bioconductor: ArrayExpress | Projects

10.1016/j.molcel.2007.03.002

A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast
Cited by: 188
Author(s): Daniel H. Lackner, Traude H. Beilharz, Samuel Marguerat, Juan Mata, Stephen Watt, Falk Schubert, Thomas Preiß, Jürg Bähler
Software Mentions: 1
Published: about 19 years ago

10.1128/mBio.00430-16

The Acinetobacter baumannii Two-Component System AdeRS Regulates Genes Required for Multidrug Efflux, Biofilm Formation, and Virulence in a Strain-Specific Manner
Cited by: 95
Author(s): Grace E. Richmond, Laura P. Evans, Michael Anderson, Matthew E. Wand, Laura C. Bonney, Alasdair Ivens, Kim Lee Chua, Mark A. Webber, J. Mark Sutton, Marnie L. Peterson, Laura J. V. Piddock
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2229-12-204

Expression of geminiviral AC2 RNA silencing suppressor changes sugar and jasmonate responsive gene expression in transgenic tobacco plants
Cited by: 39
Author(s): Arto Soitamo, Balaji Jada, Kirsi Lehto
Software Mentions: 1
Published: over 14 years ago

10.1016/j.mcpro.2021.100071

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future
Cited by: 21
Author(s): Nuno Bandeira, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, Juan Antonio Vizcaíno
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.00642-16

DamX Controls Reversible Cell Morphology Switching in Uropathogenic Escherichia coli
Cited by: 43
Author(s): Surabhi Khandige, Cecilie Antoinette Asferg, Karina Juhl Rasmussen, Martin Jakob Larsen, Martin Overgaard, Thomas Emil Andersen, Jakob Møller‐Jensen
Software Mentions: 1
Published: over 9 years ago

10.1128/mBio.00968-17

Lack of AcrB Efflux Function Confers Loss of Virulence on Salmonella enterica Serovar Typhimurium
Cited by: 92
Author(s): Xuan Wang-Kan, Jessica M A Blair, Barbara Chirullo, Jonathan W. Betts, Roberto M. La Ragione, Alasdair Ivens, Vito Ricci, Timothy J. Opperman, Laura J. V. Piddock
Software Mentions: 1
Published: over 8 years ago

10.1111/mmi.12381

Genome‐wide profiling of chromosome interactions in <scp>P</scp> lasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
Cited by: 47
Author(s): Jacob E. Lemieux, Sue Kyes, Thomas D. Otto, Avi Feller, Richard T. Eastman, Robert Pinches, Matthew Berriman, Xin‐zhuan Su, Chris Newbold
Software Mentions: 1
Published: over 12 years ago

10.1111/mmi.12358

Induced ectopic expression of <scp>HigB</scp> toxin in <scp>M</scp>ycobacterium tuberculosis results in growth inhibition, reduced abundance of a subset of <scp>mRNAs</scp> and cleavage of <scp>tmRNA</scp>
Cited by: 46
Author(s): Dorothée L. Schuessler, Teresa Cortes, Amanda S. Fivian‐Hughes, Kathryn Lougheed, Evelyn Harvey, Roger S. Buxton, E. A. Davis, Douglas B. Young
Software Mentions: 1
Published: over 12 years ago

10.1111/mmi.13091

Deciphering the metabolic response of <scp> M </scp> ycobacterium tuberculosis to nitrogen stress
Cited by: 33
Author(s): Katrina Williams, Victoria A Jenkins, Geraint Barton, William A Bryant, Nitya Krishnan, Brian Robertson
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2229-12-17

Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source-sink tissues in a segregating potato population
Cited by: 16
Author(s): Bjorn Kloosterman, A. M. Anithakumari, Pierre-Yves Chibon, Marian Oortwijn, Gerard C van der Linden, R.G.F. Visser, Christian W.B. Bachem
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2229-11-39

Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
Cited by: 45
Author(s): Yoshiharu Y. Yamamoto, Yohei Yoshioka, Mitsuro Hyakumachi, Kyonoshin Maruyama, Kazuko Yamaguchi-Shinozaki, Mutsutomo Tokizawa, Hiroyuki Koyama
Software Mentions: 1
Published: over 15 years ago

10.1002/1878-0261.12894

Multiomics integrative analysis reveals antagonistic roles of CBX2 and CBX7 in metabolic reprogramming of breast cancer
Cited by: 17
Author(s): Mohammad Askandar Iqbal, Shumaila Siddiqui, Asad Ur Rehman, Farid Ahmad Siddiqui, Prithvi Singh, Bhupender Kumar, Daman Saluja
Software Mentions: 1
Published: about 5 years ago

