cortés, C. (2001) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2001.00320.x · Cited by 374 · see citing works

The neurobiology of adolescence: Changes in brain architecture, functional dynamics, and behavioral tendencies

Sturman, D. A., & Moghaddam, B. (2011) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2011.04.003 · Cited by 341 · see citing works

Low ambient humidity impairs barrier function and innate resistance against influenza infection

Kudo, E., Song, E., Yockey, L. J., Rakib, T., Wong, P., Homer, R., & Iwasaki, A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1902840116 · Cited by 336 · see citing works

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice

Ericsson, A. C., Davis, J. W., Spollen, W. G., Bivens, N. J., Givan, S. A., Hagan, C. E., McIntosh, M., & Franklin, C. L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0116704 · Cited by 311 · see citing works

Brain function and chromatin plasticity

Dulac, C. G. (2010) · Nature · doi:10.1038/nature09231 · Cited by 299 · see citing works

Influences of laboratory environment on behavior

Chesler, E. J., Wilson, S. G., Lariviere, W. R., Rodriguez‐Zas, S. L., & Mogil, J. S. (2002) · Nature Neuroscience · doi:10.1038/nn1102-1101 · Cited by 275 · see citing works

The postnatal development of the hypothalamic–pituitary–adrenal axis in the mouse

Schmidt, M. V., Enthoven, L., van der Mark, M. H., Levine, S. D., de Kloet, E. R., & Oitzl, M. S. (2003) · International Journal of Developmental Neuroscience · doi:10.1016/s0736-5748(03)00030-3 · Cited by 271 · see citing works

Accounting for reciprocal host–microbiome interactions in experimental science

Stappenbeck, T. S., & Virgin, H. W. (2016) · Nature · doi:10.1038/nature18285 · Cited by 270 · see citing works

Lifetime development of behavioural phenotype in the house mouse (Mus musculus)

Brust, V., Schindler, P. M., & Lewejohann, L. (2015) · Frontiers in Zoology · doi:10.1186/1742-9994-12-s1-s17 · Cited by 269 · see citing works

Reproducibility of preclinical animal research improves with heterogeneity of study samples

Voelkl, B., Vogt, L., Sena, E. S., & Würbel, H. (2018) · PLOS Biology · doi:10.1371/journal.pbio.2003693 · Cited by 262 · see citing works

Understanding the potency of stressful early life experiences on brain and body function

McEwen, B. S. (2008) · Metabolism · doi:10.1016/j.metabol.2008.07.006 · Cited by 260 · see citing works

Insulin signaling in the hippocampus and amygdala regulates metabolism and neurobehavior

Soto, M., Cai, W., Konishi, M., & Kahn, C. R. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817391116 · Cited by 246 · see citing works

Neuronal Plasticity: Beyond the Critical Period

Hübener, M., & Bonhoeffer, T. (2014) · Cell · doi:10.1016/j.cell.2014.10.035 · Cited by 237 · see citing works

Behaviour and the standardization fallacy

Würbel, H. (2000) · Nature Genetics · doi:10.1038/81541 · Cited by 235 · see citing works

Involvement of Notch signaling in hippocampal synaptic plasticity

Wang, Y., Chan, S. L., Miele, L., Yao, P. J., Mackes, J., Ingram, D. K., Mattson, M. P., & Furukawa, K. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308126101 · Cited by 235 · see citing works

Systematic variation improves reproducibility of animal experiments

Richter, S. H., Garner, J. P., Auer, C., Kunert, J., & Würbel, H. (2010) · Nature Methods · doi:10.1038/nmeth0310-167 · Cited by 219 · see citing works

Early life stress alters transcriptomic patterning across reward circuitry in male and female mice

Peña, C. J., Smith, M., Ramakrishnan, A., Cates, H. M., Bagot, R. C., Kronman, H. G., Patel, B., Chang, A. B., Purushothaman, I., Dudley, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13085-6 · Cited by 219 · see citing works

Contribution of the Ventral Subiculum to Inhibitory Regulation of the Hypothalamo‐Pituitary‐Adrenocortical Axis

Herman, J. P., Cullinan, W. E., Morano, M. I., Akil, H., & Watson, S. J. (1995) · Journal of Neuroendocrinology · doi:10.1111/j.1365-2826.1995.tb00784.x · Cited by 214 · see citing works

Rein in the four horsemen of irreproducibility

Bishop, D. (2019) · Nature · doi:10.1038/d41586-019-01307-2 · Cited by 206 · see citing works

Variation in the gut microbiota of laboratory mice is related to both genetic and environmental factors.

