bioconductor: ArrayExpress | Projects

10.1099/mic.0.000296

Developmental delay in a Streptomyces venezuelae glgE null mutant is associated with the accumulation of α-maltose 1-phosphate
Cited by: 11
Author(s): Farzana Miah, Maureen J. Bibb, J. Elaine Barclay, Kim Findlay, Stephen Bornemann
Software Mentions: 1
Published: almost 10 years ago

10.1186/2040-2392-5-21

Altered brain gene expression but not steroid biochemistry in a genetic mouse model of neurodevelopmental disorder
Cited by: 20
Author(s): Simon Trent, JP Fry, Obah A. Ojarikre, William Davies
Software Mentions: 1
Published: about 12 years ago

10.1093/molbev/msu299

Expression Profile and Gene Age Jointly Shaped the Genome-Wide Distribution of Premature Termination Codons in a Drosophila melanogaster Population
Cited by: 19
Author(s): Haiwang Yang, Bin He, Huijing Ma, Shun-Chern Tsaur, Chenyu Ma, Ying Wu, Chau‐Ti Ting, Yong E. Zhang
Software Mentions: 1
Published: over 11 years ago

10.1186/1756-6606-6-12

Synaptosomal-associated protein 25 mutation induces immaturity of the dentate granule cells of adult mice
Cited by: 51
Author(s): Koji Ohira, Katsunori Kobayashi, Keiko Toyama, Hironori Nakamura, Hirotaka Shoji, Keizo Takao, Rika Takeuchi, Shun Yamaguchi, Masakazu Kataoka, Shintaro Otsuka, Masami Takahashi, Tsuyoshi Miyakawa
Software Mentions: 1
Published: about 13 years ago

10.1186/1476-4598-9-123

MicroRNAs involvement in fludarabine refractory chronic lymphocytic leukemia
Cited by: 98
Author(s): Manuela Ferracin, Barbara Zagatti, Lara Rizzotto, Francesco Cavazzini, Angelo Veronese, Maria Ciccone, Elena Saccenti, Laura Lupini, Andrea Grilli, Cristiano De Angeli, Massimo Negrini, Antonio Cuneo
Software Mentions: 1
Published: almost 16 years ago

10.1186/1476-4598-9-88

Organ-, inflammation- and cancer specific transcriptional fingerprints of pancreatic and hepatic stellate cells
Cited by: 90
Author(s): Mert Erkan, Nadine Weis, Pan Zheng, Christian Schwager, Tamar Samkharadze, Xiaohua Jiang, Ute Wirkner, Nathalia A. Giese, Wilhelm Ansorge, Jürgen Debus, Peter E. Huber, Helmut Friess, Amir Abdollahi, Jörg Kleeff
Software Mentions: 1
Published: almost 16 years ago

10.1186/1476-4598-13-20

Oncogenic transformation of mesenchymal stem cells decreases Nrf2 expression favoring in vivo tumor growth and poorer survival
Cited by: 36
Author(s): Juan M. Funes, Stephen Henderson, Rachel Kaufman, James M. Flanagan, Mathew Robson, R. Barbara Pedley, Salvador Moncada, Chris Boshoff
Software Mentions: 1
Published: over 12 years ago

10.1186/s12943-017-0717-5

Phospholipid Phosphatase 4 promotes proliferation and tumorigenesis, and activates Ca2+-permeable Cationic Channel in lung carcinoma cells
Cited by: 55
Author(s): Xin Zhang, Lan Zhang, Bihua Lin, Xingxing Chai, Ronggang Li, Yuehua Liao, Xing-Hui Deng, Qiongru Liu, Wenli Yang, Yubo Cai, Wei Zhou, Zhichao Lin, Wenhai Huang, Meigong Zhong, Fangyong Lei, Jiangxue Wu, Shuaishuai Yu, Xiaoping Li, Shangren Li, Yueyue Li, Jincheng Zeng, Wansheng Long, Dong Ren, Yanming Huang
Software Mentions: 1
Published: over 8 years ago

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

10.1016/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

10.1111/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

10.1002/1878-0261.12894

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

10.15252/msb.20156658

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

10.1002/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

10.7717/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

10.3390/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

10.1098/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/journal.pone.0141710

Expression of CCL20 and Its Corresponding Receptor CCR6 Is Enhanced in Active Inflammatory Bowel Disease, and TLR3 Mediates CCL20 Expression in Colonic Epithelial Cells
Cited by: 51
Author(s): Helene Kolstad Skovdahl, Atle van Beelen Granlund, Ann Elisabet Østvik, Ingrid Bakke, Sverre Helge Torp, Jan Kristian Damås, Arne K. Sandvik
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0009867

