bioconductor: ArrayExpress | Projects

10.3390/cancers12051136

Increased Level of Long Non-Coding RNA MALAT1 Is a Common Feature of Amoeboid Invasion
Cited by: 4
Author(s): Ladislav Merta, Aneta Gandalovičová, Vladimı́r Čermák, Michal Dibus, Tony Gutschner, Sven Diederichs, Daniel Rösel, Jan Brábek
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1005873

A FAIR guide for data providers to maximise sharing of human genomic data
Cited by: 24
Author(s): Manuel Corpas, Nadezda V. Kovalevskaya, Amanda McMurray, Fiona Nielsen
Software Mentions: 2
Published: over 8 years ago

10.1093/bib/bbw044

Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned
Cited by: 9
Author(s): Gerald Li, Peter Bankhead, Philip D. Dunne, Paul G. O’Reilly, Jacqueline James, Manuel Salto-Tellez, Peter Hamilton, Darragh G. McArt
Software Mentions: 2
Published: over 10 years ago

10.1093/hmg/ddx424

Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort
Cited by: 72
Author(s): Ana Viñuela, Andrew Anand Brown, Alfonso Buil, Pei-Chien Tsai, Matthew N. Davies, Jordana T. Bell, Emmanouil T. Dermitzakis, Timothy D. Spector, Kerrin S. Small
Software Mentions: 2
Published: almost 9 years ago

10.3390/cancers11040507

Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer
Cited by: 8
Author(s): Shujun Huang, Wayne Xu, Pingzhao Hu, Ted M. Lakowski
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers13184577

The Stress-Inducible BCL2A1 Is Required for Ovarian Cancer Metastatic Progression in the Peritoneal Microenvironment
Cited by: 5
Author(s): Rui Liang, Mingo M. H. Yung, Fengjiao He, Peili Jiao, Ki Chan, Hextan Ys Ngan, David W. Chan
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0237463

Bio-activating ultrafine grain titanium: RNA sequencing reveals enhanced mechano-activation of osteoconduction on nanostructured substrates
Cited by: 4
Author(s): Rebecca A. Reiss, Terry C. Lowe, Johnny A. Sena, Oleg Makhnin, Melanie C. Connick, Patrick Erik Illescas, Casey F. Davis
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers13153755

Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma
Cited by: 6
Author(s): Laure Dutrieux, Yea-Lih Lin, Malik Lutzmann, Raphaël Rodriguez, Michel Cogné, Philippe Pasero, Jérôme Moreaux
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0031475

LAL Regulators SCO0877 and SCO7173 as Pleiotropic Modulators of Phosphate Starvation Response and Actinorhodin Biosynthesis in Streptomyces coelicolor
Cited by: 32
Author(s): Susana Guerra, Antonio Rodríguez‐García, Javier Santos‐Aberturas, Cláudia M. Vicente, Tamara D. Payero, Juan F. Martı́n, Jesús F. Aparicio
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0005662

Accumulating Progenitor Cells in the Luminal Epithelial Cell Layer Are Candidate Tumor Initiating Cells in a Pten Knockout Mouse Prostate Cancer Model
Cited by: 66
Author(s): Hanneke Korsten, Angelique Ziel-van der Made, Xiaoqian Ma, Theodorus H. van der Kwast, Jan Trapman
Software Mentions: 2
Published: over 17 years ago

10.1186/s12859-015-0519-y

Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity
Cited by: 17
Author(s): Xindong Zhang, Lin Gao, Zhiping Liu, Luonan Chen
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-14-436

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Cited by: 15
Author(s): Katrina Williams, William A Bryant, Victoria A Jenkins, Geraint Barton, Adam A. Witney, John W. Pinney, Brian D. Robertson
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pcbi.1000779

A Quick Guide to Large-Scale Genomic Data Mining
Cited by: 38
Author(s): Curtis Huttenhower, Oliver Hofmann
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0005657