Hufeldt, M. R., Nielsen, D. S., Vogensen, F. K., Midtvedt, T., & Hansen, A. K. (2010) · PubMed Central · Cited by 202 · see citing works

A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks

Karin, O., Raz, M., Tendler, A., Bar, A., Korem Kohanim, Y., Milo, T., & Alon, U. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209510 · Cited by 200 · see citing works

Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models

Robertson, S. J., Lemire, P., Maughan, H., Goethel, A., Turpin, W., Bedrani, L., Guttman, D. S., Croitoru, K., Girardin, S. E., & Philpott, D. J. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.023 · Cited by 194 · see citing works

Mice selected for high versus low stress reactivity: A new animal model for affective disorders

Touma, C., Bunck, M., Glasl, L., Nußbaumer, M., Palme, R., Stein, H., Wolferstätter, M., Zeh, R., Zimbelmann, M., Holsboer, F., et al. (2008) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2008.03.013 · Cited by 188 · see citing works

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities

Rausch, P., Basic, M., Batra, A., Bischoff, S. C., Blaut, M., Clavel, T., Gläsner, J., Gopalakrishnan, S., Graßl, G. A., Günther, C., et al. (2016) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2016.03.004 · Cited by 177 · see citing works

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Rittschof, C. C., Bukhari, S. A., Sloofman, L. G., Troy, J. M., Caetano-Anollés, D., Cash-Ahmed, A. C., Kent, M., Lu, X., Sanogo, Y. O., Weisner, P. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420369111 · Cited by 161 · see citing works

An adverse early life environment can enhance stress resilience in adulthood

Santarelli, S., Zimmermann, C. A., Kalideris, G., Lesuis, S. L., Arloth, J., Uribe, A., Dournes, C., Balsevich, G., Hartmann, J., Masana, M., et al. (2017) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2017.01.021 · Cited by 154 · see citing works

Effect of voluntary wheel running on circadian corticosterone release and on HPA axis responsiveness to restraint stress in Sprague-Dawley rats

Fediuc, S., Campbell, J. E., & Riddell, M. C. (2006) · Journal of Applied Physiology · doi:10.1152/japplphysiol.01416.2005 · Cited by 148 · see citing works

Effect of Population Heterogenization on the Reproducibility of Mouse Behavior: A Multi-Laboratory Study

Richter, S. H., Garner, J. P., Zipser, B., Lewejohann, L., Sachser, N., Touma, C., Schindler, B., Chourbaji, S., Brandwein, C., Gass, P., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016461 · Cited by 143 · see citing works

Phenotypic Plasticity, Developmental Instability, and Robustness: The Concepts and How They Are Connected

Klingenberg, C. P. (2019) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00056 · Cited by 139 · see citing works

Improving reproducibility in animal research by splitting the study population into several ‘mini-experiments’

von Kortzfleisch, V. T., Karp, N. A., Palme, R., Kaiser, S., Sachser, N., & Richter, S. H. (2020) · Scientific Reports · doi:10.1038/s41598-020-73503-4 · Cited by 137 · see citing works

Distinct Proteomic, Transcriptomic, and Epigenetic Stress Responses in Dorsal and Ventral Hippocampus

Floriou‐Servou, A., von Ziegler, L., Stalder, L., Sturman, O., Privitera, M., Rassi, A., Cremonesi, A., Thöny, B., & Bohacek, J. (2018) · Biological Psychiatry · doi:10.1016/j.biopsych.2018.02.003 · Cited by 126 · see citing works

Interpretation of multivariate outliers for compositional data

Filzmoser, P., Hron, K., & Reimann, C. (2011) · Computers & Geosciences · doi:10.1016/j.cageo.2011.06.014 · Cited by 122 · see citing works

Stress: Physiology, Biochemistry, and Pathology

Fink, G. (2019) · Elsevier eBooks · doi:10.1016/c2016-0-04243-2 · Cited by 112 · see citing works

Mouse models of maternal immune activation: Mind your caging system!