10.1038/s41380-019-0505-2

Familial t(1;11) translocation is associated with disruption of white matter structural integrity and oligodendrocyte–myelin dysfunction
Cited by: 17
Author(s): Navneet A. Vasistha, Mandy Johnstone, Samantha K. Barton, Steffen Mayerl, Bhuvaneish T. Selvaraj, Pippa A. Thomson, Owen Dando, Ellen Grünewald, Clara Alloza, Mark E. Bastin, Matthew R. Livesey, Kyriakos D. Economides, Dario Magnani, Paraskevi Makedonopolou, Karen Burr, David Story, Douglas Blackwood, DJ Wyllie, Andrew M. McIntosh, J. Kirsty Millar, Charles ffrench‐Constant, Giles E. Hardingham, Stephen M. Lawrie, Siddharthan Chandran
Software Mentions: 1
Published: over 6 years ago

10.15252/msb.20156525

The bimodally expressed micro <scp>RNA</scp> miR‐142 gates exit from pluripotency
Cited by: 26
Author(s): Hanna L. Sladitschek, Pierre Neveu
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2229-14-155

Salicylic acid signaling inhibits apoplastic reactive oxygen species signaling
Cited by: 61
Author(s): Enjun Xu, Mikael Brosché
Software Mentions: 1
Published: over 12 years ago

10.15252/msb.20156658

The BioStudies database
Cited by: 25
Author(s): Johanna McEntyre, Ugis Sarkans, Alvis Brāzma
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2229-10-108

Expression profiling of Crambe abyssinicaunder arsenate stress identifies genes and gene networks involved in arsenic metabolism and detoxification
Cited by: 66
Author(s): Bibin Paulose, Suganthi Kandasamy, Om Parkash Dhankher
Software Mentions: 1
Published: almost 16 years ago

10.1002/msb.134886

Periodic <scp>mRNA</scp> synthesis and degradation co‐operate during cell cycle gene expression
Cited by: 75
Author(s): Philipp Eser, Carina Demel, Kerstin Maier, Björn Schwalb, Nicole Pirkl, Dietmar E. Martin, Patrick Cramer, Achim Tresch
Software Mentions: 1
Published: over 12 years ago

10.15252/msb.20199043

A gene regulatory network controls the balance between mesendoderm and ectoderm at pluripotency exit
Cited by: 16
Author(s): Hanna L. Sladitschek, Pierre Neveu
Software Mentions: 1
Published: over 6 years ago

10.1016/j.vaccine.2010.06.005

An investigation of clinical and immunological events following repeated aerodigestive tract challenge infections with live Mycobacterium bovis Bacille Calmette Guérin
Cited by: 8
Author(s): Fernanda Schreiber, Zhiming Huo, Rafaela Giemza, Maria Woodrow, Nicola Fenner, Zoe Stephens, Gordon Dougan, Steven Prideaux, L.R.R. Castello-Branco, David J. M. Lewis
Software Mentions: 1
Published: almost 16 years ago

10.1016/j.vetpar.2015.08.023

Variable exon usage of differentially-expressed genes associated with resistance of sheep to Teladorsagia circumcincta
Cited by: 3
Author(s): Hazel Wilkie, Siyang Xu, Anton Gossner
Software Mentions: 1
Published: over 10 years ago

10.1186/1743-422X-11-27

Gene expression profiling of CD4+T cells in treatment-naive HIV, HCV mono- or co-infected Chinese
Cited by: 4
Author(s): Yi Liu, Jin Zhao, Jing Lü, Ying Cui, Lin Chen, Jinquan Cheng, Yan Sun, Zhi Li, Ruotin Men, Li Yang, Hsiang‐Fu Kung, Zhengrong Yang, Ming‐Liang He
Software Mentions: 1
Published: about 12 years ago

10.3390/v12010076

Comparative Transcriptome Analysis Provides Molecular Insights into the Interaction of Beet necrotic yellow vein virus and Beet soil-borne mosaic virus with Their Host Sugar Beet
Cited by: 11
Author(s): J. Gil, Daniel Wibberg, Omid Eini, Eugene I. Savenkov, Mark Varrelmann, Sebastian Liebe
Software Mentions: 1
Published: over 6 years ago

