bioconductor: gcrma | Projects | Ecosyste.ms: Papers

10.1002/cam4.3842

Subgrouping by gene expression profiles to improve relapse risk prediction in paediatric B‐precursor acute lymphoblastic leukaemia
Cited by: 1
Author(s): Qingsheng Huang, Jiayong Zhong, Huan Gao, Kuanrong Li, Huiying Liang
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-11-285

Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
Cited by: 34
Author(s): Qianqian Zhu, Jeffrey C. Miecznikowski, Marc S. Halfon
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-11-104

Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements
Cited by: 32
Author(s): Jakub Mieczkowski, Magdalena E. Tyburczy, Michał Dąbrowski, Piotr Pokarowski
Software Mentions: 3
Published: over 14 years ago

10.1186/s13045-016-0247-4

Targeting of BMI-1 with PTC-209 shows potent anti-myeloma activity and impairs the tumour microenvironment
Cited by: 38
Author(s): Arnold Bolomsky, Karin Schlangen, Wolfgang Schreiner, Niklas Zojer, Heinz Ludwig
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0004868

Role of 3′UTRs in the Translation of mRNAs Regulated by Oncogenic eIF4E—A Computational Inference
Cited by: 19
Author(s): Arti Santhanam, Eckart Bindewald, Vinagolu K. Rajasekhar, Ola Larsson, Nahum Sonenberg, Nancy H. Colburn, Bruce A. Shapiro
Software Mentions: 2
Published: over 15 years ago

10.1111/j.1474-9726.2009.00467.x

Gene expression profiles associated with aging and mortality in humans
Cited by: 55
Author(s): Richard A. Kerber, Elizabeth O’Brien, Richard M. Cawthon
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-8-439

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips
Cited by: 23
Author(s): Ernest Turro, Natalia Bochkina, Anne-Mette K. Hein, Sylvia Richardson
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2105-8-48

Improved precision and accuracy for microarrays using updated probe set definitions
Cited by: 153
Author(s): Rickard Sandberg, Ola Larsson
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2407-11-45

Effects of EpCAM overexpression on human breast cancer cell lines
Cited by: 64
Author(s): Johanna M. Gostner, Dominic Fong, Oliver A. Wrulich, Florian Lehne, Marion Zitt, Michael Hermann, Sylvia Krobitsch, Agnieszka Martowicz, Guenther Gastl, Gilbert Spizzo
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2407-9-243

Low expression of a few genes indicates good prognosis in estrogen receptor positive breast cancer
Cited by: 31
Author(s): Steven Buechler
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2164-9-341

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design
Cited by: 53
Author(s): Alessandro Fazio, Michael C. Jewett, Pascale Daran‐Lapujade, Roberta Mustacchi, Renata Usaite, Jack T. Pronk, Christopher T. Workman, Jens Nielsen
Software Mentions: 2
Published: about 16 years ago

10.1186/1471-2164-11-359

Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor
Cited by: 98
Author(s): Raoul Frijters, Wilco W. M. Fleuren, Erik J. M. Toonen, Jan Tuckermann, Holger M. Reichardt, Hans van der Maaden, Andrea van Elsas, Marie-José van Lierop, Wim H.A. Dokter, Jacob de Vlieg, Wynand Alkema
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-10-49

Infection and genotype remodel the entire soybean transcriptome
Cited by: 45
Author(s): Long Zhou, Santiago X. Mideros, Lei Bao, Regina Hanlon, Francisco Arredondo, Sucheta Tripathy, Konstantinos Krampis, Adam Jerauld, Clive Evans, S. K. St. Martin, M. A. Saghai Maroof, Ina Hoeschele, Anne E. Dorrance, Brett M. Tyler
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-13-124

Comparative modular analysis of gene expression in vertebrate organs
Cited by: 10
Author(s): Barbara Piasecka, Zoltán Kutalik, Julien Roux, Sven Bergmann, Marc Robinson‐Rechavi
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-13-225

Probing the Xenopus laevis inner ear transcriptome for biological function
Cited by: 10
Author(s): TuShun R. Powers, Selene Virk, Casilda Trujillo-Provencio, Elba E. Serrano
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-9-601

