Bioconductor: open software development for computational biology and bioinformatics

A prospective phase II trial exploring the association between tumor microenvironment biomarkers and clinical activity of ipilimumab in advanced melanoma

Hamid, O., Schmidt, H., Nissan, A., Ridolfi, L., Aamdal, S., Hansson, J., Guida, M., Hyams, D. M., Gómez, H., Bastholt, L., et al. (2011) · Journal of Translational Medicine · doi:10.1186/1479-5876-9-204 · Cited by 534

Intraprostatic Androgens and Androgen-Regulated Gene Expression Persist after Testosterone Suppression: Therapeutic Implications for Castration-Resistant Prostate Cancer

Mostaghel, E. A., Page, S. T., Lin, D. W., Fazli, L., Coleman, I. M., True, L. D., Knudsen, B., Hess, D. L., Nelson, C. C., Matsumoto, A. M., et al. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-3332 · Cited by 529

Deactivation of Hepatic Stellate Cells During Liver Fibrosis Resolution in Mice

Troeger, J. S., Mederacke, I., Gwak, G., Dapito, D. H., Mu, X., Hsu, C. C., Pradere, J., Friedman, R. A., & Schwabe, R. F. (2012) · Gastroenterology · doi:10.1053/j.gastro.2012.06.036 · Cited by 515

Genome-wide analysis of noncoding regulatory mutations in cancer

Weinhold, N., Jacobsen, A., Schultz, N., Sander, C., & Lee, W. (2014) · Nature Genetics · doi:10.1038/ng.3101 · Cited by 484

Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion

Dayeh, T., Volkov, P., Salö, S., Hall, E., Nilsson, E., Olsson, A. H., Kirkpatrick, C. L., Wollheim, C. B., Eliasson, L., Rönn, T., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004160 · Cited by 523

Tumor-Infiltrating Macrophages Are Associated with Metastasis Suppression in High-Grade Osteosarcoma: A Rationale for Treatment with Macrophage Activating Agents

Buddingh, E. P., Kuijjer, M. L., Duim, R. A. J., Bürger, H., Agelopoulos, K., Myklebost, O., Serra, M., Mertens, F., Hogendoorn, P. C. W., Lankester, A. C., et al. (2011) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-10-2047 · Cited by 508

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502

PHAST and RPHAST: phylogenetic analysis with space/time models

Hubisz, M. J., Pollard, K. S., & Siepel, A. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbq072 · Cited by 490

Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours

Rebouissou, S., Amessou, M., Couchy, G., Poussin, K., Imbeaud, S., Pilati, C., Izard, T., Balabaud, C., Bioulac-Sage, P., & Zucman-Rossi, J. (2009) · Nature · doi:10.1038/nature07475 · Cited by 477

Suppression of lung adenocarcinoma progression by Nkx2-1

Winslow, M. M., Dayton, T. L., Verhaak, R. G. W., Kim-Kiselak, C., Snyder, E. L., Feldser, D. M., Hubbard, D. D., DuPage, M. J., Whittaker, C. A., Hoersch, S., et al. (2011) · Nature · doi:10.1038/nature09881 · Cited by 467

A genome-wide association study of alcohol dependence

Bierut, L. J., Agrawal, A., Bucholz, K. K., Doheny, K. F., Laurie, C., Pugh, E., Fisher, S., Fox, L., Howells, W., Bertelsen, S., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911109107 · Cited by 457

Comparison of co-expression measures: mutual information, correlation, and model based indices

Song, L., Langfelder, P., & Horvath, S. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-328 · Cited by 460

Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes

Hannon, E., Lunnon, K., Schalkwyk, L., & Mill, J. (2015) · Epigenetics · doi:10.1080/15592294.2015.1100786 · Cited by 455

Kupffer Cells Promote Hepatic Steatosis Via Interleukin-1β–Dependent Suppression of Peroxisome Proliferator-Activated Receptor α Activity

Stienstra, R., Saudale, F., Duval, C., Keshtkar, S., Groener, J. E. M., van Rooijen, N., Staels, B., Kersten, S., & Müller, M. (2010) · Hepatology · doi:10.1002/hep.23337 · Cited by 452

Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways

Lim, E., Wu, D., Pal, B., Bouras, T., Asselin-Labat, M.-L., Vaillant, F., Yagita, H., Lindeman, G. J., Smyth, G. K., & Visvader, J. E. (2010) · Breast Cancer Research · doi:10.1186/bcr2560 · Cited by 440

Iron regulates phosphorylation of Smad1/5/8 and gene expression of Bmp6, Smad7, Id1, and Atoh8 in the mouse liver