10.12688/wellcomeopenres.12199.1

Methyl donor deficient diets cause distinct alterations in lipid metabolism but are poorly representative of human NAFLD
Cited by: 12
Author(s): Marcus J. Lyall, Jessy Cartier, James Richards, Diego Cobice, John P. Thomson, Richard R. Meehan, Stephen M. Anderton, Amanda J. Drake
Software Mentions: 1
Published: over 8 years ago

10.12688/wellcomeopenres.14576.2

DOLORisk: study protocol for a multi-centre observational study to understand the risk factors and determinants of neuropathic pain
Cited by: 20
Author(s): Mathilde M.V. Pascal, Andreas C. Themistocleous, Ralf Baron, Andreas Binder, Didier Bouhassira, Geert Crombez, Nanna Brix Finnerup, Janne Gierthmühlen, Yelena Granovsky, Leif Groop, Harry L. Hébert, Troels Staehelin Jensen, Kristinn Johnsen, Mark I. McCarthy, Meng Wang, Colin N.A. Palmer, Andrew S.C. Rice, Jordi Serra, Romà Solà, David Yarnitsky, Blair H. Smith, Nadine Attal, David L.H. Bennett
Software Mentions: 1
Published: about 7 years ago

10.1007/s10354-016-0488-4

New insights in Rett syndrome using pathway analysis for transcriptomics data
Cited by: 9
Author(s): Friederike Ehrhart, Susan L. Coort, Elisa Cirillo, Eric Smeets, Chris T. Evelo, Leopold Curfs
Software Mentions: 1
Published: over 9 years ago

10.1186/s12957-018-1320-y

Clinical value of miR-198-5p in lung squamous cell carcinoma assessed using microarray and RT-qPCR
Cited by: 19
Author(s): Yue‐Ya Liang, Jiacheng Huang, Rongjiang Tang, Wenjie Chen, Peng Chen, Wei‐Luan Cen, Ke Shi, Gao Li, Xiang Gao, An‐Gui Liu, Xuebiao Peng, Su-Hua Huang, Ye‐Ying Fang, Yutong Gu
Software Mentions: 1
Published: about 8 years ago

10.1186/s12957-020-01975-9

Immunohistochemical basigin expression level in thyroid cancer tissues
Cited by: 2
Author(s): Wanping Guo, Deng Tang, Yu‐Yan Pang, Xiao‐Jiao Li, Gang Chen, Zhi‐Guang Huang, Xiao‐Zhun Tang, Quirino Lai, Jin-Yan Gan, Xiaoli Huang, Xiaofan Liu, Zhixiao Wei, Wei Ma
Software Mentions: 1
Published: over 5 years ago

10.1186/1755-8417-2-2

Unraveling the disease pathogenesis behind lethal hydrolethalus syndrome revealed multiple changes in molecular and cellular level
Cited by: 10
Author(s): Heli Honkala, Jenni Lahtela, Hazel M. Fox, Massimiliano Gentile, Niklas Pakkasjärvi, Riitta Salonen, Kirmo Wartiovaara, Matti Jauhiainen, Marjo Kestilä
Software Mentions: 1
Published: almost 17 years ago

10.3390/pathogens5030051

FlpS, the FNR-Like Protein of Streptococcus suis Is an Essential, Oxygen-Sensing Activator of the Arginine Deiminase System
Cited by: 10
Author(s): Jörg Willenborg, Anna Koczula, Marcus Fulde, Astrid de Greeff, Andreas Beineke, Wolfgang Eisenreich, Claudia Huber, Maren Seitz, Peter Valentin‐Weigand, Ralph Goethe
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2229-9-28

Differential patterns of reactive oxygen species and antioxidative mechanisms during atrazine injury and sucrose-induced tolerance in Arabidopsis thaliana plantlets
Cited by: 264
Author(s): Fanny Ramel, Cécile Sulmon, Matthieu Bogard, Ivan Couée, Gwenola Gouesbet
Software Mentions: 1
Published: about 17 years ago

10.1186/2050-6511-15-5

Skin sensitizers differentially regulate signaling pathways in MUTZ-3 cells in relation to their individual potency
Cited by: 34
Author(s): Ann-Sofie Albrekt, Henrik Johansson, Anna Börje, Carl Borrebaeck, Malin Lindstedt
Software Mentions: 1
Published: about 12 years ago

10.7717/peerj.10141

Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues
Cited by: 28
Author(s): Sevcan Atay
Software Mentions: 1
Published: over 5 years ago