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3
Cited by: 85
Author(s): Jakub Orzechowski Westholm, Niklas Nordberg, Eva Murén, Adam Ameur, Jan Komorowski, Hans Ronne
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2164-11-640

Gene expression profile of the skin in the 'hairpoor' (HrHp) mice by microarray analysis
Cited by: 12
Author(s): Bong-Kyu Kim, In‐Cheol Baek, Hwa Young Lee, Jeong-Ki Kim, Hyo Jeong Song, Sungjoo Kim Yoon
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2172-13-12

Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling
Cited by: 44
Author(s): Ruben Smeets, Wilco W. M. Fleuren, Xiaotian He, Paul Vink, Frank Wijnands, Monika Górecka, Henri Klop, Sussane Bauerschmidt, Anja Garritsen, Hans J. P. M. Koenen, Irma Joosten, Annemieke M. H. Boots, Wynand Alkema
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2202-8-100

Analysis of gene expression during neurite outgrowth and regeneration
Cited by: 38
Author(s): Moriah L. Szpara, Karen Vranizan, Yu Chuan Tai, Corey S. Goodman, Terence P. Speed, John Ngai
Software Mentions: 2
Published: almost 17 years ago

10.1155/2015/635748

MicroRNA and mRNA Features of Malignant Pleural Mesothelioma and Benign Asbestos-Related Pleural Effusion
Cited by: 42
Author(s): Güntülü Ak, Sandra Tomaszek, Farhad Kosari, Muzaffer Metintaş, James R. Jett, Selma Metintaş, Hüseyin Yıldırım, Emine Dündar, Jie Dong, Marie Christine Aubry, Dennis A. Wigle, Charles F. Thomas
Software Mentions: 2
Published: almost 10 years ago

10.1186/1754-6834-6-22

The influence of HMF and furfural on redox-balance and energy-state of xylose-utilizing Saccharomyces cerevisiae
Cited by: 145
Author(s): Magnus Ask, Maurizio Bettiga, Valeria Mapelli, Lisbeth Olsson
Software Mentions: 2
Published: over 11 years ago

10.1186/1476-4598-8-80

Chemoresistance acquisition induces a global shift of expression of aniogenesis-associated genes and increased pro-angogenic activity in neuroblastoma cells
Cited by: 28
Author(s): Martin Michaelis, Denise Klassert, Susanne Barth, Tatyana Suhan, Rainer Breitling, Bernd Mayer, Nora Hinsch, Hans Wilhelm Doerr, Jaroslav Činátl, Jindřich Činátl
Software Mentions: 2
Published: about 15 years ago

10.1111/mpp.12048

Transcriptomic characterization of two major <scp>F</scp>usarium resistance quantitative trait loci (<scp>QTL</scp>s), <scp>F</scp>hb1 and <scp>Q</scp>fhs.ifa‐<scp>5A</scp>, identifies novel candidate genes
Cited by: 101
Author(s): Wolfgang Schweiger, Barbara Steiner, Christian Ametz, Gerald Siegwart, Gerlinde Wiesenberger, Franz Berthiller, Marc Lemmens, Haiyan Jia, Gerhard Adam, Gary J. Muehlbauer, David P. Kreil, Hermann Buerstmayr
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pcbi.1000189

Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs
Cited by: 8
Author(s): Ran Elkon, Reuven Agami
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pgen.1002794

Gene Expression Profiles in Parkinson Disease Prefrontal Cortex Implicate FOXO1 and Genes under Its Transcriptional Regulation
Cited by: 70
Author(s): Alexandra Dumitriu, Jeanne C. Latourelle, Tiffany C. Hadzi, Nathan Pankratz, Dan Garza, John P. Miller, Jeffery M. Vance, Tatiana Foroud, Thomas G. Beach, Richard H. Myers
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1006757