Mueller, F. S., Polesel, M., Richetto, J., Meyer, U., & Weber‐Stadlbauer, U. (2018) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2018.07.014 · Cited by 107 · see citing works

ALK5-dependent TGF-β signaling is a major determinant of late-stage adult neurogenesis

He, Y., Zhang, H., Yung, A. R., Villeda, S., Jaeger, P. A., Olayiwola, O., Fainberg, N. A., & Wyss‐Coray, T. (2014) · Nature Neuroscience · doi:10.1038/nn.3732 · Cited by 102 · see citing works

Chromatin organization in the female mouse brain fluctuates across the oestrous cycle

Jarić, I., Rocks, D., Greally, J. M., Suzuki, M., & Kundaković, M. (2019) · Nature Communications · doi:10.1038/s41467-019-10704-0 · Cited by 102 · see citing works

Principles of Laboratory Animal Science: A Contribution to the Humane Use and Care of Animals and to the Quality of Experimental Results

van Zutphen, L. F. M., Baumans, V., & Beynen, A. C. (1993) · Medical Entomology and Zoology · Cited by 100 · see citing works

Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse

Eppig, J. T. (2017) · ILAR Journal · doi:10.1093/ilar/ilx013 · Cited by 99 · see citing works

Reduced body weight is a common effect of gene knockout in mice

Reed, D. R., Lawler, M. P., & Tordoff, M. G. (2008) · BMC Genetics · doi:10.1186/1471-2156-9-4 · Cited by 98 · see citing works

Environmental programming of susceptibility and resilience to stress in adulthood in male mice

Peña, C. J., Nestler, E. J., & Bagot, R. C. (2019) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2019.00040 · Cited by 97 · see citing works

Variations on the Notch pathway in neural development

Justice, N. J., & Jan, Y. N. (2002) · Current Opinion in Neurobiology · doi:10.1016/s0959-4388(02)00291-x · Cited by 95 · see citing works

Collagen XIX is expressed by interneurons and contributes to the formation of hippocampal synapses

Su, J., Gorse, K. M., Ramirez, F., & Fox, M. A. (2009) · The Journal of Comparative Neurology · doi:10.1002/cne.22228 · Cited by 95 · see citing works

Reproducibility Crisis: Are We Ignoring Reaction Norms?

Voelkl, B., & Würbel, H. (2016) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2016.05.003 · Cited by 94 · see citing works

Housing temperature affects the acute and chronic metabolic adaptations to exercise in mice

McKie, G. L., Medak, K. D., Knuth, C. M., Shamshoum, H., Townsend, L. K., Peppler, W. T., & Wright, D. C. (2019) · The Journal of Physiology · doi:10.1113/jp278221 · Cited by 91 · see citing works

Sex and Estrous Cycle Effects on Anxiety- and Depression-Related Phenotypes in a Two-Hit Developmental Stress Model

Jarić, I., Rocks, D., Cham, H., Herchek, A., & Kundaković, M. (2019) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2019.00074 · Cited by 86 · see citing works

Genetic Variables That Influence Phenotype

Linder, C. C. (2006) · ILAR Journal · doi:10.1093/ilar.47.2.132 · Cited by 85 · see citing works

Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet

Rasmussen, T. S., de Vries, L., Kot, W., Hansen, L. H., Castro-Mejía, J. L., Vogensen, F. K., Hansen, A. K., & Nielsen, D. S. (2019) · Viruses · doi:10.3390/v11050435 · Cited by 85 · see citing works

Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research

Eppig, J. T., Smith, C. L., Blake, J. A., Ringwald, M., Kadin, J. A., Richardson, J. E., & Bult, C. J. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6427-7_3 · Cited by 82 · see citing works

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility

Parker, K. D., Albeke, S. E., Gigley, J. P., Goldstein, A. M., & Ward, N. L. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01598 · Cited by 81 · see citing works

The influence of genetic background on spontaneous and genetically engineered mouse models of complex diseases.