Kautz, L., Meynard, D., Monnier, A., Darnaud, V., Bouvet, R., Wang, R.-H., Deng, C., Vaulont, S., Mosser, J., Coppin, H., et al. (2008) · Blood · doi:10.1182/blood-2008-03-143354 · Cited by 437

Nuclear FAK Controls Chemokine Transcription, Tregs, and Evasion of Anti-tumor Immunity

Serrels, A., Lund, T., Serrels, B., Byron, A., McPherson, R. C., von Kriegsheim, A., Gómez-Cuadrado, L., Canel, M., Muir, M., Ring, J. E., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.001 · Cited by 407

MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling

Huang, S., Hölzel, M., Knijnenburg, T., Schlicker, A., Roepman, P., McDermott, U., Garnett, M., Grernrum, W., Sun, C., Prahallad, A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.10.035 · Cited by 430

MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis

Terunuma, A., Putluri, N., Mishra, P., Mathé, E. A., Dorsey, T. H., Yi, M., Wallace, T. A., Issaq, H. J., Zhou, M., Killian, J. K., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci71180 · Cited by 428

Predictability of biomass burning in response to climate changes

Daniau, A. ‐., Bartlein, P. J., Harrison, S. P., Prentice, I. C., Brewer, S., Friedlingstein, P., Harrison‐Prentice, T. I., Inoue, J., Izumi, K., Marlon, J. R., et al. (2012) · Global Biogeochemical Cycles · doi:10.1029/2011gb004249 · Cited by 417

A Modified γ-Retrovirus Vector for X-Linked Severe Combined Immunodeficiency

Hacein-Bey-Abina, S., Pai, S.-Y., Gaspar, H. B., Armant, M., Berry, C. C., Blanche, S., Bleesing, J., Blondeau, J., de Boer, H., Buckland, K. F., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1404588 · Cited by 412

ROCK and JAK1 Signaling Cooperate to Control Actomyosin Contractility in Tumor Cells and Stroma

Sanz-Moreno, V., Gaggioli, C., Yeo, M., Albrengues, J., Wallberg, F., Viros, A., Hooper, S., Mitter, R., Féral, C. C., Cook, M., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.018 · Cited by 409

DNA methylation contributes to natural human variation

Heyn, H., Moran, S., Hernando-Herraez, I., Sayols, S., Gomez, A., Sandoval, J., Monk, D., Hata, K., Marques-Bonet, T., Wang, L., et al. (2013) · Genome Research · doi:10.1101/gr.154187.112 · Cited by 408

Integrated genomics and proteomics define huntingtin CAG length-dependent networks in mice

Langfelder, P., Cantle, J. P., Chatzopoulou, D., Wang, N., Gao, F., Al-Ramahi, I., Lu, X.-H., Ramos, E. M., El-Zein, K., Zhao, Y., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4256 · Cited by 385

Relationship Between Methylome and Transcriptome in Patients With Nonalcoholic Fatty Liver Disease

Murphy, S. K., Yang, H., Moylan, C. A., Pang, H., Dellinger, A., Abdelmalek, M. F., Garrett, M. E., Ashley–Koch, A., Suzuki, A., Tillmann, H. L., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.07.047 · Cited by 391

Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor

Mohammed, H., D’Santos, C., Serandour, A. A., Ali, H. R., Brown, G. D., Atkins, A., Rueda, O. M., Holmes, K. A., Theodorou, V., Robinson, J. L. L., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.010 · Cited by 400

Lifespan extension induced by AMPK and calcineurin is mediated by CRTC-1 and CREB

Mair, W., Morantte, I., Rodrigues, A. P. C., Manning, G., Montminy, M., Shaw, R. J., & Dillin, A. (2011) · Nature · doi:10.1038/nature09706 · Cited by 393

Statistical Design and Analysis of RNA Sequencing Data

Auer, P. L., & Doerge, R. W. (2010) · Genetics · doi:10.1534/genetics.110.114983 · Cited by 393

Robustly detecting differential expression in RNA sequencing data using observation weights

Zhou, X., Lindsay, H., & Robinson, M. D. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku310 · Cited by 387

Mistimed sleep disrupts circadian regulation of the human transcriptome

Archer, S. N., Laing, E. E., Möller-Levet, C. S., van der Veen, D. R., Bucca, G., Lazar, A. S., Santhi, N., Slak, A., Kabiljo, R., von Schantz, M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1316335111 · Cited by 386

SIRT6 is responsible for more efficient DNA double-strand break repair in long-lived species