Highly Active Microbial Phosphoantigen Induces Rapid yet Sustained MEK/Erk- and PI-3K/Akt-Mediated Signal Transduction in Anti-Tumor Human γδ T-Cells
Cited by: 47
Author(s): Daniel V. Correia, Francisco d’Orey, Bruno Cardoso, Telma Lança, Ana Rita Grosso, Ana deBarros, Leila R. Martins, João T. Barata, Bruno Silva‐Santos
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-10-S3-S15

Improving gene expression similarity measurement using pathway-based analytic dimension
Cited by: 4
Author(s): Changwon Keum, Jung Hoon Woo, Won Seok Oh, Sue-Nie Park, Kyoung Tai No
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pone.0241174

Comprehensive analysis of differential expression profiles via transcriptome sequencing in SH-SY5Y cells infected with CV-A16
Cited by: 1
Author(s): Yuanliang Hu, Yang Zhen, Shenglan Wang, Danxiong Sun, Mi Zhong, Mudong Wen, Longding Liu, Yunhui Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2121-10-87

Global transcriptional response after exposure of fission yeast cells to ultraviolet light
Cited by: 6
Author(s): Henriette C. Skjølberg, Øyvind Fensgård, Hilde Nilsen, Beáta Grallert, Erik Boye
Software Mentions: 2
Published: almost 17 years ago

10.1155/2020/9015713

Classification of Thyroid Nodules with Stacked Denoising Sparse Autoencoder
Cited by: 3
Author(s): Zexin Li, Kaiji Yang, Lili Zhang, Chiju Wei, Peixuan Yang, Weilai Xu
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-8-S1-S21

The Genopolis Microarray Database
Cited by: 8
Author(s): Andrea Splendiani, Marco Brandizi, Gaël Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri, Paola Ricciardi‐Castagnoli
Software Mentions: 2
Published: over 19 years ago

10.1371/journal.pone.0042161

Identification of Pluripotent and Adult Stem Cell Genes Unrelated to Cell Cycle and Associated with Poor Prognosis in Multiple Myeloma
Cited by: 18
Author(s): Alboukadel Kassambara, Dirk Hose, Jérôme Moreaux, Thierry Rème, Jennifer Torrent, Jean François Rossi, Hartmut Goldschmidt, Bernard Klein
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-213X-11-2

Targets downstream of Cdk8 in Dictyostelium development
Cited by: 4
Author(s): David Greene, Gareth Bloomfield, Jason Skelton, Alasdair Ivens, Catherine J. Pears
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0234803

Genetic analysis of body weight in wild populations of medaka fish from different latitudes
Cited by: 3
Author(s): Tamiris I. Yassumoto, Mana Nakatsukasa, Atsushi J. Nagano, Masaki Yasugi, Takashi Yoshimura, Ai Shinomiya
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0236006

Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China
Cited by: 18
Author(s): Tong-Wei Guan, Yijin Lin, Meng-Ying Ou, Ke-Bao Chen
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-7-190

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation
Cited by: 15
Author(s): Leandro Hermida, Olivier Schaad, Philippe Demougin, Patrick Descombes, Michael Primig
Software Mentions: 2
Published: over 20 years ago

10.1167/iovs.61.4.24

The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension
Cited by: 13
Author(s): Ilona Liesenborghs, Lars Eijssen, Martina Kutmon, Theo G. M. F. Gorgels, Chris T. Evelo, Henny J. M. Beckers, Carroll A.B. Webers, Jan S.A.G. Schouten
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-13-187

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit
Cited by: 32
Author(s): Viviana Lima-Silva, Abel Rosado, Vítor Amorim‐Silva, Antonio Muñoz‐Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta, Miguel A. Botella
Software Mentions: 2
Published: over 14 years ago

10.1186/1752-0509-8-S2-I1

Data integration in the era of omics: current and future challenges
Cited by: 295
Author(s): David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew E. Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam‐Rudloff, Ana Conesa, Jesper Tegnér
Software Mentions: 2
Published: almost 13 years ago

10.1186/bcr2256

Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression
Cited by: 46
Author(s): Cecilia Williams, Luísa A. Helguero, Karin Edvardsson, Lars Arne Haldosén, Jan‐Åke Gustafsson
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0083772