Linder, C. C. (2001) · PubMed · Cited by 80 · see citing works

A big-data approach to understanding metabolic rate and response to obesity in laboratory mice

Corrigan, J. K., Ramachandran, D., He, Y., Palmer, C. J., Jurczak, M. J., Chen, R., Li, B., Friedline, R. H., Kim, J. K., Ramsey, J. J., et al. (2020) · eLife · doi:10.7554/elife.53560 · Cited by 80 · see citing works

Developmental programming of the HPA axis and related behaviours: epigenetic mechanisms

Matthews, S. G., & McGowan, P. O. (2019) · Journal of Endocrinology · doi:10.1530/joe-19-0057 · Cited by 77 · see citing works

Notch1 Regulates Hippocampal Plasticity Through Interaction with the Reelin Pathway, Glutamatergic Transmission and CREB Signaling

Brai, E., Marathe, S. V., Astori, S., Fredj, N. B., Perry, E., Lamy, C. M., Scotti, A. L., & Alberi, L. A. (2015) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2015.00447 · Cited by 73 · see citing works

Chemical signaling between gut microbiota and host chromatin: What is your gut really saying?

Krautkramer, K. A., Rey, F. E., & Denu, J. M. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.r116.761577 · Cited by 70 · see citing works

Meta-analysis of variation suggests that embracing variability improves both replicability and generalizability in preclinical research

Usui, T., Macleod, M. R., McCann, S., Senior, A. M., & Nakagawa, S. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001009 · Cited by 70 · see citing works

Systematic heterogenization for better reproducibility in animal experimentation

Richter, S. H. (2017) · Lab Animal · doi:10.1038/laban.1330 · Cited by 69 · see citing works

Increasing the statistical power of animal experiments with historical control data

Bonapersona, V., Hoijtink, H., RELACS, Sarabdjitsingh, R. A., & Joëls, M. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00792-3 · Cited by 69 · see citing works

Wnt-5a/Frizzled9 Receptor Signaling through the Gαo-Gβγ Complex Regulates Dendritic Spine Formation

Ramírez, V. T., Ramos‐Fernández, E., Henríquez, J. P., Lorenzo, A., & Inestrosa, N. C. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.722132 · Cited by 64 · see citing works

Phenotypic Plasticity through Transcriptional Regulation of the Evolutionary Hotspot Gene tan in Drosophila melanogaster

Gibert, J., Mouchel‐Vielh, E., Castro, S. D., & Peronnet, F. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006218 · Cited by 59 · see citing works

The standardization fallacy

Voelkl, B., Würbel, H., Krzywinski, M. I., & Altman, N. (2021) · Nature Methods · doi:10.1038/s41592-020-01036-9 · Cited by 57 · see citing works

The Very Idea of Modern Science

Agassi, J. (2013) · Boston studies in the philosophy of science · doi:10.1007/978-94-007-5351-8 · Cited by 53 · see citing works

Canonical TGF-β Signaling Is Required for the Balance of Excitatory/Inhibitory Transmission within the Hippocampus and Prepulse Inhibition of Acoustic Startle

Sun, M., Gewirtz, J. C., Bofenkamp, L., Wickham, R. J., Ge, H., & O’Connor, M. B. (2010) · Journal of Neuroscience · doi:10.1523/jneurosci.0789-10.2010 · Cited by 50 · see citing works

Replications, Comparisons, Sampling and the Problem of Representativeness in Animal Cognition Research

Farrar, B. G., Voudouris, K., & Clayton, N. S. (2021) · Animal Behavior and Cognition · doi:10.26451/abc.08.02.14.2021 · Cited by 50 · see citing works