Tian, X., Firsanov, D., Zhang, Z., Cheng, Y., Luo, L., Tombline, G., Tan, R., Simon, M., Henderson, S., Steffan, J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.043 · Cited by 353

Impaired Mitochondrial Biogenesis in Adipose Tissue in Acquired Obesity

Heinonen, S., Buzkova, J., Muniandy, M., Kaksonen, R., Ollikainen, M., Ismail, K., Hakkarainen, A., Lundbom, J., Lundbom, N., Vuolteenaho, K., et al. (2015) · Diabetes · doi:10.2337/db14-1937 · Cited by 362

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX

Ko, M., An, J., Bandukwala, H. S., Chavez, L., Äijö, T., Pastor, W. A., Segal, M. F., Li, H., Koh, K. P., Lähdesmäki, H., et al. (2013) · Nature · doi:10.1038/nature12052 · Cited by 373

Downstream of Mutant KRAS, the Transcription Regulator YAP Is Essential for Neoplastic Progression to Pancreatic Ductal Adenocarcinoma

Zhang, W., Nandakumar, N., Shi, Y., Manzano, M., Smith, A., Graham, G., Gupta, S., Vietsch, E. E., Laughlin, S. Z., Wadhwa, M., et al. (2014) · Science Signaling · doi:10.1126/scisignal.2005049 · Cited by 360

Elucidating Compound Mechanism of Action by Network Perturbation Analysis

Woo, J. H., Shimoni, Y., Yang, W. S., Subramaniam, P., Iyer, A., Nicoletti, P., Rodríguez Martínez, M., López, G., Mattioli, M., Realubit, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.056 · Cited by 351

The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila

Liu, N., Landreh, M., Cao, K., Abe, M., Hendriks, G.-J., Kennerdell, J. R., Zhu, Y., Wang, L.-S., & Bonini, N. M. (2012) · Nature · doi:10.1038/nature10810 · Cited by 356

BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation

Raffel, S., Falcone, M., Kneisel, N., Hansson, J., Wang, W., Lutz, C., Bullinger, L., Poschet, G., Nonnenmacher, Y., Barnert, A., et al. (2017) · Nature · doi:10.1038/nature24294 · Cited by 354

MHC-I expression renders catecholaminergic neurons susceptible to T-cell-mediated degeneration

Cebrián, C., Zucca, F. A., Mauri, P., Steinbeck, J. A., Studer, L., Scherzer, C. R., Kanter, E., Budhu, S., Mandelbaum, J., Vonsattel, J. P., et al. (2014) · Nature Communications · doi:10.1038/ncomms4633 · Cited by 338

Podocyte-Selective Deletion of Dicer Induces Proteinuria and Glomerulosclerosis

Shi, S., Yu, L., Chiu, C., Sun, Y., Chen, J., Khitrov, G., Merkenschlager, M., Holzman, L. B., Zhang, W., Mundel, P., et al. (2008) · Journal of the American Society of Nephrology · doi:10.1681/asn.2008030312 · Cited by 349

The tumor-promoting actions of TNF-α involve TNFR1 and IL-17 in ovarian cancer in mice and humans

Charles, K. A., Kulbe, H., Soper, R., Escorcio-Correia, M., Lawrence, T., Schultheis, A., Chakravarty, P., Thompson, R. G., Kollias, G., Smyth, J. F., et al. (2009) · Journal of Clinical Investigation · doi:10.1172/jci39065 · Cited by 338

Long-term IL-33–producing epithelial progenitor cells in chronic obstructive lung disease

Byers, D. E., Alexander-Brett, J., Patel, A. C., Agapov, E., Dang-Vu, G., Jin, X., Wu, K., You, Y., Alevy, Y., Girard, J.-P., et al. (2013) · Journal of Clinical Investigation · doi:10.1172/jci65570 · Cited by 337

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

Fortin, J.-P., & Hansen, K. D. (2015) · Genome Biology · doi:10.1186/s13059-015-0741-y · Cited by 333

TFEB and TFE3 cooperate in the regulation of the innate immune response in activated macrophages

Pastore, N., Brady, O. A., Diab, H. I., Martina, J. A., Sun, L., Huynh, T., Lim, J.-A., Zare, H., Raben, N., Ballabio, A., et al. (2016) · Autophagy · doi:10.1080/15548627.2016.1179405 · Cited by 331

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

Chandra, T., Kirschner, K., Thuret, J.-Y., Pope, B. D., Ryba, T., Newman, S., Ahmed, K., Samarajiwa, S. A., Salama, R., Carroll, T., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.010 · Cited by 308