10.1186/s12903-019-0738-0

Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO)
Cited by: 26
Author(s): Asami Suzuki, Tetsuro Horie, Yukihiro Numabe
Software Mentions: 1
Published: about 7 years ago

10.3390/pharmaceutics11040152

Translational PBPK Modeling of the Protein Therapeutic and CD95L Inhibitor Asunercept to Develop Dose Recommendations for Its First Use in Pediatric Glioblastoma Patients
Cited by: 17
Author(s): Nina Hanke, Claudia Kunz, Meinolf Thiemann, Harald Fricke, Thorsten Lehr
Software Mentions: 1
Published: about 7 years ago

10.1111/acel.12160

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging
Cited by: 40
Author(s): Erik B. van den Akker, Willemijn M. Passtoors, Ritsert C. Jansen, Erik W. van Zwet, Jelle J. Goeman, Marc Hulsman, Valur Emilsson, Markus Perola, Gonneke Willemsen, Brenda W. J. H. Penninx, B.T. Heijmans, Andrea B. Maier, Dorret I. Boomsma, Joost N. Kok, P. Eline Slagboom, Marcel J. T. Reinders, Marian Beekman
Software Mentions: 1
Published: over 12 years ago

10.1098/rstb.2019.0413

Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis rcd1 mutant
Cited by: 15
Author(s): Alexey Shapiguzov, Lauri Nikkanen, Duncan Fitzpatrick, Julia P. Vainonen, Richard Gossens, Saleh Alseekh, Fayezeh Aarabi, Arjun Tiwari, Olga Blokhina, Klára Panzarová, Zuzana Benedikty, Esa Tyystjärvi, Alisdair R. Fernie, Martin Trtílek, Eva‐Mari Aro, Eevi Rintamäki, Jaakko Kangasjärvi
Software Mentions: 1
Published: almost 6 years ago

10.1098/rstb.2010.0286

Computational biology for ageing
Cited by: 37
Author(s): Daniela Wieser, Irene Papatheodorou, Matthias Ziehm, Janet M. Thornton
Software Mentions: 1
Published: over 15 years ago

10.1093/pcp/pcv165

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression
Cited by: 143
Author(s): Yosuke Aoki, Yasunobu Okamura, Shu Tadaka, Kengo Kinoshita, Takeshi Obayashi
Software Mentions: 1
Published: over 10 years ago

10.1093/pcp/pcx191

ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index
Cited by: 196
Author(s): Takeshi Obayashi, Yosuke Aoki, Shu Tadaka, Yuki Kagaya, Kengo Kinoshita
Software Mentions: 1
Published: over 8 years ago

10.1111/tpj.14898

TERMINAL FLOWER‐1/CENTRORADIALIS inhibits tuberisation via protein interaction with the tuberigen activation complex
Cited by: 21
Author(s): Xing Zhang, Raymond Campbell, Laurence J. M. Ducreux, Jennifer Morris, Pete E. Hedley, Elena Mellado‐Ortega, Alison G. Roberts, Jennifer Stephens, Glenn Bryan, L. Torrance, Sean Chapman, Salomé Prat, Mark A. Taylor
Software Mentions: 1
Published: over 5 years ago

10.1186/s13007-016-0144-4

Measures for interoperability of phenotypic data: minimum information requirements and formatting
Cited by: 98
Author(s): Hanna Ćwiek‐Kupczyńska, Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun Chen, Guillaume Cornut, Fabio Fiorani, Wojciech Frohmberg, Astrid Junker, Christian Klukas, Matthias Lange, Cezary Mazurek, Anahita Nafissi, Pascal Neveu, Jan van Oeveren, Cyril Pommier, Hendrik Poorter, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Marco van Schriek, Ümit Seren, Björn Usadel, Stéphan Weise, Paul J. Kersey, Paweł Krajewski
Software Mentions: 1
Published: over 9 years ago

10.1128/mBio.00109-21

Metabolomics Reveal Potential Natural Substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium
Cited by: 14
Author(s): Xuan Wang-Kan, Giovanny Rodrı́guez-Blanco, Andrew D. Southam, Catherine Winder, Warwick B. Dunn, Alasdair Ivens, Laura J. V. Piddock
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2202-6-28

Transcriptome analysis in primary neural stem cells using a tag cDNA amplification method
Cited by: 12
Author(s): Maria Sievertzon, Valtteri Wirta, Alex Mercer, Konstantinos Meletis, Rikard Erlandsson, Lilian Wikström, Jonas Frisén, Joakim Lundeberg
Software Mentions: 1
Published: almost 21 years ago