Transcriptome Analysis of Nodes and Buds from High and Low Tillering Switchgrass Inbred Lines
Cited by: 9
Author(s): Wang Yixing, Xin Zeng, Lila Peal, Yuhong Tang, Yanqi Wu, Ramamurthy Mahalingam
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-7-205

SIMAGE: si mulation of DNA-m icroa rray g ene e xpression data
Cited by: 23
Author(s): Casper J. Albers, Ritsert C. Jansen, Jan Kok, Oscar P. Kuipers, Sacha A. F. T. van Hijum
Software Mentions: 2
Published: over 20 years ago

10.1371/journal.pone.0042490

Gene Profile of Chemokines on Hepatic Stellate Cells of Schistosome-Infected Mice and Antifibrotic Roles of CXCL9/10 on Liver Non-Parenchymal Cells
Cited by: 26
Author(s): Yuejin Liang, Jie Luo, Qiao Lu, Ying Zhou, Hai Wei Wu, Dan Zheng, Yong ya Ren, Ke Sun, Yong Wang, Zhao Song Zhang
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0026801

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
Cited by: 104
Author(s): Alicia N. Massa, Kevin L. Childs, Haining Lin, Glenn J. Bryan, Giovanni Giuliano, C. Robin Buell
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pgen.1007440

Antimicrobial peptides modulate long-term memory
Cited by: 45
Author(s): Raquel Barajas-Azpeleta, Jianping Weng, Jason Gill, Ryan Welte, Chris Seidel, Sean A. McKinney, Stephane Dissel, Kausik Si
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0238190

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria
Cited by: 26
Author(s): Abdurrahman Hassan Jibril, Iruka N. Okeke, Anders Dalsgaard, Eglė Kudirkienė, Olabisi C. Akinlabi, Muhammad Bashir Bello
Software Mentions: 2
Published: about 6 years ago

10.1038/onc.2015.526

A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer
Cited by: 28
Author(s): Anna Moles, Jacqueline Butterworth, Ana M. Sánchez, Jill E. Hunter, Jack Leslie, Hélène Sellier, Dina Tiniakos, Simon Cockell, Derek A. Mann, Fiona Oakley, Neil D. Perkins
Software Mentions: 2
Published: over 10 years ago

10.1038/s41388-018-0588-2

LCE: an open web portal to explore gene expression and clinical associations in lung cancer
Cited by: 70
Author(s): Ling Cai, Shing-Jong Lin, Luc Girard, Yunyun Zhou, Lin Yang, Bo Ci, Qinbo Zhou, Danni Luo, Bo Yao, Jing Tang, Jeffrey D. Allen, Kenneth E. Huffman, Adi F. Gazdar, John V. Heymach, Ignacio I. Wistuba, Guanghua Xiao, John D. Minna, Yang Xie
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0242939

DamID identifies targets of CEH-60/PBX that are associated with neuron development and muscle structure in Caenorhabditis elegans
Cited by: 5
Author(s): Pieter Van de Walle, Celia Muñoz-Jiménez, Peter Askjaer, Liliane Schoofs, Liesbet Temmerman
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2202-6-55

Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation
Cited by: 7
Author(s): Maria Sievertzon, Valtteri Wirta, Alex Mercer, Jonas Frisén, Joakim Lundeberg
Software Mentions: 2
Published: about 21 years ago

10.1186/bcr2109

PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Cited by: 25
Author(s): Anna Git, Inmaculada Spiteri, Cherie Blenkiron, Mark J. Dunning, Jessica C. Pole, Suet-Feung Chin, Yanzhong Wang, James Smith, Frederick J. Livesey, Carlos Caldas
Software Mentions: 2
Published: over 18 years ago

10.1016/j.jmb.2020.10.008

TET1 Interacts Directly with NANOG via Independent Domains Containing Hydrophobic and Aromatic Residues
Cited by: 2
Author(s): Raphaël Pantier, Nicholas P. Mullin, Elisa Hall-Ponselé, Ian Chambers
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0229415