Genetic analysis of complex traits in the emerging Collaborative Cross

Aylor, D. L., Valdar, W., Foulds-Mathes, W., Buus, R. J., Verdugo, R. A., Baric, R. S., Ferris, M. T., Frelinger, J. A., Heise, M., Frieman, M. B., et al. (2011) · Genome Research · doi:10.1101/gr.111310.110 · Cited by 328

Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus

Suderman, M., McGowan, P. O., Sasaki, A., Huang, T. C. T., Hallett, M. T., Meaney, M. J., Turecki, G., & Szyf, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121260109 · Cited by 327

Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd‐hyperaccumulator Thlaspi caerulescens

VAN DE MORTEL, J. E., SCHAT, H., MOERLAND, P. D., VAN THEMAAT, E. V. L., VAN DER ENT, S., BLANKESTIJN, H., GHANDILYAN, A., TSIATSIANI, S., & AARTS, M. G. M. (2008) · Plant, Cell & Environment · doi:10.1111/j.1365-3040.2007.01764.x · Cited by 326

The Capsaspora genome reveals a complex unicellular prehistory of animals

Suga, H., Chen, Z., de Mendoza, A., Sebé-Pedrós, A., Brown, M. W., Kramer, E., Carr, M., Kerner, P., Vervoort, M., Sánchez-Pons, N., et al. (2013) · Nature Communications · doi:10.1038/ncomms3325 · Cited by 317

TREM2 regulates microglial cell activation in response to demyelination in vivo

Cantoni, C., Bollman, B., Licastro, D., Xie, M., Mikesell, R., Schmidt, R., Yuede, C. M., Galimberti, D., Olivecrona, G., Klein, R. S., et al. (2015) · Acta Neuropathologica · doi:10.1007/s00401-015-1388-1 · Cited by 296

The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells

Provençal, N., Suderman, M. J., Guillemin, C., Massart, R., Ruggiero, A., Wang, D., Bennett, A. J., Pierre, P. J., Friedman, D. P., Côté, S. M., et al. (2012) · The Journal of Neuroscience · doi:10.1523/jneurosci.1470-12.2012 · Cited by 312

When is hub gene selection better than standard meta-analysis?

Langfelder, P., Mischel, P. S., & Horvath, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061505 · Cited by 313

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice

Lewis, M. A., Quint, E., Glazier, A. M., Fuchs, H., De Angelis, M. H., Langford, C., van Dongen, S., Abreu-Goodger, C., Piipari, M., Redshaw, N., et al. (2009) · Nature Genetics · doi:10.1038/ng.369 · Cited by 302

APC and Oncogenic KRAS Are Synergistic in Enhancing Wnt Signaling in Intestinal Tumor Formation and Progression

Janssen, K., Alberici, P., Fsihi, H., Gaspar, C., Breukel, C., Franken, P., Rosty, C., Abal, M., El Marjou, F., Smits, R., et al. (2006) · Gastroenterology · doi:10.1053/j.gastro.2006.08.011 · Cited by 298

Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

Litvak, V., Ramsey, S. A., Rust, A. G., Zak, D. E., Kennedy, K. A., Lampano, A. E., Nykter, M., Shmulevich, I., & Aderem, A. (2009) · Nature Immunology · doi:10.1038/ni.1721 · Cited by 295

Interferon-γ links ultraviolet radiation to melanomagenesis in mice

Zaidi, M. R., Davis, S., Noonan, F. P., Graff-Cherry, C., Hawley, T. S., Walker, R. L., Feigenbaum, L., Fuchs, E., Lyakh, L., Young, H. A., et al. (2011) · Nature · doi:10.1038/nature09666 · Cited by 293

Time of exercise specifies the impact on muscle metabolic pathways and systemic energy homeostasis

Sato, S., Basse, A. L., Schönke, M., Chen, S., Samad, M., Altıntaş, A., Laker, R. C., Dalbram, E., Barrès, R., Baldi, P., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.03.013 · Cited by 298

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development

Marques, S., van Bruggen, D., Vanichkina, D. P., Floriddia, E. M., Munguba, H., Väremo, L., Giacomello, S., Falcão, A. M., Meijer, M., Björklund, Å. K., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.07.005 · Cited by 290

Mitochondrial function in the brain links anxiety with social subordination

Hollis, F., van der Kooij, M. A., Zanoletti, O., Lozano, L., Cantó, C., & Sandi, C. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512653112 · Cited by 288