Brg1 chromatin remodeling ATPase balances germ layer patterning by amplifying the transcriptional burst at midblastula transition
Cited by: 3
Author(s): Gerd K. Wagner, Nishant Singhal, Dario Nicetto, Tobias Straub, Elisabeth Kremmer, Ralph A.W. Rupp
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1007242

Impaired proteoglycan glycosylation, elevated TGF-β signaling, and abnormal osteoblast differentiation as the basis for bone fragility in a mouse model for gerodermia osteodysplastica
Cited by: 33
Author(s): Wing Lee Chan, Magdalena Steiner, Tomasz M. Witkos, Johannes Egerer, Björn Busse, Shuji Mizumoto, Jan M. Pestka, Haikuo Zhang, Ingrid Haußer, Layal Abo Khayal, Claus‐Eric Ott, Mateusz Kolanczyk, Bettina M. Willie, Thorsten Schinke, Chiara Paganini, Antonio Rossi, Kazuyuki Sugahara, Michael Amling, Petra Knaus, D Chan, Martin Lowe, Stefan Mundlos, Uwe Kornak
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0048385

Org 214007-0: A Novel Non-Steroidal Selective Glucocorticoid Receptor Modulator with Full Anti-Inflammatory Properties and Improved Therapeutic Index
Cited by: 28
Author(s): M.J.C. van Lierop, Wynand Alkema, Anke Laskewitz, R. Dijkema, Hans M. van der Maaden, Martin J. Smit, Ralf Plate, Paolo Conti, Christan G.J.M. Jans, Cornelis M. Timmers, C. A. A. Van Boeckel, Scott J. Lusher, Ross McGuire, René C. van Schaik, Jacob de Vlieg, Ruben Smeets, Claudia L. Hofstra, Annemieke M. H. Boots, Marcel van Duin, Benno Ingelse, W.G.E.J. Schoonen, Aldo Grefhorst, Theo H. van Dijk, Folkert Kuipers, Wim H.A. Dokter
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0083674

Behaviorally Activated mRNA Expression Profiles Produce Signatures of Learning and Enhanced Inhibition in Aged Rats with Preserved Memory
Cited by: 31
Author(s): Rebecca P. Haberman, Carlo Colantuoni, Ming Teng Koh, Michela Gallagher
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0007919

Akt and SHIP Modulate Francisella Escape from the Phagosome and Induction of the Fas-Mediated Death Pathway
Cited by: 32
Author(s): Murugesan V. S. Rajaram, Jonathan P. Butchar, Kishore V. L. Parsa, Thomas Cremer, Amal O. Amer, Larry S. Schlesinger, Susheela Tridandapani
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0006779

New Alzheimer Amyloid β Responsive Genes Identified in Human Neuroblastoma Cells by Hierarchical Clustering
Cited by: 14
Author(s): Markus Uhrig, Carina Ittrich, Verena Wiedmann, Yuri P. Knyazev, Annette Weninger, Matthias Riemenschneider, Tobias Hartmann
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0083719

The Glycome of Normal and Malignant Plasma Cells
Cited by: 13
Author(s): Thomas Michel, Anja Seckinger, Dirk Hose, Mindaugas Andrulis, Jérôme Moreaux, Thomas Hielscher, Martina Willhauck‐Fleckenstein, Anette Merling, Uta Bertsch, Anna Jauch, Hartmut Goldschmidt, Bernard Klein, Reinhard Schwartz‐Albiez
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0024153

Inactivation of a Single Copy of Crebbp Selectively Alters Pre-mRNA Processing in Mouse Hematopoietic Stem Cells
Cited by: 6
Author(s): Madeleine E. Lemieux, Zhongqing Cheng, Qing Zhou, Ruth White, John E. Cornell, Andrew L. Kung, Vivienne I. Rebel
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0002924

Microarray Analysis of Human Monocytes Infected with Francisella tularensis Identifies New Targets of Host Response Subversion
Cited by: 110
Author(s): Jonathan P. Butchar, Thomas Cremer, Corey D. Clay, Mikhail A. Gavrilin, Mark D. Wewers, Clay B. Marsh, Larry S. Schlesinger, Susheela Tridandapani
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0052177