Identification of two novel adenoviruses in smooth-billed ani and tropical screech owl
Cited by: 10
Author(s): Ana Paula Jejesky de Oliveira, Maria Cristina Valdetaro Rangel, Márton Z. Vidovszky, João Luiz Rossi, Fernando Vicentini, Balázs Harrach, Győző L. Kaján
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-7-49

Development of a chicken 5 K microarray targeted towards immune function
Cited by: 31
Author(s): Jacqueline Smith, David Speed, Paul Hocking, Richard Talbot, W.G.J. Degen, Virgil E.J.C. Schijns, Elizabeth J. Glass, David W. Burt
Software Mentions: 2
Published: over 20 years ago

10.3892/or.2014.3579

Human cancer databases (Review)
Cited by: 63
Author(s): Athanasia Pavlopoulou, Demetrios Α. Spandidos, Ioannis Michalopoulos
Software Mentions: 2
Published: almost 12 years ago

10.7554/eLife.44344

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
Cited by: 102
Author(s): Christopher D. Todd, Özgen Deniz, Darren Taylor, Miguel R. Branco
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1005251

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding
Cited by: 34
Author(s): Xin Xie, Michael J. T. Stubbington, Jesper K. Nissen, Kristian G. Andersen, Daniel Hebenstreit, Sarah A. Teichmann, Alexander G. Betz
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-021-04359-2

Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders
Cited by: 0
Author(s): Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi, Benoît Ballester
Software Mentions: 2
Published: about 5 years ago

10.1186/bcr2192

A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer
Cited by: 117
Author(s): Fabien Reyal, Martin H. van Vliet, Nicola J. Armstrong, Hugo M. Horlings, Karin E. de Visser, M Kok, Andrew E. Teschendorff, Stella Mook, Laura van ’t Veer, Carlos Caldas, Rémy Salmon, Marc J. van de Vijver, Lodewyk F.A. Wessels
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0040521

Molecular Resistance Fingerprint of Pemetrexed and Platinum in a Long-Term Survivor of Mesothelioma
Cited by: 33
Author(s): Oluf Dimitri Røe, Adam Szulkin, Endre Anderssen, Arnar Flatberg, Helmut Sandeck, Tore Amundsen, Sten Even Erlandsen, Katalin Dobra, Stein Sundstrøm
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0045527

Reconstruction of the Evolutionary History of Saccharomyces cerevisiae x S. kudriavzevii Hybrids Based on Multilocus Sequence Analysis
Cited by: 28
Author(s): David Peris, Christian A. Lopes, Armando Arias, Eladio Barrio
Software Mentions: 2
Published: about 14 years ago

10.1111/acel.13092

Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver
Cited by: 20
Author(s): Andrew Price, Mohan C. Manjegowda, Jessica Kain, Swetha Anandh, Irina M. Bochkis
Software Mentions: 2
Published: almost 7 years ago

10.1186/bcr2334

Genomic profiling of breast tumours in relation to BRCAabnormalities and phenotypes
Cited by: 131
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Óskar Þór Jóhannsson, Katrín Ólafsdóttir, Margrét Steinarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-11-7

Decoding pooled RNAi screens by means of barcode tiling arrays
Cited by: 10
Author(s): Michael Boettcher, Johannes Fredebohm, Amin Moghaddas Gholami, Yafit Hachmo, Iris Dotan, Dan Canaani, Jörg D. Hoheisel
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pone.0111668

A Network-Based Classification Model for Deriving Novel Drug-Disease Associations and Assessing Their Molecular Actions
Cited by: 42
Author(s): Min Kyu Oh, Jaegyoon Ahn, Yoon Yong-Jin
Software Mentions: 2
Published: almost 12 years ago

10.7554/eLife.12717

Zeb1 controls neuron differentiation and germinal zone exit by a mesenchymal-epithelial-like transition
Cited by: 58
Author(s): Shalini Singh, Danielle Howell, Niraj Trivedi, Ketty Kessler, Taren Ong, Pedro Rosmaninho, Alexandre A.S.F. Raposo, Giles Robinson, Martine F. Roussel, Diogo S. Castro, David J. Solecki
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0256158

