Ecosyste.ms: Papers

10.1186/1471-2105-16-S11-S2

VisRseq: R-based visual framework for analysis of sequencing data
Cited by: 59
Author(s): Hamid Younesy, Torsten B. Möller, Matthew C. Lorincz, Mehdi Karimi, Steven J.M. Jones
Software Mentions: 15
Published: about 9 years ago

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 12 years ago

10.1186/1471-2105-9-46

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
Cited by: 16
Author(s): Yuerong Zhu, Yuelin J. Zhu, Wei Xu
Software Mentions: 7
Published: almost 17 years ago

10.1186/gb-2008-9-7-r118

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
Cited by: 86
Author(s): Vu T. Chu, Raphaël Gottardo, Adrian E. Raftery, Roger E. Bumgarner, Ka Yee Yeung
Software Mentions: 7
Published: almost 17 years ago

10.1186/1471-2105-9-86

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Cited by: 75
Author(s): Frédéric Chalmel, Michael Primig
Software Mentions: 6
Published: almost 17 years ago

10.1186/s12864-015-1787-7

Identification and functional analysis of early gene expression induced by circadian light-resetting in Drosophila
Cited by: 20
Author(s): Adeolu B. Adewoye, Charalambos P. Kyriacou, Eran Tauber
Software Mentions: 5
Published: over 9 years ago

10.1016/j.devcel.2016.08.013

Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis
Cited by: 61
Author(s): Stefano Bencivenga, Antonio Serrano-Mislata, Maxwell S. Bush, Samantha Fox, Robert Sablowski
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2164-8-455

Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells
Cited by: 49
Author(s): Yan Xu, Machiko Ikegami, Yanhua Wang, Yasushi Matsuzaki, Jeffrey A. Whitsett
Software Mentions: 3
Published: almost 18 years ago

10.1038/s41598-018-33475-y

Mechanisms Underlying the Regulation of HP1γ by the NGF-PKA Signaling Pathway
Cited by: 3
Author(s): Seungmae Seo, Angela Mathison, Adrienne Grzenda, Jewel L. Podratz, Ézéquiel Calvo, Stephen Brimijoin, Anthony J. Windebank, Juan Iovanna, Gwen Lomberk, Raúl Urrutia
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2229-9-132

Genome scale transcriptome analysis of shoot organogenesis in Populus
Cited by: 43
Author(s): Yanghuan Bao, Palitha Dharmawardhana, Todd C. Mockler, Steven H. Strauss
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2229-9-29

Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants
Cited by: 46
Author(s): Debra J. Skinner, Charles S. Gasser
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2229-11-149

Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening
Cited by: 123
Author(s): Ana Margarida Fortes, Ana Patrícia, Marta S. Silva, Kashif Ali, Lisete Sousa, Federica Maltese, Young Hae Choi, Jérôme Grimplet, J. M. Martínez-Zapater, Robert Verpoorte, M. S. Pais
Software Mentions: 2
Published: almost 14 years ago

10.1186/bcr2827

During hormone depletion or tamoxifen treatment of breast cancer cells the estrogen receptor apoprotein supports cell cycling through the retinoic acid receptor α1 apoprotein
Cited by: 23
Author(s): Marcela d’Alincourt Salazar, Maya Ratnam, Mugdha Patki, Ivana Kisovic, Robert Trumbly, Mohamed Imran, Manohar Ratnam
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0060422

Search for Transcriptional and Metabolic Markers of Grape Pre-Ripening and Ripening and Insights into Specific Aroma Development in Three Portuguese Cultivars
Cited by: 58
Author(s): Ana Patrícia, Alexander Erban, Lisete Sousa, M. S. Pais, Joachim Kopka, Ana Margarida Fortes
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0064829

Transcriptome Analysis Reveals New Insights into the Modulation of Endometrial Stromal Cell Receptive Phenotype by Embryo-Derived Signals Interleukin-1 and Human Chorionic Gonadotropin: Possible Involvement in Early Embryo Implantation
Cited by: 35
Author(s): Amélie Bourdiec, Ézéquiel Calvo, Ch.V. Rao, Ali Akoum
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1002315

Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis
Cited by: 175
Author(s): Marta L. DeDiego, José L. Nieto-Torres, Jose M. Jiménez-Guardeño, José Ángel Regla-Nava, Enrique Álvarez, Juan Carlos Oliveros, Jincun Zhao, Craig Fett, Stanley Perlman, Luis Enjuanes
Software Mentions: 2
Published: about 13 years ago