Inhibition of the Pim1 Oncogene Results in Diminished Visual Function
Cited by: 20
Author(s): Jun Yin, Lisa Shine, Francis Raycroft, Sudhakar Deeti, Alison Reynolds, Kristin M. Ackerman, Antonino Glaviano, Sean O’Farrell, Olivia O'Leary, Claire Kilty, Ciarán Kennedy, Sarah McLoughlin, Megan Rice, Eileen G. Russell, Desmond G. Higgins, David R. Hyde, Breandán N Kennedy
Software Mentions: 2
Published: almost 12 years ago

10.15252/emmm.201505495

Therapeutic potential of targeting micro <scp>RNA</scp> ‐10b in established intracranial glioblastoma: first steps toward the clinic
Cited by: 113
Author(s): Nadiya M. Teplyuk, Erik J. Uhlmann, Galina Gabriely, Natalia Volfovsky, Yan Wang, Jian Teng, Priya Karmali, Eric G. Marcusson, Merlene Peter, Athul Mohan, Yevgenya Kraytsberg, Ron Cialic, E. Antonio Chiocca, Jakub Godlewski, Bakhos A. Tannous, Anna M. Krichevsky
Software Mentions: 2
Published: over 8 years ago

10.1289/ehp.11229

Murine Lung Responses to Ambient Particulate Matter: Genomic Analysis and Influence on Airway Hyperresponsiveness
Cited by: 55
Author(s): Ting Wang, Liliana Moreno‐Vinasco, Yong Huang, Gabriel Lang, Jered Linares, Sascha N. Goonewardena, Alayna Grabavoy, Jonathan M. Samet, Alison S. Geyh, Patrick N. Breysse, Yves A. Lussier, Viswanathan Natarajan, Joe G.N. Garcia
Software Mentions: 2
Published: almost 16 years ago

10.3389/fonc.2018.00645

BCL2-Family Dysregulation in B-Cell Malignancies: From Gene Expression Regulation to a Targeted Therapy Biomarker
Cited by: 49
Author(s): Benoît Tessoulin, Antonin Papin, Patricia Gomez‐Bougie, Céline Bellanger, Martine Amiot, Catherine Pellat‐Deceunynck, David Chiron
Software Mentions: 2
Published: almost 6 years ago

10.1093/jxb/erw350

The build-up of osmotic stress responses within the growing root apex using kinematics and RNA-sequencing
Cited by: 12
Author(s): Mathilde Royer, David Cohen, Nathalie Aubry, Vera Vendramin, Simone Scalabrin, Federica Cattonaro, Marie‐Béatrice Bogeat‐Triboulot, Irène Hummel
Software Mentions: 2
Published: about 8 years ago

10.1038/srep30975

Thermal fluctuations affect the transcriptome through mechanisms independent of average temperature
Cited by: 48
Author(s): Jesper Givskov Sørensen, Mads Fristrup Schou, Torsten Nygaard Kristensen, Volker Loeschcke
Software Mentions: 2
Published: about 8 years ago

10.1038/srep34949

Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research
Cited by: 90
Author(s): Christopher S. Hughes, Melissa K. McConechy, Dawn R. Cochrane, Tayyebeh M. Nazeran, Anthony N. Karnezis, David G. Huntsman, Gregg B. Morin
Software Mentions: 2
Published: about 8 years ago

10.1038/srep43941

Androgen receptor is a potential novel prognostic marker and oncogenic target in osteosarcoma with dependence on CDK11
Cited by: 12
Author(s): Yunfei Liao, Slim Sassi, Stefan Halvorsen, Yong Feng, Jacson K. Shen, Yan Gao, Gregory M. Coté, Edwin Choy, David C. Harmon, Henry J. Mankin, Francis J. Hornicek, Zhenfeng Duan
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-29085-3

Menthol, a unique urinary volatile compound, is associated with chronic inflammation in interstitial cystitis
Cited by: 17
Author(s): Muhammad Shahid, Min Young Lee, Austin Yeon, Eunho Cho, Vikram Sairam, Luis Valdiviez, Sungyong You, Jayoung Kim
Software Mentions: 2
Published: about 6 years ago