Cohort profile: Epigenetics in Pregnancy (EPIPREG) – population-based sample of European and South Asian pregnant women with epigenome-wide DNA methylation (850k) in peripheral blood leukocytes
Cited by: 7
Author(s): Nicolás Fragoso-Bargas, Julia O Opsahl, Nadezhda Kiryushchenko, Yvonne Böttcher, Sindre Lee, Elisabeth Qvigstad, Kåre Rønn Richardsen, Christin W. Waage, Line Sletner, Anne Karen Jenum, Rashmi B. Prasad, Leif Groop, Gunn-Helen Moen, Kåre I. Birkeland, Christine Sommer
Software Mentions: 2
Published: about 5 years ago

10.1186/bcr3403

Embryonic mammary signature subsets are activated in Brca1 -/- and basal-like breast cancers
Cited by: 47
Author(s): Marketa Zvelebil, Erik Oliemuller, Qiong Gao, Olivia Wansbury, Alan Mackay, Howard Kendrick, Matthew J. Smalley, Jorge S. Reis‐Filho, Beatrice A. Howard
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.33506

Epidermal LysM receptor ensures robust symbiotic signalling in Lotus japonicus
Cited by: 48
Author(s): Eiichi Murakami, Jeryl Cheng, Kira Gysel, Zoltán Bozsóki, Yasuyuki Kawaharada, Christian T. Hjuler, Kasper K. Sørensen, Ke Tao, Simon Kelly, Francesco Venice, Andrea Genre, Mikkel B. Thygesen, Noor de Jong, Maria Vinther, Dorthe Bødker Jensen, Knud J. Jensen, Mickaël Blaise, Lene Heegaard Madsen, Kasper R. Andersen, Jens Stougaard, Simona Radutoiu
Software Mentions: 2
Published: over 8 years ago

10.1186/s13058-015-0539-6

Mouse mammary stem cells express prognostic markers for triple-negative breast cancer
Cited by: 32
Author(s): Kelly Soady, Howard Kendrick, Qiong Gao, Andrew Tutt, Marketa Zvelebil, Liliana Ordonez, Jelmar Quist, David Wei-Min Tan, Clare M. Isacke, Anita Grigoriadis, Matthew J. Smalley
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0006447

Mining Biological Pathways Using WikiPathways Web Services
Cited by: 107
Author(s): Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Martijn P. van Iersel, Chris T. Evelo, Bruce R. Conklin
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0022196

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes
Cited by: 119
Author(s): Kevin L. Childs, Rebecca M. Davidson, C. Robin Buell
Software Mentions: 2
Published: about 15 years ago

10.7554/eLife.65722

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Cited by: 18
Author(s): Rong Yu, Egor Vorontsov, Carina Sihlbom, Jens Nielsen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0230822

Characterization of the fungal community in the canopy air of the invasive plant Ageratina adenophora and its potential to cause plant diseases
Cited by: 7
Author(s): Chinho Lin, Kai Fang, Xing-Fan Dong, Ai-Ling Yang, Yuxuan Li, Hanbo Zhang
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.18715

A computational interactome and functional annotation for the human proteome
Cited by: 59
Author(s): José Ignacio Garzón, Lei Deng, Diana Murray, Sagi Shapira, Donald Petrey, Barry Honig
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0232297

Association between the rs1544410 polymorphism in the vitamin D receptor (VDR) gene and insulin secretion after gestational diabetes mellitus
Cited by: 6
Author(s): Nael Shaat, Anastasia Katsarou, Bushra Shahida, Rashmi B. Prasad, Karl Kristensen, Tereza Planck
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.33761

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair
Cited by: 116
Author(s): Nataša Savić, Femke Ringnalda, Helen Lindsay, Christian Berk, Katja Bargsten, Yizhou Li, Dario Neri, Mark D. Robinson, Constance Ciaudo, Jonathan Hall, Martin Jínek, Gerald Schwank
Software Mentions: 2
Published: over 8 years ago

