bioconductor: ArrayExpress | Projects

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: almost 21 years ago

10.1186/1753-6561-5-S4-S4

Jejunal gene expression patterns correlate with severity of systemic infection in chicken
Cited by: 4
Author(s): Dirkjan Schokker, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 1
Published: about 15 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

10.1186/1471-2229-10-77

Large impact of the apoplast on somatic embryogenesis in Cyclamen persicum offers possibilities for improved developmental control in vitro
Cited by: 30
Author(s): Claudia Hoenemann, Sandra Richardt, Katja Krüger, Andreas Zimmer, Annette Hohe, Stefan A. Rensing
Software Mentions: 1
Published: about 16 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: about 12 years ago

10.1186/1471-2229-8-76

Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism
Cited by: 70
Author(s): Wieslawa I. Mentzen, Peng Jisheng, Nick Ransom, Basil J. Nikolau, Eve Syrkin Wurtele
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12859-019-2651-6

Identification of trans-eQTLs using mediation analysis with multiple mediators
Cited by: 31
Author(s): Nayang Shan, Zuoheng Wang, Lin Hou
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2229-12-74

Effects of yeast trehalose-6-phosphate synthase 1 on gene expression and carbohydrate contents of potato leaves under drought stress conditions
Cited by: 57
Author(s): Mihály Kondrák, Ferenc Marincs, Ferenc Antal, Zsófia Juhász, Zsófia Bánfalvi
Software Mentions: 1
Published: about 14 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: almost 15 years ago

10.1186/1471-2229-7-56

Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis
Cited by: 151
Author(s): Xiaoping Tan, Blake C. Meyers, Alexander Kozik, Marilyn A. L. West, Michèle Morgante, Dina A. St. Clair, Andrew F. Bent, Richard W. Michelmore
Software Mentions: 1
Published: over 18 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

10.1186/1471-2229-9-19

TRUNCATULIX - a data warehouse for the legume community
Cited by: 11
Author(s): Kolja Henckel, Kai J. Runte, Thomas Bekel, Michael Dondrup, Tobias Jakobi, H. Küster, Alexander Goesmann
Software Mentions: 1
Published: over 17 years ago

10.3390/ijms20225783

Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing
Cited by: 19
Author(s): Yi Feng, Qiran Sun, Guifen Zhang, Ting Wu, Xinzhong Zhang, Xuefeng Xu, Zhenhai Han, Yi Wang
Software Mentions: 1
Published: over 6 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

10.1186/1471-2229-9-15

Validation of candidate genes putatively associated with resistance to SCMV and MDMV in maize (Zea mays L.) by expression profiling
Cited by: 53
Author(s): Anna Użarowska, Giuseppe Dionisio, Barbara Sarholz, Hans‐Peter Piepho, Ming Xu, Christina Ingvardsen, G. Wenzel, Thomas Lübberstedt
Software Mentions: 1
Published: over 17 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

10.1186/1471-2229-10-202

Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.)
Cited by: 59
Author(s): Pete E. Hedley, Joanne Russell, Linzi Jorgensen, Sandra Gordon, Jenny Morris, Christine A. Hackett, Linda Cardle, Rex Brennan
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-7-489

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Cited by: 197
Author(s): Tim Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert, Joseph A. White, Patricia L. Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brāzma
Software Mentions: 1
Published: over 19 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: almost 17 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

10.1186/1471-2229-12-204

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

10.1371/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: over 6 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: over 14 years ago

10.1038/s41598-018-37591-7

Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 1
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Connor Rogerson, Christopher W. Bleaney, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 1
Published: over 7 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: over 16 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

10.1038/s41598-019-42750-5

Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
Cited by: 5
Author(s): Michael Laimighofer, Ramona Lickert, R. Fuerst, Fabian J. Theis, Christiane Winkler, Ezio Bonifacio, Anette‐Gabriele Ziegler, Jan Krumsiek
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.03743

The transcription factor Pitx2 positions the embryonic axis and regulates twinning
Cited by: 33
Author(s): Angela Torlopp, Mohsin A.F. Khan, Nidia M M Oliveira, Ingrid Lekk, Luz Mayela Soto‐Jiménez, Alona Sosinsky, Claudio D. Stern
Software Mentions: 1
Published: over 11 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

10.1371/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: about 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: about 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: almost 13 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: about 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

10.1186/1471-2229-10-108

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: about 16 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: about 11 years ago

10.1038/s41598-019-43795-2

Replication termination without a replication fork trap
Cited by: 20
Author(s): Elisa Galli, Jean-Luc Ferat, Jean-Michel Desfontaines, Marie-Eve Val, Ove Skovgaard, François‐Xavier Barre, Christophe Possoz
Software Mentions: 1
Published: about 7 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: over 8 years ago

10.1038/s41598-019-46664-0

Virus Genotype-Dependent Transcriptional Alterations in Lipid Metabolism and Inflammation Pathways in the Hepatitis C Virus-infected Liver
Cited by: 18
Author(s): W. d’Avigdor, Magdalena A. Budzinska, M Lee, Roselind S. Lam, James G. Kench, Michael Stapelberg, Susan V. McLennan, Geoffrey C. Farrell, Jacob George, Geoffrey W. McCaughan, Thomas Tu, Nicholas Shackel
Software Mentions: 1
Published: almost 7 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

10.1186/1471-2229-9-28

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: over 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: over 12 years ago

10.1186/1471-2105-11-150

Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes
Cited by: 41
Author(s): Sigrid Rouam, Thierry Moreau, Philippe Broët
Software Mentions: 1
Published: about 16 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: about 7 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

10.1371/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

10.1186/1471-2105-9-183

Data capture in bioinformatics: requirements and experiences with Pedro
Cited by: 16
Author(s): Daniel Jameson, Kevin Garwood, Christopher Garwood, Tim Booth, Pinar Alper, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: about 18 years ago

10.1038/s41598-019-49124-x

Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis
Cited by: 8
Author(s): Perumal Gnanakkumaar, Ram Murugesan, Shiek S. S. J. Ahmed
Software Mentions: 1
Published: almost 7 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: about 21 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: about 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

10.1186/1471-2202-11-14

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: over 16 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: about 19 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

10.1186/1471-2474-13-130

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: almost 14 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: almost 14 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.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

10.1186/1471-2199-8-119

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

10.1371/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: about 16 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

10.1186/1471-2180-7-88

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.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: almost 9 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: over 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: over 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

10.1186/1471-2180-12-104

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

10.1186/1471-2180-13-224

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.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: about 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: almost 14 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

10.1371/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: almost 13 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

10.7554/eLife.09886

Protein kinase C coordinates histone H3 phosphorylation and acetylation
Cited by: 13
Author(s): Zoulfia Darieva, Aaron Webber, Stacey Warwood, Andrew D. Sharrocks
Software Mentions: 1
Published: over 10 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

10.1186/1471-2180-8-73

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: about 18 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

10.1186/1471-2180-12-212

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.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: almost 13 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: almost 18 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: almost 10 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: over 18 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

10.1371/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

10.1186/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

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962