10.1038/s41389-020-00253-3

Cyclin D1 targets hexokinase 2 to control aerobic glycolysis in myeloma cells
Cited by: 20
Author(s): Mélody Caillot, Jérôme Bourgeais, Hassan Dakik, Élodie Costé, Nathalie M. Mazure, Éric Lelièvre, Olivier Coqueret, Olivier Hérault, Frédéric Mazurier, Brigitte Sola
Software Mentions: 2
Published: about 4 years ago

10.1186/gb-2005-6-4-r33

Promoter features related to tissue specificity as measured by Shannon entropy
Cited by: 387
Author(s): Jonathan Schug, Schuller Winfried-Paul, Claudia Kappen, J. Michael Salbaum, Maja Bućan, Christian J. Stoeckert
Software Mentions: 1
Published: over 19 years ago

10.3390/cells9112449

The Remaining Mysteries about Brown Adipose Tissues
Cited by: 7
Author(s): Miwako Nishio, Kumiko Saeki
Software Mentions: 1
Published: almost 4 years ago

10.1186/gb-2011-12-12-r119

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)
Cited by: 69
Author(s): Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse
Software Mentions: 1
Published: almost 14 years ago

10.1186/gb-2014-15-1-r12

Global target mRNA specification and regulation by the RNA-binding protein ZFP36
Cited by: 134
Author(s): Neelanjan Mukherjee, Nicholas C. Jacobs, Markus Hafner, Elizabeth A. Kennington, Jeffrey D. Nusbaum, Thomas Tuschl, Perry J. Blackshear, Uwe Ohler
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13059-015-0593-5

Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks
Cited by: 44
Author(s): Vez Repunte‐Canonigo, William Shin, Leandro F. Vendruscolo, Céline Lefèbvre, Lena van der Stap, Tatsuyuki Kawamura, Joel E. Schlosburg, Mariano J. Alvarez, George F. Koob, Andrea Califano, Pietro Paolo Sanna
Software Mentions: 1
Published: over 9 years ago

10.3390/cancers8090079

Wnt5a Signaling in Cancer
Cited by: 174
Author(s): Marwa Asem, Steven Buechler, Rebecca J. Wates, Daniel Miller, M. Sharon Stack
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0095556

HD CAGnome: A Search Tool for Huntingtin CAG Repeat Length-Correlated Genes
Cited by: 3
Author(s): Ekaterina I. Galkina, Ae Sun Shin, Kathryn R. Coser, Toshi Shioda, Isaac S. Kohane, Ihn Sik Seong, Vanessa C. Wheeler, James F. Gusella, Marcy E. MacDonald, Jongmin Lee
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0082833

Prognostic Value of Discs Large Homolog 7 Transcript Levels in Prostate Cancer
Cited by: 24
Author(s): Christian R. Gómez, Farhad Kosari, Jan Marie Munz, Claire A. Schreiber, Gaylord J. Knutson, Cristiane M. Ida, Abdelouahid El Khattouti, R. Jeffrey Karnes, John C. Cheville, George Vasmatzis, Stanimir Vuk‐Pavlović
Software Mentions: 1
Published: almost 11 years ago

10.1186/s40478-019-0853-9

A metastable subproteome underlies inclusion formation in muscle proteinopathies
Cited by: 15
Author(s): Prajwal Ciryam, Matthew Antalek, Fernando Maureira Cid, Gian Gaetano Tartaglia, Christopher M. Dobson, Anne Katrin Guettsches, Britta Eggers, Matthias Vorgerd, Katrin Marcus, Rudolf A. Kley, Richard I. Morimoto, Conrad C. Weihl
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0104742

Overexpression of Gremlin-1 in Patients with Loeys-Dietz Syndrome: Implications on Pathophysiology and Early Disease Detection
Cited by: 12
Author(s): Jasmin Wellbrock, Sara Sheikhzadeh, Leticia Oliveira‐Ferrer, Hauke Stamm, Mathias Hillebrand, Britta Keyser, Marianne Klokow, Gabi Vohwinkel, Veronika Bonk, Benjamin Otto, Thomas Streichert, Stefan Balabanov, Christian Hagel, Meike Rybczynski, Frank Bentzien, Carsten Bokemeyer, Yskert Von Kodolitsch, Walter Fiedler
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0006279