10.1590/1414-431X2020e10388

Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification
Cited by: 0
Author(s): Lucas Delmonico, John C. Obenauer, Thomas P. Stockfisch, Marcia V. Fournier
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0236460

Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy
Cited by: 12
Author(s): Thanawat Rattanathammethee, Pimchanok Tuitemwong, Parameth Thiennimitr, Phinitphong Sarichai, Sarisa Na Pombejra, Pokpong Piriyakhuntorn, Sasinee Hantrakool, Chatree Chai‐Adisaksopha, Ekarat Rattarittamrong, Adisak Tantiworawit, Lalita Norasetthada
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0121846

Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes
Cited by: 6
Author(s): Avinash M. Veerappa, Sangeetha Vishweswaraiah, Kusuma Lingaiah, Megha Murthy, Raviraj V. Suresh, Dinesh S. Manjegowda, Nallur B. Ramachandra
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-7-240

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies
Cited by: 5
Author(s): Paul Honoré, Samuel Granjeaud, Rebecca Tagett, S. Deraco, Emmanuel Beaudoing, Jacques Rougemont, Stéphane Debono, Pascal Hingamp
Software Mentions: 2
Published: about 20 years ago

10.1371/journal.pone.0256588

Characterization of microRNA expression in B cells derived from Japanese black cattle naturally infected with bovine leukemia virus by deep sequencing
Cited by: 5
Author(s): Chihiro Ochiai, Sonoko Miyauchi, Yuta Kudo, Yuta Naruke, Syuji Yoneyama, Keisuke Tomita, Leng Dongze, Yusuke Chiba, To-ichi Hirata, Toshihiro Ichijo, Kazuya Nagai, Sota Kobayashi, Shinji Yamada, Hirokazu Hikono, Kenji Murakami
Software Mentions: 2
Published: about 5 years ago

10.1002/biot.201100305

Molecular signatures from omics data: From chaos to consensus
Cited by: 103
Author(s): Jaeyun Sung, Yuliang Wang, Sriram Chandrasekaran, Daniela Witten, Nathan D. Price
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0230802

Detection of novel coronaviruses in bats in Myanmar
Cited by: 66
Author(s): Marc Valitutto, Ohnmar Aung, Kyaw Yan Naing Tun, Megan E. Vodzak, Dawn Zimmerman, Jennifer H. Yu, Ye Tun Win, Min Thein Maw, Wai Zin Thein, Htay Htay Win, Jasjeet K. Dhanota, Victoria Ontiveros, Brett Smith, Alexandre Tremeau-Brevard, Tracey Goldstein, Christine K. Johnson, Suzan Murray, Jonna A. K. Mazet
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2210-8-16

Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in Atlantic salmon (Salmo salar L.)
Cited by: 23
Author(s): Pål A. Olsvik, Kai Kristoffer Lie, Eva Mykkeltvedt, Ole Bent Samuelsen, Kjell Petersen, Anne-Kristin Stavrum, Bjørn Tore Lunestad
Software Mentions: 2
Published: about 18 years ago

10.1111/acel.12676

Age‐associated dysregulation of protein metabolism in the mammalian oocyte
Cited by: 80
Author(s): Francesca E. Duncan, Susmita Jasti, Ariel Paulson, John M. Kelsh, Barbara Fegley, Jennifer L. Gerton
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms141123160

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System
Cited by: 4
Author(s): Paolo Martini, Gabriele Sales, Enrica Calura, Mattia Brugiolo, Gerolamo Lanfranchi, Chiara Romualdi, Stefano Cagnin
Software Mentions: 2
Published: almost 13 years ago

10.3390/ijms151017601

Hope for GWAS: Relevant Risk Genes Uncovered from GWAS Statistical Noise
Cited by: 2
Author(s): Catarina Correia, Yoan Diekmann, Astrid M. Vicente, José B. Pereira-Leal
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0110840

Measuring the Effect of Inter-Study Variability on Estimating Prediction Error
Cited by: 19
Author(s): Shuyi Ma, Jaeyun Sung, Andrew T. Magis, Yuliang Wang, Donald Geman, Nathan D. Price
Software Mentions: 2
Published: about 12 years ago