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

Metabolic adaptation establishes disease tolerance to sepsis

Weis, S., Carlos, A. R., Moita, M. R., Singh, S., Blankenhaus, B., Cardoso, S., Larsen, R., Rebelo, S., Schäuble, S., Del Barrio, L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.05.031 · Cited by 284

Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways †

Nishimura, Y., Martin, C. L., Vazquez-Lopez, A., Spence, S. J., Alvarez-Retuerto, A. I., Sigman, M., Steindler, C., Pellegrini, S., Schanen, N. C., Warren, S. T., et al. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddm116 · Cited by 276

A comparison of statistical methods for detecting differentially expressed genes from RNA‐seq data

Kvam, V. M., Liu, P., & Si, Y. (2012) · American Journal of Botany · doi:10.3732/ajb.1100340 · Cited by 281

De novo mutations in regulatory elements in neurodevelopmental disorders

Short, P. J., McRae, J. F., Gallone, G., Sifrim, A., Won, H., Geschwind, D. H., Wright, C. F., Firth, H. V., FitzPatrick, D. R., Barrett, J. C., et al. (2018) · Nature · doi:10.1038/nature25983 · Cited by 274

Foxp2 regulates gene networks implicated in neurite outgrowth in the developing brain

Vernes, S. C., Oliver, P. L., Spiteri, E., Lockstone, H. E., Puliyadi, R., Taylor, J. M., Ho, J., Mombereau, C., Brewer, A., Lowy, E., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002145 · Cited by 276

Blood coagulation protein fibrinogen promotes autoimmunity and demyelination via chemokine release and antigen presentation

Ryu, J. K., Petersen, M. A., Murray, S. G., Baeten, K. M., Meyer-Franke, A., Chan, J. P., Vagena, E., Bedard, C., Machado, M. R., Coronado, P. E. R., et al. (2015) · Nature Communications · doi:10.1038/ncomms9164 · Cited by 271

A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing

Martí, E., Pantano, L., Bañez-Coronel, M., Llorens, F., Miñones-Moyano, E., Porta, S., Sumoy, L., Ferrer, I., & Estivill, X. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq575 · Cited by 276

Impact of age, BMI and HbA1c levels on the genome-wide DNA methylation and mRNA expression patterns in human adipose tissue and identification of epigenetic biomarkers in blood

Ronn, T., Volkov, P., Gillberg, L., Kokosar, M., Perfilyev, A., Jacobsen, A. L., Jorgensen, S. W., Brons, C., Jansson, P.-A., Eriksson, K.-F., et al. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv124 · Cited by 270

Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis

Pollari, S., Käkönen, S.-M., Edgren, H., Wolf, M., Kohonen, P., Sara, H., Guise, T., Nees, M., & Kallioniemi, O. (2011) · Breast Cancer Research and Treatment · doi:10.1007/s10549-010-0848-5 · Cited by 269

The impact of gut microbiota on gender-specific differences in immunity

Fransen, F., van Beek, A. A., Borghuis, T., Meijer, B., Hugenholtz, F., van der Gaast-de Jongh, C., Savelkoul, H. F., de Jonge, M. I., Faas, M. M., Boekschoten, M. V., et al. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00754 · Cited by 266

Genomic and proteomic profiling reveals reduced mitochondrial function and disruption of the neuromuscular junction driving rat sarcopenia

Ibebunjo, C., Chick, J. M., Kendall, T., Eash, J. K., Li, C., Zhang, Y., Vickers, C., Wu, Z., Clarke, B. A., Shi, J., et al. (2013) · Molecular and Cellular Biology · doi:10.1128/mcb.01036-12 · Cited by 267

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

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

Intensity-based hierarchical bayes method improves testing for differentially expressed genes in microarray experiments

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Circadian Desynchrony Promotes Metabolic Disruption in a Mouse Model of Shiftwork

Barclay, J. L., Husse, J., Bode, B., Naujokat, N., Meyer-Kovac, J., Schmid, S. M., Lehnert, H., & Oster, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037150 · Cited by 259

Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis

Hou, W., & Ji, Z. (2024) · Nature Methods · doi:10.1038/s41592-024-02235-4 · Cited by 277

Increased NOS2 predicts poor survival in estrogen receptor-negative breast cancer patients

Glynn, S. A., Boersma, B. J., Dorsey, T. H., Yi, M., Yfantis, H. G., Ridnour, L. A., Martin, D. N., Switzer, C. H., Hudson, R. S., Wink, D. A., et al. (2010) · Journal of Clinical Investigation · doi:10.1172/jci42059 · Cited by 254

Molecular and cellular reorganization of neural circuits in the human lineage

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