How the Intestinal Peptide Transporter PEPT-1 Contributes to an Obesity Phenotype in Caenorhabditits elegans
Cited by: 52
Author(s): Britta Spanier, Katrin Lasch, Silke Marsch, Jacqueline Benner, Wenjuan Liao, Hao Hu, Hermine Kienberger, Wolfgang Eisenreich, Hannelore Daniel
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0066574

A Molecular Predictor Reassesses Classification of Human Grade II/III Gliomas
Cited by: 7
Author(s): Thierry Rème, Jean‐Philippe Hugnot, Ivan Bièche, Valérie Rigau, Fanny Burel‐Vandenbos, Vincent Prévot, Marc Baroncini, Denys Fontaine, Hugues Chevassus, Sophie Vacher, Rosette Lidereau, Hugues Duffau, Luc Bauchet, Dominique Joubert
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0120352

Assembly and Interrogation of Alzheimer’s Disease Genetic Networks Reveal Novel Regulators of Progression
Cited by: 83
Author(s): S. Aubry, William Shin, John F. Crary, Roger Lefort, Yasir H. Qureshi, Céline Lefèbvre, Andrea Califano, Michael L. Shelanski
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0028455

Genomic Approach to Study Floral Development Genes in Rosa sp.
Cited by: 43
Author(s): Annick Dubois, Arnaud Remay, Olivier Raymond, Sandrine Balzergue, Aurélie Chauvet, Marion Maene, Yann Pécrix, Shuhua Yang, Julien Jeauffre, Tatiana Thouroude, Véronique Boltz, Marie‐Laure Martin‐Magniette, Stéphane Janczarski, Fabrice Legeai, Jean-Pierre Renou, Philippe Vergne, Manuel Le Bris, Fabrice Foucher, Mohammed Bendahmane
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0190341

Transcriptome dynamic of Arabidopsis roots infected with Phytophthora parasitica identifies VQ29, a gene induced during the penetration and involved in the restriction of infection
Cited by: 20
Author(s): Jo-Yanne Le Berre, Mathieu Gourgues, Birgit Samans, Harald Keller, Franck Panabières, Agnès Attard
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-11-630

Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes
Cited by: 177
Author(s): David Cohen, Marie‐Béatrice Bogeat‐Triboulot, Émilie Tisserant, Sandrine Balzergue, Marie‐Laure Martin‐Magniette, Gaëlle Lelandais, Nathalie Ningre, Jean-Pierre Renou, Jean-Philippe Tamby, Didier Le Thiec, Irène Hummel
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0031917

A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants
Cited by: 110
Author(s): Samantha Rayson, Luis Arciga-Reyes, Lucie Wootton, Marta de Torres Zabala, William Truman, Neil Graham, Murray Grant, Brendan Davies
Software Mentions: 1
Published: over 12 years ago

10.1186/1742-4690-3-32

Induction of the HIV-1 Tat co-factor cyclin T1 during monocyte differentiation is required for the regulated expression of a large portion of cellular mRNAs
Cited by: 26
Author(s): Wendong Yu, Yan Wang, Chad A. Shaw, F. Xiao-Feng Qin, Andrew P. Rice
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0203965

LDH-A regulates the tumor microenvironment via HIF-signaling and modulates the immune response
Cited by: 69
Author(s): Inna Serganova, Ilan Cohen, Kiranmayi Vemuri, Masahiro Shindo, Masatomo Maeda, Mayuresh Mane, Е. А. Мороз, Raya Khanin, Jaya M. Satagopan, Jason A. Koutcher, Ronald G. Blasberg
Software Mentions: 1
Published: about 6 years ago

