10.1186/1471-2164-10-467

An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)
Cited by: 59
Author(s): Albert Mascarell-Creus, Joaquı́n Cañizares, Josep Vilarrasa-Blasi, Santiago Mora-Garcı́a, José Blanca, Daniel González-Ibeas, Montserrat Saladié, Cristina Roig, Wim Deleu, Belén Picó-Silvent, Núria López‐Bigas, Miguel A. Aranda, Jordi García-Más, F. Nuez, Pere Puigdomènech, Ana I. Caño‐Delgado
Software Mentions: 3
Published: almost 17 years ago

10.1186/ar2855

Insights in to the pathogenesis of axial spondyloarthropathy based on gene expression profiles
Cited by: 45
Author(s): Srilakshmi M Sharma, Dongseok Choi, Stephen R. Planck, Christina A. Harrington, Carrie R. Austin, J. A. Lewis, Tessa N. Diebel, Tammy M. Martin, Justine R. Smith, James T. Rosenbaum
Software Mentions: 3
Published: over 17 years ago

10.1111/1751-7915.13863

Transcriptome analysis reveals the roles of nitrogen metabolism and sedoheptulose bisphosphatase pathway in methanol‐dependent growth of Corynebacterium glutamicum
Cited by: 4
Author(s): Liwen Fan, Yu Wang, Jin Qian, Ning Gao, Zhihui Zhang, Xiaomeng Ni, Letian Sun, Qianqian Yuan, Ping Zheng, Jibin Sun
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-94396-x

Niche partitioning among dead wood-dependent beetles
Cited by: 1
Author(s): Jakub Horák
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-12-411

EPEPT: A web service for enhanced P-value estimation in permutation tests
Cited by: 5
Author(s): Theo Knijnenburg, Jake Lin, Hector Rovira, John P. Boyle, Ilya Shmulevich
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0081468

Quantitative Identification of Mutant Alleles Derived from Lung Cancer in Plasma Cell-Free DNA via Anomaly Detection Using Deep Sequencing Data
Cited by: 62
Author(s): Yoji Kukita, Junji Uchida, Shigeyuki Oba, Kazumi Nishino, Toru Kumagai, Koki Taniguchi, Takako Okuyama, Fumio Imamura, Kikuya Kato
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12863-017-0568-5

IntroMap: a signal analysis based method for the detection of genomic introgressions
Cited by: 3
Author(s): Daniel J. Shea, Mitsuru Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0128776

Individual Consistency and Phenotypic Plasticity in Rockhopper Penguins: Female but Not Male Body Mass Links Environmental Conditions to Reproductive Investment
Cited by: 14
Author(s): Nina Dehnhard, Marcel Eens, Laurent Demongin, Petra Quillfeldt, Maud Poisbleau
Software Mentions: 3
Published: over 11 years ago

10.3390/s18051465

Smart Waste Collection System with Low Consumption LoRaWAN Nodes and Route Optimization
Cited by: 48
Author(s): Álvaro Lozano, Javier Caridad, Juan F. De Paz, Gabriel Villarrubia González, Javier Bajo
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-020-03658-4

Performance evaluation of lossy quality compression algorithms for RNA-seq data
Cited by: 1
Author(s): Rongshan Yu, Wenxian Yang, Wang Shun
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0113862

The Accuracy, Feasibility and Challenges of Sequencing Short Tandem Repeats Using Next-Generation Sequencing Platforms
Cited by: 26
Author(s): Monika Závodná, Andrew T. M. Bagshaw, Rüdiger Bräuning, Neil J. Gemmell
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12859-021-03980-5

ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data
Cited by: 7
Author(s): Elisa Pischedda, Cristina M. Crava, Martina Carlassara, Susanna Zucca, Laila Gasmi, Mariangela Bonizzoni
Software Mentions: 3
Published: over 5 years ago

10.1186/s12862-019-1353-z

Origin and diversification of the plasminogen activation system among chordates
Cited by: 26
Author(s): Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Berthou, Frank Panitz
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0020924

The Reconstruction of Condition-Specific Transcriptional Modules Provides New Insights in the Evolution of Yeast AP-1 Proteins
Cited by: 17
Author(s): Christel Goudot, Catherine Etchebest, Frédéric Devaux, Gaëlle Lelandais
Software Mentions: 3
Published: over 15 years ago

10.1186/s12862-019-1522-0

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)
Cited by: 11
Author(s): Akira Iguchi, Yuki Yoshioka, Zac H. Forsman, Ingrid S. Knapp, Robert J. Toonen, Yuki Hongo, Satoshi Nagai, Nina Yasuda
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0048743

Internal Habitat Quality Determines the Effects of Fragmentation on Austral Forest Climbing and Epiphytic Angiosperms
Cited by: 9
Author(s): Ainhoa Magrach, Asier R. Larrinaga, Luis Santamarı́a
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0090240

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene
Cited by: 33
Author(s): Yvette A. Halley, Scot E. Dowd, Jared E. Decker, Paul Seabury, Eric K. Bhattarai, Charles D. Johnson, Dale Rollins, Ian R. Tizard, Donald J. Brightsmith, Markus J. Peterson, Jeremy F. Taylor, Christopher M. Seabury
Software Mentions: 3
Published: over 12 years ago

10.1186/s12859-015-0812-9

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles
Cited by: 5
Author(s): Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens
Software Mentions: 3
Published: almost 11 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0249859