10.1186/1471-2202-11-14

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
Cited by: 365
Author(s): Tim R. Mercer, Irfan A. Qureshi, Şölen Gokhan, Marcel E. Dinger, Guangyu Li, John S. Mattick, Mark F. Mehler
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pbio.0020317

Submission of Microarray Data to Public Repositories
Cited by: 113
Author(s): Catherine A. Ball, Alvis Brāzma, Helen C. Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna Assunta Sansone, Gavin Sherlock, Paul T. Spellman, C. J. Stoeckert, Yoshio Tateno, Ron Taylor, Joseph A. White, Neil Winegarden
Software Mentions: 1
Published: over 21 years ago

10.1371/journal.pbio.0030384

Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning
Cited by: 394
Author(s): Benoît Guillemette, Alain R. Bataille, Nicolas Gévry, Maryse Adam, Mathieu Blanchette, François Robert, Luc Gaudreau
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pbio.0030297

Bioinformatics and Data Management Support for Environmental Genomics
Cited by: 23
Author(s): Dawn Field, Bela Tiwari, Jason Snape
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pbio.3001311

MHC class I H2-Kb negatively regulates neural progenitor cell proliferation by inhibiting FGFR signaling
Cited by: 12
Author(s): Karin Lin, Gregor Bieri, Géraldine Gontier, Sören Müller, Lucas K. Smith, Cedric E Snethlage, Charles White, Sun Y. Maybury-Lewis, Saul Villeda
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2202-8-34

Reduced expression of TAC1, PENK and SOCS2 in Hcrtr-2 mutated narcoleptic dog brain
Cited by: 7
Author(s): Julia Hedlund Lindberg, Peter Saetre, Seiji Nishino, Emmanuel Mignot, Elena Jazin
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pcbi.1002278

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Cited by: 65
Author(s): Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1003597

Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation
Cited by: 10
Author(s): Marcus J. Tindall, Angela Clerk
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2474-13-130

Expression profile analysis of mycotoxin-related genes in cartilage with endemic osteochondropathy kashin-beck disease
Cited by: 7
Author(s): Na Zhang, Xiong Guo, Weizhuo Wang, Shixun Wu, Wei-Juan Ma, Yan Hua
Software Mentions: 1
Published: over 13 years ago

10.18632/aging.101078

Human exceptional longevity: transcriptome from centenarians is distinct from septuagenarians and reveals a role of Bcl-xL in successful aging
Cited by: 37
Author(s): Consuelo Borrás, Kheira M. Abdelaziz, Juan Gambini, Eva Serna, Marta Inglés, Mónica De la Fuente, Idoia García, Ander Matheu, Paula Sanchís, Ángel Belenguer, Alessandra Errigo, Juan A. Avellana, Ana Barettino, Carla Lloret-Fernández, Nuria Flames, Giovanni Mario Pes, Leocadio Rodríguez‐Mañas, José Viña
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2199-8-112

Checkpoint independence of most DNA replication origins in fission yeast
Cited by: 36
Author(s): Katie L Mickle, Sunita Ramanathan, Adam P. Rosebrock, Anna Maria Oliva, Amna Chaudari, Chulee Yompakdee, David Scott, Janet Leatherwood, Joel A. Huberman
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pcbi.1000940

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions
Cited by: 63
Author(s): Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel T. Dudley, Szu Chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush, Minnie M. Sarwal, Atul J. Butte
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1000851

Large-Scale Analysis of Network Bistability for Human Cancers
Cited by: 75
Author(s): Tetsuya Shiraishi, Shinako Matsuyama, Hiroaki Kitano
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pcbi.1002126

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
Cited by: 80
Author(s): Tim D. Williams, Nahid Turan, Amer Diab, Huifeng Wu, Carolynn Mackenzie, Kerry L. Bartie, Olga Hrydziuszko, Brett P. Lyons, Grant D. Stentiford, John Herbert, Kuruvilla Joseph Abraham, Ioanna Katsiadaki, Michael J. Leaver, John B. Taggart, Stephen George, Mark R. Viant, Kevin Chipman, Francesco Falciani
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2199-8-119

Checkpoint effects and telomere amplification during DNA re-replication in fission yeast
Cited by: 10
Author(s): Katie L Mickle, Anna Maria Oliva, Joel A. Huberman, Janet Leatherwood
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2199-11-95