Practical Guidelines for High-Resolution Epigenomic Profiling of Nucleosomal Histones in Postmortem Human Brain Tissue

Kundaković, M., Jiang, Y. P., Kavanagh, D. H., Dincer, A., Brown, L. M., Pothula, V., Zharovsky, E., Park, R., Jacobov, R., Magro, I. L., et al. (2016) · Biological Psychiatry · doi:10.1016/j.biopsych.2016.03.1048 · Cited by 49 · see citing works

Leucine-rich repeat-containing synaptic adhesion molecules as organizers of synaptic specificity and diversity

Schroeder, A., & de Wit, J. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-017-0023-8 · Cited by 48 · see citing works

Modeling the Sex Differences and Interindividual Variability in the Activity of the Hypothalamic-Pituitary-Adrenal Axis

Rao, R., & Androulakis, I. P. (2017) · Endocrinology · doi:10.1210/en.2017-00544 · Cited by 47 · see citing works

The Impact of Preclinical Irreproducibility on Drug Development

Freedman, L. P., & Gibson, M. (2014) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.9 · Cited by 43 · see citing works

Collagen-derived matricryptins promote inhibitory nerve terminal formation in the developing neocortex

Su, J., Jiang, C., Lippold, K. M., Monavarfeshani, A., Carrillo, G. L., Jenkins, R., & Fox, M. A. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201509085 · Cited by 43 · see citing works

Shared and distinctive features of the gut microbiome of C57BL/6 mice from different vendors and production sites, and in response to a new vivarium

Long, L. L., Svenson, K. L., Mourino, A. J., Michaud, M., Fahey, J. R., Waterman, L., Vandegrift, K. L., & Adams, M. D. (2021) · Lab Animal · doi:10.1038/s41684-021-00777-0 · Cited by 42 · see citing works

Bidirectional modulation of hippocampal synaptic plasticity by Dopaminergic D4-receptors in the CA1 area of hippocampus

Navakkode, S., Chew, K. C. M., Tay, S. J. N., Lin, Q., Behnisch, T., & Soong, T. W. (2017) · Scientific Reports · doi:10.1038/s41598-017-15917-1 · Cited by 40 · see citing works

Adolescent Brain Vulnerability and Psychopathology Through the Generations: Role of Diet and Dopamine

O’Connor, R. M., & Cryan, J. F. (2013) · Biological Psychiatry · doi:10.1016/j.biopsych.2013.10.022 · Cited by 39 · see citing works

What is the optimum design for my animal experiment?

Karp, N. A., & Fry, D. (2021) · BMJ Open Science · doi:10.1136/bmjos-2020-100126 · Cited by 39 · see citing works

MULTOVL: fast multiple overlaps of genomic regions

Aszódi, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts607 · Cited by 37 · see citing works

Reproducibility in the absence of selective reporting: An illustration from large‐scale brain asymmetry research

Kong, X., ENIGMA Laterality Working Group, & Francks, C. (2020) · Human Brain Mapping · doi:10.1002/hbm.25154 · Cited by 36 · see citing works

Housing mice in the individually ventilated or open cages—Does it matter for behavioral phenotype?

Åhlgren, J., & Võikar, V. (2019) · Genes Brain & Behavior · doi:10.1111/gbb.12564 · Cited by 35 · see citing works

Living inside the box: environmental effects on mouse models of human disease

Sundberg, J. P., & Schofield, P. N. (2018) · Disease Models & Mechanisms · doi:10.1242/dmm.035360 · Cited by 34 · see citing works

The Effect of Cage Space on Behavior and Reproduction in Crl:CD1(Icr) and C57BL/6NCrl Laboratory Mice

Gaskill, B. N., & Pritchett‐Corning, K. R. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127875 · Cited by 32 · see citing works

Hippo Signaling: Emerging Pathway in Stress-Related Psychiatric Disorders?