Oral Activated Charcoal Prevents Experimental Cerebral Malaria in Mice and in a Randomized Controlled Clinical Trial in Man Did Not Interfere with the Pharmacokinetics of Parenteral Artesunate
Cited by: 10
Author(s): J. Brian de Souza, Uduak Okomo, Alexander Nast, Naveed Aziz, Benjamin M. J. Owens, Harsimran Kaur, Momodou Jasseh, Sant Muangnoicharoen, Percy F. Sumariwalla, David C. Warhurst, Stephen A. Ward, David J. Conway, Luis Ulloa, Kevin J. Tracey, Brian M. J. Foxwell, Paul M. Kaye, Michael Walther
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0183410

snoRNA and piRNA expression levels modified by tobacco use in women with lung adenocarcinoma
Cited by: 25
Author(s): Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton Carvalho, Fábio Passetti
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0013658

Whole Blood Transcriptomics in Cardiac Surgery Identifies a Gene Regulatory Network Connecting Ischemia Reperfusion with Systemic Inflammation
Cited by: 34
Author(s): Orfeas Liangos, Sophie Domhan, Christian Schwager, Martin Zeier, Peter E. Huber, Francesco Addabbo, Michael S. Goligorsky, Lynn Hlatky, Bertrand L. Jaber, Amir Abdollahi
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0013079

QKI-7 Regulates Expression of Interferon-Related Genes in Human Astrocyte Glioma Cells
Cited by: 8
Author(s): Lin Jiang, Peter Saetre, Katarzyna J. Radomska, Elena Jazin, Eva Carlström
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0049077

Gadd45α: A Novel Diabetes-Associated Gene Potentially Linking Diabetic Cardiomyopathy and Baroreflex Dysfunction
Cited by: 13
Author(s): Ning Wang, Chao Yang, Fang Xie, Lichao Sun, Xiaolin Su, Ying Wang, Ran Wei, Rong Zhang, Xia Li, Baofeng Yang, Jing Ai
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0118511

MicroRNA-572 Improves Early Post-Operative Cognitive Dysfunction by Down-Regulating Neural Cell Adhesion Molecule 1
Cited by: 31
Author(s): Xiuchong Yu, Shupeng Liu, Jinbao Li, Xiaoping Fan, Yuanjie Chen, Xiaoying Bi, Shanrong Liu, Xiaoming Deng
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0055506

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
Cited by: 34
Author(s): David Cohen, Marie‐Béatrice Bogeat‐Triboulot, Silvère Vialet-Chabrand, Rémy Merret, Pierre‐Emmanuel Courty, Sébastien Moretti, François Bizet, Agnès Guilliot, Irène Hummel
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0199991

PASI: A novel pathway method to identify delicate group effects
Cited by: 4
Author(s): Maria K. Jaakkola, Aidan McGlinchey, Рику Клен, Laura L. Elo
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0123342

Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain
Cited by: 39
Author(s): Ann-Kristin Reinhold, Laura Batti, Daniel Bilbao, Andreas Buneß, Heike L. Rittner, Paul A. Heppenstall
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0045200

Transcriptomic Assay of CD8+ T Cells in Treatment-Naïve HIV, HCV-Mono-Infected and HIV/HCV-Co-Infected Chinese
Cited by: 7
Author(s): Jin Zhao, Yi Liu, Jing Lu, Zheng Yang, Ying Chen, Chenli Zheng, Dan Huang, Yufeng Li, Lin Chen, Jinquan Cheng, Hsiang‐Fu Kung, Ming‐Liang He
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0073072

Transmembrane Prostatic Acid Phosphatase (TMPAP) Interacts with Snapin and Deficient Mice Develop Prostate Adenocarcinoma
Cited by: 27
Author(s): Ileana B. Quintero, Annakaisa Herrala, César L. Araujo, Anitta E. Pulkka, Sampsa Hautaniemi, Kristian Ovaska, Evgeny Pryazhnikov, Evgeny Kulesskiy, Maija Ruuth, Ylermi Soini, Raija Sormunen, Leonard Khirug, Pirkko Vihko
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0007158

miR-155 Inhibition Sensitizes CD4+ Th Cells for TREG Mediated Suppression
Cited by: 81
Author(s): Heiko Stahl, Tanja Fauti, Nina D. Ullrich, Tobias Bopp, Jan Kubach, Werner Rust, Paul Labhart, Vassili Alexiadis, Christian Becker, Mathias Hafner, Andreas Weith, Martin Lenter, Helmut Jonuleit, Edgar Schmitt, Detlev Mennerich
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0152786