Overexpression of miR-128 specifically inhibits the truncated isoform of NTRK3 and upregulates BCL2 in SH-SY5Y neuroblastoma cells
Cited by: 78
Author(s): Monia Guidi, Margarita Muiños‐Gimeno, Birgit Kagerbauer, Eulàlia Martı́, Xavier Estivill, Yolanda Espinosa‐Parrilla
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pgen.1004243

The Membrane-Associated Transcription Factor NAC089 Controls ER-Stress-Induced Programmed Cell Death in Plants
Cited by: 160
Author(s): Zhenle Yang, Mei-Jing Wang, Ling Sun, Sun-Jie Lu, Dongling Bi, Li‐Zhong Sun, Ze‐Ting Song, Shuang-Shuang Zhang, Shun-Fan Zhou, Jian‐Xiang Liu
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2180-7-88

Comparative gene expression profiling in two congenic mouse strains following Bordetella pertussis infection
Cited by: 7
Author(s): Sander Banus, Rob J. Vandebriel, Jeroen L. A. Pennings, Eric R. Gremmer, Piet W. Wester, Henk J. van Kranen, Timo M. Breit, Peter Démant, Frits R. Mooi, Barbara Hoebee, Tjeerd G. Kimman
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pgen.1003594

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts
Cited by: 38
Author(s): Daria V. Zhernakova, Eleonora de Klerk, Harm-Jan Westra, Anastasios Mastrokolias, Shoaib Amini, Yavuz Ariyürek, Ritsert C. Jansen, Brenda W. J. H. Penninx, Jouke Jan Hottenga, Gonneke Willemsen, Eco J. C. de Geus, Dorret I. Boomsma, Jan H. Veldink, Leonard H van den Berg, Cisca Wijmenga, Johan T. den Dunnen, Gert‐Jan B. van Ommen, Peter A C ‘t Hoen, Lude Franke
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1002362

Caenorhabditis elegans Cyclin D/CDK4 and Cyclin E/CDK2 Induce Distinct Cell Cycle Re-Entry Programs in Differentiated Muscle Cells
Cited by: 32
Author(s): Jerome Korzelius, Suzan Ruijtenberg, Martine B.W. Prinsen, Vincent Portegijs, Teije C. Middelkoop, Marian J. A. Groot Koerkamp, Frank C. P. Holstege, Mike Boxem, Sander van den Heuvel
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1000599

A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene
Cited by: 290
Author(s): Chris Church, Sheena Lee, Eleanor A. L. Bagg, James S. McTaggart, Robert M. J. Deacon, Thomas A. Gerken, Angela Lee, Lee Moir, Jasmin Mecinović, Mohamed M. Quwailid, Christopher J. Schofield, Frances M. Ashcroft, Roger D. Cox
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1003160

Insulin and IGF1 Receptors Are Essential for XX and XY Gonadal Differentiation and Adrenal Development in Mice
Cited by: 110
Author(s): Jean-Luc Pitetti, Pierre Calvel, Yannick Romero, Béatrice Conne, Vy Truong, Marilena D. Papaioannou, Olivier Schaad, Mylène Docquier, Pedro Luis Herrera, Dagmar Wilhelm, Serge Nef
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2180-12-104

The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated
Cited by: 120
Author(s): Alex J. McCarthy, Jodi A. Lindsay
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1008549

Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs
Cited by: 15
Author(s): Satesh Ramdhani, Elisa Navarro, Evan Udine, Anastasia G. Efthymiou, Brian M Schilder, Madison Parks, Alison M. Goate, Towfique Raj
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2180-13-224

Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions
Cited by: 8
Author(s): Yared H. Kidane, Christopher B. Lawrence, T. M. Murali
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1000846

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome
Cited by: 220
Author(s): Juan M. Vaquerizas, Ritsuko Suyama, Jop Kind, Kota Miura, Nicholas M. Luscombe, Asifa Akhtar
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2180-9-246

Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Cited by: 7
Author(s): J. F. Yuan, Zhang Sj, Osman Jafer, RA Furlong, OE Chausiaux, Carole A. Sargent, Zhang Gh, Nabeel A. Affara
Software Mentions: 1
Published: over 16 years ago

10.1186/s40246-020-00269-1

Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals
Cited by: 4
Author(s): Andreanna Burman, Rolando García-Milián, Shannon Whirledge
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2105-10-S12-S10

Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
Cited by: 4
Author(s): Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1000479

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference
Cited by: 117
Author(s): Eric A. Stone, Julien F. Ayroles
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1000470

SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing
Cited by: 75
Author(s): Anu Tyagi, Jessica Ryme, David Brodin, A K Ostlund Farrants, Neus Visa
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1003734