Stepan, J., Anderzhanova, E. A., & Gassen, N. C. (2018) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2018.00715 · Cited by 32 · see citing works

A reaction norm perspective on reproducibility

Voelkl, B., & Würbel, H. (2021) · Theory in Biosciences · doi:10.1007/s12064-021-00340-y · Cited by 29 · see citing works

Supplier-origin mouse microbiomes significantly influence locomotor and anxiety-related behavior, body morphology, and metabolism

Ericsson, A. C., Hart, M. L., Kwan, J. Y., Lanoue, L., Bower, L. R., Araiza, R. S., Lloyd, K. C. K., & Franklin, C. L. (2021) · Communications Biology · doi:10.1038/s42003-021-02249-0 · Cited by 27 · see citing works

Genes, Environments, and Phenotypic Plasticity in Immunology

Martin, L. B., Hanson, H. E., Hauber, M. E., & Ghalambor, C. K. (2021) · Trends in Immunology · doi:10.1016/j.it.2021.01.002 · Cited by 26 · see citing works

Incorporating inter-individual variability in experimental design improves the quality of results of animal experiments

van der Goot, M. H., van der Kooij, M., Stolte, S., Baars, A. M., Arndt, S. S., & van Lith, H. A. (2021) · PLoS ONE · doi:10.1371/journal.pone.0255521 · Cited by 22 · see citing works

On the usefulness of animals as a model system (part I): Overview of criteria and focus on robustness

Pallocca, G. (2022) · ALTEX · doi:10.14573/altex.2203291 · Cited by 17 · see citing works

Environmental enrichment influences novelty reactivity, novelty preference, and anxiety via distinct genetic mechanisms in C57BL/6J and DBA/2J mice

Dickson, P. E., & Mittleman, G. (2021) · Scientific Reports · doi:10.1038/s41598-021-83574-6 · Cited by 16 · see citing works

Reporting phenotypes in mouse models when considering body size as a potential confounder

Oellrich, A., Meehan, T. F., Parkinson, H., Sarntivijai, S., White, J. K., & Karp, N. A. (2016) · Journal of Biomedical Semantics · doi:10.1186/s13326-016-0050-8 · Cited by 12 · see citing works

Beyond Standardization: Improving External Validity and Reproducibility in Experimental Evolution

Desjardins, E., Kurtz, J., Kranke, N., Lindeza, A. S., & Richter, S. H. (2021) · BioScience · doi:10.1093/biosci/biab008 · Cited by 12 · see citing works

From genetic variation to phenotype via chromatin

Stower, H. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3622 · Cited by 9 · see citing works

Signalling cognition: The gut microbiota and hypothalamic-pituitary-adrenal axis

Rusch, J. A., Layden, B. T., & Dugas, L. R. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1130689 · Cited by 415 · see citing works

Environmental enrichment in farm, zoo, companion and experimental animals

Vučinić, M. M. (2009) · Veterinarski glasnik · doi:10.2298/vetgl0904227v · Cited by 1 · see citing works

Effects of cage enrichment on heart rate, blood pressure, and activity of female Sprague-Dawley and spontaneously hypertensive rats at rest and after acute challenges.

Azar, T. A., Sharp, J. L., & Lawson, D. M. (2012) · PubMed Central · Cited by 12 · see citing works

Brain-derived neurotrophic factor in serum as an animal welfare indicator of environmental enrichment in pigs

Rault, J., Lawrence, A. J., & Ralph, C. R. (2018) · Domestic Animal Endocrinology · doi:10.1016/j.domaniend.2018.05.007 · Cited by 36 · see citing works

Effects of environmental enrichment on cognitive function and hippocampal NGF in the non-handled rats

Pham, T. M., Söderström, S., Winblad, B., & Mohammed, A. H. (1999) · Behavioural Brain Research · doi:10.1016/s0166-4328(99)00019-4 · Cited by 162 · see citing works

Behavioral effects of enrichment on singly‐housed, yearling rhesus monkeys: An analysis including three enrichment conditions and a control group

Schapiro, S. J., & Bloomsmith, M. A. (1995) · American Journal of Primatology · doi:10.1002/ajp.1350350202 · Cited by 60 · see citing works