10.1186/s12885-018-4995-0

Triptolide as a novel agent in pancreatic cancer: the validation using patient derived pancreatic tumor cell line
Cited by: 18
Author(s): Seung Tae Kim, Sun Young Kim, Jeeyun Lee, Kyung Kim, Se Hoon Park, Young Suk Park, Ho Yeong Lim, Won Ki Kang, Joon Oh Park
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms150713111

DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide
Cited by: 64
Author(s): Laura Baranello, Fedor Kouzine, Damian Wójtowicz, Kairong Cui, Teresa M. Przytycka, Keji Zhao, David Levens
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2105-8-399

fREDUCE: Detection of degenerate regulatory elements using correlation with expression
Cited by: 14
Author(s): Randy Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li, Shoudan Liang
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0039860

MassTRIX Reloaded: Combined Analysis and Visualization of Transcriptome and Metabolome Data
Cited by: 78
Author(s): Brigitte Wägele, Michael Witting, Philippe Schmitt‐Kopplin, Karsten Suhre
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-12-S13-S20

Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression
Cited by: 44
Author(s): Sheng-An Lee, Theresa Tsun-Hui Tsao, Ko-Chun Yang, Han Lin, Yu‐Hung Kuo, Chien-Hsiang Hsu, Wen‐Kuei Lee, Kuo-Chuan Huang, Cheng−Yan Kao
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.0030187

Adaptive Gene Expression Divergence Inferred from Population Genomics
Cited by: 52
Author(s): Alisha K. Holloway, Mara Lawniczak, Jason G. Mezey, David J. Begun, Corbin D. Jones
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pcbi.1002240

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome
Cited by: 498
Author(s): David Venet, Jacques Emile Dumont, Vincent Detours
Software Mentions: 1
Published: almost 13 years ago

10.1038/leu.2013.345

Blocking ETV6/RUNX1-induced MDM2 overexpression by Nutlin-3 reactivates p53 signaling in childhood leukemia
Cited by: 31
Author(s): Ulrike Kaindl, Maria Morak, C Portsmouth, A Mecklenbräuker, Max Kauer, Marion Zeginigg, Andishe Attarbaschi, Oskar A. Haas, Renate Panzer‐Grümayer
Software Mentions: 1
Published: almost 11 years ago

10.1186/bcr3230

Cross-species genomic and functional analyses identify a combination therapy using a CHK1 inhibitor and a ribonucleotide reductase inhibitor to treat triple-negative breast cancer
Cited by: 25
Author(s): Christina N. Bennett, Christine C. Tomlinson, Aleksandra M. Michalowski, Isabel Chu, Dror Luger, Lara Mittereder, Olga Aprelikova, James Shou, Helen Piwinica-Worms, Natasha J. Caplen, Melinda G. Hollingshead, Jeffrey E. Green
Software Mentions: 1
Published: about 12 years ago

10.1186/1755-8794-2-25

Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis
Cited by: 12
Author(s): Erik F. Hensen, Jelle J. Goeman, Jan Oosting, Andel G. L. van der Mey, Pancras C.W. Hogendoorn, C.W.R.J. Cremers, Peter Devilee, Cees J. Cornelisse
Software Mentions: 1
Published: over 15 years ago

10.1038/tp.2017.6

Chemistry-based molecular signature underlying the atypia of clozapine
Cited by: 13
Author(s): Timothy Cardozo, Evgeny Shmelkov, Klára Felsövályi, J Swetnam, Tracy Butler, Dolores Malaspina, Sergey V. Shmelkov
Software Mentions: 1
Published: over 7 years ago

10.1186/1741-7015-10-39

Bioinformatic identification of proteins with tissue-specific expression for biomarker discovery
Cited by: 45
Author(s): Ioannis Prassas, Caitlin C. Chrystoja, Shalini Makawita, Eleftherios P. Diamandis
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-11-229

Age-related molecular genetic changes of murine bone marrow mesenchymal stem cells
Cited by: 117
Author(s): Amber Wilson, Lina A. Shehadeh, Hong Yu, Keith A. Webster
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-14-100