Comparative Oncogenomic Analysis of Copy Number Alterations in Human and Zebrafish Tumors Enables Cancer Driver Discovery
Cited by: 31
Author(s): Guangjun Zhang, Sebastian Hoersch, Adam Amsterdam, Charles A. Whittaker, Eline Beert, Julian M. Catchen, Sarah Farrington, John H. Postlethwait, Eric Legius, Nancy Hopkins, Jacqueline A. Lees
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1006000

Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
Cited by: 50
Author(s): Katarina Truvé, Peter J. Dickinson, Anqi Xiong, Daniel York, Kartika Jayashankar, Gerli Pielberg, Michele Koltookian, Eva Murén, Hans Henrik Fuxelius, Holger Weishaupt, Fredrik J. Swartling, Gerhard Andersson, Åke Hedhammar, Erik Bongcam‐Rudloff, Karin Forsberg-Nilsson, Danika L. Bannasch, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1002398

Widespread Cotranslational Formation of Protein Complexes
Cited by: 104
Author(s): Caia D. S. Duncan, Juan Mata
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2180-8-73

Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni
Cited by: 20
Author(s): Sandra Rodin, Anders F. Andersson, Valtteri Wirta, Lena Eriksson, Marianne Ljungström, Britta Björkholm, Hans Lindmark, Lars Engstrand
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pgen.1005153

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression
Cited by: 43
Author(s): Marta Garrido, Benjamin Frage, Patrick R. Wright, Anke Becker
Software Mentions: 1
Published: almost 11 years ago

10.1093/hmg/ddw417

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus
Cited by: 25
Author(s): Christopher A. Odhams, Andrea Cortini, Lingyan Chen, Amy L. Roberts, Ana Viñuela, Alfonso Buil, Kerrin S. Small, Emmanouil T. Dermitzakis, David L. Morris, Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1007256

Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome
Cited by: 35
Author(s): Anurag Kumar Sinha, Christophe Possoz, Adeline Durand, Jean-Michel Desfontaines, François‐Xavier Barre, David R. F. Leach, Bertrand Michel
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2180-12-212

Insight into the bacterial gut microbiome of the North American moose (Alces alces)
Cited by: 45
Author(s): Suzanne L. Ishaq, André‐Denis G. Wright
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1000286

Field-Caught Permethrin-Resistant Anopheles gambiae Overexpress CYP6P3, a P450 That Metabolises Pyrethroids
Cited by: 293
Author(s): Pie Müller, Emma Warr, Bradley J. Stevenson, Pasquale Pignatelli, John C. Morgan, Andrew Steven, Alexander Egyir Yawson, Sara N. Mitchell, Hilary Ranson, Janet Hemingway, Mark J. I. Paine, Martin J. Donnelly
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pgen.1003163

Increased Maternal Genome Dosage Bypasses the Requirement of the FIS Polycomb Repressive Complex 2 in Arabidopsis Seed Development
Cited by: 55
Author(s): David Kradolfer, Lars Hennig, Claudia Köhler
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2180-10-106

The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori
Cited by: 3
Author(s): François P. Douillard, Kevin Ryan, Michael Lane, Delphine L. Caly, Stanley A. Moore, Charles W. Penn, Jason Hinds, Paul W. O’Toole
Software Mentions: 1
Published: about 16 years ago

10.1186/s12911-021-01634-3

A framework for validating AI in precision medicine: considerations from the European ITFoC consortium
Cited by: 18
Author(s): Rosy Tsopra, Xose M Fernandez-Suarez, Claudio Luchinat, Lilia Alberghina, Hans Lehrach, Marco Vanoni, Felix Dreher, Osman Uğur Sezerman, Marc Cuggia, Marie de Tayrac, Edvīns Miklaševičs, Lucian Mihai Itu, Marius Geantă, Lesley A. Ogilvie, Florence Godey, C. Boldisor, Boris Campillo‐Gimenez, Cosmina Cioroboiu, Costin Florian Ciușdel, Simona M. Coman, Oliver Hijano Cubelos, Alexandru Itu, Bodo Lange, Matthieu Le Gallo, Alexandra Lespagnol, Giancarlo Mauri, H Okan Soykam, Bastien Rance, Paola Turano, Leonardo Tenori, Alessia Vignoli, Christoph Wierling, Nora Benhabilès, Anita Burgun
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pmed.1002786

Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures
Cited by: 115
Author(s): Hayley Warsinske, Rohit Vashisht, Purvesh Khatri
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12920-017-0293-y

Differential gene expression in disease: a comparison between high-throughput studies and the literature
Cited by: 52
Author(s): Raul Rodriguez‐Esteban, Xiaoyu Jiang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pmed.1000046

A Compendium of Potential Biomarkers of Pancreatic Cancer
Cited by: 256
Author(s): H. C. Harsha, Kumaran Kandasamy, Prathibha Ranganathan, Sandhya Rani, Subhashri Ramabadran, Sashikanth Gollapudi, Lavanya Balakrishnan, Sutopa B. Dwivedi, Deepthi Telikicherla, Lakshmi Dhevi N. Selvan, Renu Goel, Suresh Mathivanan, Arivusudar Marimuthu, Manoj Kumar Kashyap, Robert F. Vizza, Robert J. Mayer, James A. DeCaprio, Sudhir Srivastava, Samir Hanash, Ralph H. Hruban, Akhilesh Pandey
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pntd.0005972

Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes
Cited by: 28
Author(s): Juan Mucci, Santiago J. Carmona, Romina Volcovich, Jaime Altcheh, Estefanisa Bracamonte, Jorge Diego Marco, Morten Nielsen, Carlos A. Buscaglia, Fernán Agüero
Software Mentions: 1
Published: over 8 years ago

10.1186/s13046-016-0403-2

Microarray-based identification of genes associated with cancer progression and prognosis in hepatocellular carcinoma
Cited by: 33
Author(s): Fuqiang Yin, Liuyang Shu, Xia Liu, Ting Li, Tao Peng, Yueli Nan, Shu Li, Xianmin Zeng, Xiaoqiang Qiu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0001692

Gene Amplification, ABC Transporters and Cytochrome P450s: Unraveling the Molecular Basis of Pyrethroid Resistance in the Dengue Vector, Aedes aegypti
Cited by: 156
Author(s): Vassiliki Bariami, Christopher M. Jones, Rodolphe Poupardin, John Vontas, Hilary Ranson
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pntd.0005069

Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection
Cited by: 67
Author(s): Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0002607

Bioassay-Guided Fractionation of Extracts from Codiaeum variegatum against Entamoeba histolytica Discovers Compounds That Modify Expression of Ceramide Biosynthesis Related Genes
Cited by: 14
Author(s): Emmanuel Mfotie Njoya, Christian Weber, Nora Adriana Hernández‐Cuevas, Chung-Chau Hon, Yves L. Janin, Melanie F. G. Kamini, Paul Fewou Moundipa, Nancy Guillén
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pntd.0002438

Temephos Resistance in Aedes aegypti in Colombia Compromises Dengue Vector Control
Cited by: 106
Author(s): Nelson Grisales, Rodolphe Poupardin, Santiago Gómez, Idalyd Fonseca-González, Hilary Ranson, Audrey Lenhart
Software Mentions: 1
Published: over 12 years ago

10.1186/s12920-014-0063-z

Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS)
Cited by: 22
Author(s): Maria Chiara Pelleri, Allison Piovesan, Maria Caracausi, Anna C. Berardi, Lorenza Vitale, Pierluigi Strippoli
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0052321

Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
Cited by: 37
Author(s): Candy Kumps, Annelies Fieuw, Pieter Mestdagh, Björn Menten, Steve Lefever, Filip Pattyn, Sara De Brouwer, Tom Sante, Johannes H. Schulte, Alexander Schramm, Nadine Van Roy, Tom Van Maerken, Rosa Noguera, Valérie Combaret, Christine Devalck, Frank Westermann, Geneviève Laureys, Angelika Eggert, Jo Vandesompele, Katleen De Preter, Franki Speleman
Software Mentions: 1
Published: over 13 years ago

10.1186/1755-8794-6-35

Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers
Cited by: 34
Author(s): Adam L. Cohen, Stephen R. Piccolo, Luis Cheng, Rafaella Soldi, Bing Han, W. Evan Johnson, Andrea Bild
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0043249

Induction of Endoplasmic Reticulum Stress Response by the Indole-3-Carbinol Cyclic Tetrameric Derivative CTet in Human Breast Cancer Cell Lines
Cited by: 43
Author(s): Luca Galluzzi, Mauro De Santi, Rita Crinelli, Cinzia De Marco, Nadia Zaffaroni, Andrea Duranti, Giorgio Brandi, Mauro Magnani
Software Mentions: 1
Published: over 13 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962