10.3390/ijms161226148

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders
Cited by: 41
Author(s): Martin Hofmann-Apitius, G. Ball, Stephan Gebel, Shweta Bagewadi, Bernard de Bono, Reinhard Schneider, Matt Page, Alpha Tom Kodamullil, Erfan Younesi, Christian Ebeling, Jesper Tegnér, Luc Canard
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0241914

Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves
Cited by: 4
Author(s): Ruixue Wang, Peng Yin, Ruixia Yang, Xiao Liu, Lijie Luo, Junfeng Xu
Software Mentions: 2
Published: almost 6 years ago

10.1007/s10456-015-9488-z

ADAMTS3 activity is mandatory for embryonic lymphangiogenesis and regulates placental angiogenesis
Cited by: 73
Author(s): Lauriane Janssen, Laura Dupont, Mourad Bekhouche, Agnès Noël, Cédric Leduc, Marianne Voz, Bernard Peers, Didier Cataldo, Suneel S. Apte, Johanne Dubail, Alain Colige
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0224643

Genome-wide transcriptomic analysis of the response of Botrytis cinerea to wuyiencin
Cited by: 5
Author(s): Liming Shi, Binghua Liu, Qiuhe Wei, Beibei Ge, Kecheng Zhang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0245160

Rapid detection of ERG11 polymorphism associated azole resistance in Candida tropicalis
Cited by: 6
Author(s): Saikat Paul, Rajneesh Dadwal, Shreya Singh, Dipika Shaw, Arunaloke Chakrabarti, Shivaprakash M Rudramurthy, Anup Ghosh
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0243681

Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico
Cited by: 11
Author(s): Enrique Jesús Delgado-Suárez, Tania Palós-Guitérrez, Francisco Alejandro Ruíz-López, Cindy Fabiola Hernández Pérez, Nayarit Emérita Ballesteros-Nova, Orbelín Soberanis-Ramos, Rubén Danilo Méndez-Medina, Marc W. Allard, María Salud Rubio Lozano
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0211716

Sepsis induces long-lasting impairments in CD4+ T-cell responses despite rapid numerical recovery of T-lymphocyte populations
Cited by: 22
Author(s): Christoph Ammer‐Herrmenau, Upasana Kulkarni, Nico Andreas, Martin Ungelenk, Sarina Ravens, Christian G. Hübner, Angela Kather, Ingo Kurth, Michael Bauer, Thomas Kamradt
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms20194740

The CXCR4–CXCL12-Axis Is of Prognostic Relevance in DLBCL and Its Antagonists Exert Pro-Apoptotic Effects In Vitro
Cited by: 13
Author(s): Katrin Pansy, Julia Feichtinger, Barbara Ehall, Barbara Uhl, Miriam Sedej, David Roula, Beata Pursche, Axel Wolf, Manuel Zoidl, Elisabeth Steinbauer, Verena Gruber, Hildegard Greinix, Katharina Prochazka, Gerhard G. Thallinger, Ákos Heinemann, Christine Beham–Schmid, Peter Neumeister, Tanja Wrodnigg, Karoline Fechter, Alexander Deutsch
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-016-2600-y

Gene expression comparison of resistant and susceptible Atlantic salmon fry challenged with Infectious Pancreatic Necrosis virus reveals a marked contrast in immune response
Cited by: 53
Author(s): Diego Robledo, John B. Taggart, J. Ireland, Brendan McAndrew, W. Starkey, Chris Haley, Alastair Hamilton, D. R. Guy, J. C. Mota-Velasco, Almas Gheyas, A. E. Tinch, David W. Verner–Jeffreys, Richard Paley, Georgina S. E. Rimmer, I. Tew, Stephen Bishop, James E. Bron, Ross D. Houston
Software Mentions: 2
Published: over 10 years ago

10.3390/biom9070282

Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray
Cited by: 12
Author(s): Ali Mohamed Alshabi, Basavaraj Vastrad, Ibrahim Ahmed Shaikh, Chanabasayya Vastrad
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-017-3627-4