10.1186/1755-8417-1-2

Smad4 haploinsufficiency: a matter of dosage
Cited by: 25
Author(s): Paola Alberici, Cláudia Gaspar, Patrick Franken, Marcin M. Gorski, Ingrid de Vries, Rodney J. Scott, Ari Ristimäki, Lauri A. Aaltonen, Riccardo Fodde
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0012143

The SWR1 Histone Replacement Complex Causes Genetic Instability and Genome-Wide Transcription Misregulation in the Absence of H2A.Z
Cited by: 98
Author(s): Macarena Morillo-Huesca, Marta Clemente‐Ruiz, Eloísa Andújar, Félix Prado
Software Mentions: 1
Published: about 14 years ago

10.1074/jbc.M112.434670

Krüppel-like Factor 11 Regulates the Expression of Metabolic Genes via an Evolutionarily Conserved Protein Interaction Domain Functionally Disrupted in Maturity Onset Diabetes of the Young
Cited by: 31
Author(s): Gwen Lomberk, Adrienne Grzenda, Angela Mathison, Carlos Escande, Jin San Zhang, Ézéquiel Calvo, Laurence J. Miller, Juan Iovanna, Eduardo N. Chini, Martín E. Fernández-Zapico, Raúl Urrutia
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0026570

Human Embryonic Stem Cells Derived from Embryos at Different Stages of Development Share Similar Transcription Profiles
Cited by: 22
Author(s): G. Giritharan, Duško Ilić, Matthew Gormley, Ana Krtolica
Software Mentions: 1
Published: about 13 years ago

10.1186/ar1754

Cited by: 21
Author(s): Philip Gierer, Saleh M. Ibrahim, Thomas Mittlmeier, Dirk Koczan, Steffen Moeller, Jürgen Landes, Georg Gradl, Brigitte Vollmar
Software Mentions: 1
Published: almost 20 years ago

10.1371/journal.pone.0113704

Human Staufen1 Associates to MiRNAs Involved in Neuronal Cell Differentiation and is Required for Correct Dendritic Formation
Cited by: 14
Author(s): Joan Peredo, Patricia Villacé, Juan Ortı́n, Susana de Lucas
Software Mentions: 1
Published: almost 10 years ago

10.22074/cellj.2021.7053

Identification of CCNB2 as A Potential Non-Invasive Breast Cancer Biomarker in Peripheral Blood Mononuclear Cells Using The Systems Biology Approach.
Cited by: 3
Author(s): Raheleh Moradpoor, Hakimeh Zali, Ahmad Gharebaghian, Mohammad Esmaeil Akbari, Soheila Ajdari, Mona Salimi
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-018-5080-4

Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus)
Cited by: 24
Author(s): Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang, Harold B. White
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2199-15-10

Single and combinatorial chromatin coupling events underlies the function of transcript factor krüppel-like factor 11 in the regulation of gene networks
Cited by: 6
Author(s): Ézéquiel Calvo, Adrienne Grzenda, Gwen Lomberk, Angela Mathison, Juan Iovanna, Raúl Urrutia
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-11-108

Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication
Cited by: 10
Author(s): Jenny Zetterblad, Hong Qian, Sasan Zandi, Robert Månsson, Anna Lagergren, Frida Hansson, David Bryder, Nils Paulsson, Mikael Sigvardsson
Software Mentions: 1
Published: over 14 years ago

10.1186/1756-8935-6-21

Functional impact of Aurora A-mediated phosphorylation of HP1γ at serine 83 during cell cycle progression
Cited by: 19
Author(s): Adrienne Grzenda, Phoebe H. Leonard, Seungmae Seo, Angela Mathison, Guillermo Urrutia, Ézéquiel Calvo, Juan Iovanna, Raúl Urrutia, Gwen Lomberk
Software Mentions: 1
Published: over 11 years ago

10.1186/1756-8935-6-3

Functional characterization of EZH2β reveals the increased complexity of EZH2 isoforms involved in the regulation of mammalian gene expression
Cited by: 30
Author(s): Adrienne Grzenda, Gwen Lomberk, Phyllis A. Svingen, Angela Mathison, Ézéquiel Calvo, Juan Iovanna, Yuning Xiong, William A. Faubion, Raúl Urrutia
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-10-517

An expression database for roots of the model legume Medicago truncatula under salt stress
Cited by: 68
Author(s): Daofeng Li, Zhen Su, Jiangli Dong, Tao Wang
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2105-10-292

A first principles approach to differential expression in microarray data analysis
Cited by: 2
Author(s): Robert A. Rubin
Software Mentions: 1
Published: about 15 years ago