Adipocytes as a Link Between Gut Microbiota-Derived Flagellin and Hepatocyte Fat Accumulation
Cited by: 13
Author(s): Eveliina Munukka, Petri Wiklund, Tiina Partanen, Sakari Välimäki, Eija K. Laakkonen, Maarit Lehti, Pamela Fischer-Posovzsky, Martin Wabitsch, Sulin Cheng, Pentti Huovinen, Satu Pekkala
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0048896

Survival of Staphylococcus aureus ST398 in the Human Nose after Artificial Inoculation
Cited by: 23
Author(s): Bibi C. G. C. Slingerland, Mehri Tavakol, Alex J. McCarthy, Jodi A. Lindsay, Susan V. Snijders, Jaap A. Wagenaar, Alex van Belkum, Margreet C. Vos, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0070294

Prediction Errors in Learning Drug Response from Gene Expression Data – Influence of Labeling, Sample Size, and Machine Learning Algorithm
Cited by: 15
Author(s): Immanuel Bayer, Philip Groth, Sebastian Schneckener
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0131336

MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing
Cited by: 29
Author(s): Li Zhang, Pengfei Wei, Xudong Shen, Yuanwei Zhang, Bo Xu, Jun Zhou, Song Fan, Zongyao Hao, Hao Shi, Xiansheng Zhang, Rui Kong, Lingfan Xu, Duohong Zou, Chaozhao Liang
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0002798

Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors
Cited by: 63
Author(s): Paolo Facella, Loredana Lopez, Fabrizio Carbone, David W. Galbraith, Giovanni Giuliano, Gaetano Perrotta
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0008018

Sulfur Metabolism Actively Promotes Initiation of Cell Division in Yeast
Cited by: 17
Author(s): Heidi M. Blank, Shefali Rajendra Gajjar, Andrey Belyanin, Michael Polymenis
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0161993

PKC-ALDH2 Pathway Plays a Novel Role in Adipocyte Differentiation
Cited by: 20
Author(s): Yu-Hsiang Yu, Pei Ru Liao, Chien Jung Guo, Che Hong Chen, Daria Mochly‐Rosen, Lee‐Ming Chuang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0079627

Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts
Cited by: 1
Author(s): Thong Tien Nguyen, Cathal Seoighe
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0001546

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays
Cited by: 13
Author(s): Michael A. Cook, Chi Kin Chan, Paul Jorgensen, Troy Ketela, Daniel K. C. So, Mike Tyers, Chi Yip Ho
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0048363

Functional Similarities between Pigeon ‘Milk’ and Mammalian Milk: Induction of Immune Gene Expression and Modification of the Microbiota
Cited by: 28
Author(s): Meagan J Gillespie, Dragana Stanley, Honglei Chen, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0080747

PaGenBase: A Pattern Gene Database for the Global and Dynamic Understanding of Gene Function
Cited by: 100
Author(s): Jianbo Pan, Shichang Hu, Dan Shi, Mei-Chun Cai, Yin-Bo Li, Quan Zou, Zhi-Liang Ji
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0026023

Hormone Receptor and ERBB2 Status in Gene Expression Profiles of Human Breast Tumor Samples
Cited by: 6
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0250747

Glycans unique to the relapse-prone subset within triple-negative breast cancer as revealed by lectin array-based analysis of surgical specimens
Cited by: 3
Author(s): Madoka Sakata-Matsuzawa, Kaori Denda-Nagai, Haruhiko Fujihira, Miki Noji, Katrin Ishii-Schrade, Atsushi Matsuda, Atsushi Kuno, Misato Okazaki, Keiichi Nakai, Yoshiya Horimoto, Mitsue Saito, Tatsuro Irimura
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0113053

Toward Computational Cumulative Biology by Combining Models of Biological Datasets
Cited by: 8
Author(s): Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, Samuel Kaski
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0080047

A Small RNA Encoded in the Rv2660c Locus of Mycobacterium tuberculosis Is Induced during Starvation and Infection
Cited by: 32
Author(s): Joanna Houghton, Teresa Cortes, Olga T. Schubert, Graham Rose, Angela Rodgers, Megan De Ste Croix, Rudolf Aebersold, Douglas B. Young, Kristine B. Arnvig
Software Mentions: 1
Published: over 12 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962