Exploring the nature of prediagnostic blood transcriptome markers of chronic lymphocytic leukemia by assessing their overlap with the transcriptome at the clinical stage
Cited by: 3
Author(s): Jelle Vlaanderen, Max Leenders, Marc Chadeau‐Hyam, Lützen Portengen, Soterios A. Kyrtopoulos, Ingvar A. Bergdahl, Anders Johansson, Dennie G. A. J. Hebels, Theo M. C. M. de Kok, Paolo Víneis, Roel Vermeulen
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-1181

Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome
Cited by: 13
Author(s): Samoel Renan Mello da Silva, Gabriel C. Perrone, J. Dinis, Rita Maria Cunha de Almeida
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0246144

Xylanase modulates the microbiota of ileal mucosa and digesta of pigs fed corn-based arabinoxylans likely through both a stimbiotic and prebiotic mechanism
Cited by: 14
Author(s): Amy L Petry, John F. Patience, Lucas R Koester, Nichole F. Huntley, M.R. Bedford, Stephan Schmitz‐Esser
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0072591

Comparative Gene Expression Profiling Identifies Common Molecular Signatures of NF-κB Activation in Canine and Human Diffuse Large B Cell Lymphoma (DLBCL)
Cited by: 74
Author(s): Manikhandan Mudaliar, Ross Haggart, Gino Miele, Grant C. Sellar, Karen A. L. Tan, John Goodlad, Elspeth Milne, David M. Vail, Ilene D. Kurzman, Daniel Crowther, David Argyle
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-12-429

Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data
Cited by: 47
Author(s): Gareth R. Howell, David O Walton, Benjamin L. King, Richard T. Libby, Simon W. M. John
Software Mentions: 2
Published: about 15 years ago

10.1186/s12864-015-1993-3

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
Cited by: 31
Author(s): Andrea Saß, Heleen Van Acker, Konrad U. Förstner, Filip Van Nieuwerburgh, Dieter Deforce, Jörg Vogel, Tom Coenye
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1009297

Dis3L2 regulates cell proliferation and tissue growth through a conserved mechanism
Cited by: 12
Author(s): Benjamin P. Towler, Amy L. Pashler, Hope J. Haime, Katarzyna M. Przybyl, Sandra C. Viegas, Rute G. Matos, Simon Morley, Cecília M. Arraiano, Sarah F. Newbury
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1004288

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip
Cited by: 188
Author(s): Yujia Alina Chan, Maria J. Aristizabal, Phoebe Y. T. Lu, Zongli Luo, Akil Hamza, Michæl S. Kobor, Peter C. Stirling, Philip Hieter
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1000663

Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis
Cited by: 137
Author(s): Aleksandra Erilova, Lynette Brownfield, Vivien Exner, Marisa Rosa, David Twell, Ortrun Mittelsten Scheid, Lars Hennig, Claudia Köhler
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pgen.1002505

Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes
Cited by: 56
Author(s): Josine L. Min, George Nicholson, Ingileif Halgrimsdottir, Kristian Almstrup, Andreas Petri, Amy Barrett, Mary E. Travers, Nigel W. Rayner, Reedik Mägi, Fredrik Pettersson, John Broxholme, Matt J. Neville, Quin F. Wills, Jane Cheeseman, Maxine Allen, Chris Holmes, Tim D. Spector, Jan Fleckner, Mark I. McCarthy, Fredrik Karpe, Cecilia M. Lindgren, Krina T. Zondervan
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-7-75

Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression
Cited by: 23
Author(s): Karin Richter, Valtteri Wirta, Lina Dahl, Sara Bruce, Joakim Lundeberg, Leif Carlsson, Cecilia Williams
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2105-13-S1-S10

A semantic web framework to integrate cancer omics data with biological knowledge
Cited by: 18
Author(s): Matthew Holford, James P. McCusker, Kei‐Hoi Cheung, Michael Krauthammer
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-15-231

An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation
Cited by: 12
Author(s): Mathieu Lajoie, Yu-Chih Hsu, Richard M. Gronostajski, Timothy L. Bailey
Software Mentions: 2
Published: over 12 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962