Gene expression profiling of breast cancer survivability by pooled cDNA microarray analysis using logistic regression, artificial neural networks and decision trees
Cited by: 31
Author(s): Hsiu Ling Chou, Chung Tay Yao, Sui-Lung Su, Chia-Yi Lee, Kuang Yu Hu, Harn Jing Terng, Yun Wen Shih, Yu Sheng Chang, Yu Lu, Ching-Wei Chang, Mark L. Wahlqvist, Thomas C. Wetter, Chi Ming Chu
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-015-2055-6

On the relevance of technical variation due to building pools in microarray experiments
Cited by: 1
Author(s): Henrik Rudolf, Gerd Nuernberg, Dirk Koczan, Jens Vanselow, Tanja Gempe, Martin Beye, Gérard Leboulle, Kaspar Bienefeld, Norbert Reinsch
Software Mentions: 1
Published: almost 9 years ago

10.3389/fgene.2018.00198

Kynurenine 3-Monooxygenase Gene Associated With Nicotine Initiation and Addiction: Analysis of Novel Regulatory Features at 5′ and 3′-Regions
Cited by: 8
Author(s): Hassan A. Aziz, Abdel‐Salam G. Abdel‐Salam, Mohammed A. I. Al‐Obaide, Hytham Alobydi, Saif Al-Humaish
Software Mentions: 1
Published: over 6 years ago

10.1096/fj.201900766R

ULK2 is essential for degradation of ubiquitinated protein aggregates and homeostasis in skeletal muscle
Cited by: 27
Author(s): Jordan D. Fuqua, Caleb Mere, Ana Kronemberger, Jay Blomme, Dam Bae, Kristen Turner, Matthew P. Harris, Estêvão Scudese, Mitchell Edwards, Scott M. Ebert, Luís G O de Sousa, Sue C. Bodine, Ling Yang, Christopher M. Adams, Vitor A. Lira
Software Mentions: 1
Published: about 5 years ago

10.3390/cells10040915

Rho Family GTPases and Rho GEFs in Glucose Homeostasis
Cited by: 12
Author(s): Polly Machin, Elpida Tsonou, David C. Hornigold, Heidi Welch
Software Mentions: 1
Published: over 3 years ago

10.3389/fonc.2019.00152

Construction and Validation of a 9-Gene Signature for Predicting Prognosis in Stage III Clear Cell Renal Cell Carcinoma
Cited by: 19
Author(s): Junlong Wu, Shengming Jin, Weijun Gu, Fangning Wan, Ye Zhang, Guohai Shi, Yuanyuan Qu, Dingwei Ye
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-6-6

Microarray analysis of gene expression profiles of cardiac myocytes and fibroblasts after mechanical stress, ionising or ultraviolet radiation
Cited by: 58
Author(s): Marjan Boerma, Caroline G C van der Wees, Harry Vrieling, J. Peter Svensson, J. Wondergem, Arnoud van der Laarse, Leon H.F. Mullenders, A.A. van Zeeland
Software Mentions: 1
Published: over 19 years ago

10.3389/fpls.2017.01984

An Integrated “Multi-Omics” Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality
Cited by: 41
Author(s): Marc Galland, Dongli He, Imen Lounifi, Erwann Arc, Gilles Clément, Sandrine Balzergue, Stéphanie Huguet, Gwendal Cueff, Benoit Godin, Boris Collet, Fabienne Granier, Halima Morin, Joseph Tran, Benoı̂t Valot, Loïc Rajjou
Software Mentions: 1
Published: almost 7 years ago

10.3389/fpls.2016.01837

MtNF-YA1, A Central Transcriptional Regulator of Symbiotic Nodule Development, Is Also a Determinant of Medicago truncatula Susceptibility toward a Root Pathogen
Cited by: 20
Author(s): Thomas Rey, Philippe Laporte, Maxime Bonhomme, Marie-Françoise Jardinaud, Stéphanie Huguet, Sandrine Balzergue, Bernard Dumas, Andréas Niebel, Christophe Jacquet
Software Mentions: 1
Published: almost 8 years ago

Projects: bioconductor: gcrma

Papers Mentioning gcrma 186