Physiological and genetic characterization of heat stress effects in a common bean RIL population
Cited by: 17
Author(s): Yulieth Vargas, Víctor Manuel Mayor-Durán, Hector Fabio Buendia, Henry Alonso Ruiz-Guzman, Bodo Raatz
Software Mentions: 3
Published: over 5 years ago

10.1186/1472-6815-14-9

Combined examination of sequence and copy number variations in human deafness genes improves diagnosis for cases of genetic deafness
Cited by: 23
Author(s): Haiying Ji, Jingqiao Lü, Jianjun Wang, Huawei Li, Xiaobo Lin
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0039951

Effects of Eutrophication, Seasonality and Macrofouling on the Diversity of Bacterial Biofilms in Equatorial Coral Reefs
Cited by: 42
Author(s): Yvonne Sawall, Claudio Richter, Alban Ramette
Software Mentions: 3
Published: about 14 years ago

10.1186/s12859-018-2318-8

Identification of differentially expressed genes by means of outlier detection
Cited by: 5
Author(s): Itziar Irigoien, C. Arenas
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0067410

Boosting Probabilistic Graphical Model Inference by Incorporating Prior Knowledge from Multiple Sources
Cited by: 10
Author(s): Paurush Praveen, Holger Fröhlich
Software Mentions: 3
Published: about 13 years ago

10.1186/1471-2105-16-S18-S16

Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Cited by: 23
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: almost 11 years ago

10.1111/tpj.12307

Resistance gene enrichment sequencing (<scp>R</scp>en<scp>S</scp>eq) enables reannotation of the <scp>NB</scp>‐<scp>LRR</scp> gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Cited by: 327
Author(s): Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan MacLean, Peter J. A. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D. G. Jones
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pone.0062547

p63 Attenuates Epithelial to Mesenchymal Potential in an Experimental Prostate Cell Model
Cited by: 29
Author(s): Jan Roger Olsen, Anne Margrete Øyan, Kari Rostad, Margrete R. Hellem, Jie Liu, Lisha Li, David Micklem, Hallvard Haugen, James B. Lorens, Varda Rotter, Xisong Ke, Biaoyang Lin, Karl‐Henning Kalland
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0002737

Type I Interferon: Potential Therapeutic Target for Psoriasis?
Cited by: 253
Author(s): Yihong Yao, Laura K. Richman, Chris Morehouse, Melissa de los Reyes, Brandon W. Higgs, Anmarie Boutrin, Barbara White, Anthony J. Coyle, James G. Krueger, Peter A. Kiener, Bahija Jallal
Software Mentions: 3
Published: about 18 years ago

10.3390/ani11071863

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep
Cited by: 8
Author(s): Aiju Liu, Xiaoyong Chen, Menghe Liu, Limeng Zhang, Xiaofei Ma, Shujun Tian
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0002126

Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance
Cited by: 162
Author(s): David G. Hendrickson, Daniel J. Hogan, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: over 18 years ago

10.3390/ijms17050696

Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction
Cited by: 31
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-018-2592-5

IMOS: improved Meta-aligner and Minimap2 On Spark
Cited by: 7
Author(s): Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi, Seyed Abolfazl Motahari
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0010247

Evaluation of the Psoriasis Transcriptome across Different Studies by Gene Set Enrichment Analysis (GSEA)
Cited by: 153
Author(s): Mayte Suárez‐Fariñas, Michelle A. Lowes, Lisa C. Zaba, James G. Krueger
Software Mentions: 3
Published: over 16 years ago

10.1186/s12859-020-3491-0

Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
Cited by: 6
Author(s): Jad Abbass, Jean‐Christophe Nebel
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0082638

Evaluation of Current and New Biomarkers in Severe Preeclampsia: A Microarray Approach Reveals the VSIG4 Gene as a Potential Blood Biomarker
Cited by: 33
Author(s): Julien Textoris, Delphine Ivorra, Amira Ben Amara, Florence Sabatier, Jean-Pierre Ménard, H. Heckenroth, Florence Bretelle, Jean‐Louis Mège
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2105-11-73

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Cited by: 11
Author(s): Mark Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0231738

mmannot: How to improve small–RNA annotation?
Cited by: 1
Author(s): Matthias Zytnicki, Christine Gaspin
Software Mentions: 3
Published: over 6 years ago

10.3758/s13414-015-0860-2

The long and the short of priming in visual search
Cited by: 24
Author(s): Wouter Kruijne, Martijn Meeter
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2407-14-64

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Cited by: 21
Author(s): Marion Fehlker, Matthew R. Huska, Thomas Jöns, Miguel A. Andrade‐Navarro, Wolfgang Kemmner
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0012336

Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies
Cited by: 124
Author(s): M. Jeanmougin, Aurélien de Reyniès, Laëtitia Marisa, Caroline Paccard, Grégory Nuel, Mickaël Guedj
Software Mentions: 3
Published: about 16 years ago

10.1371/journal.pone.0000242

Epigenetic Activation of a Subset of mRNAs by eIF4E Explains Its Effects on Cell Proliferation
Cited by: 203
Author(s): Yaël Mamane, Emmanuel Petroulakis, Yvan Martineau, Takaaki Sato, Ola Larsson, Vinagolu K. Rajasekhar, Nahum Sonenberg
Software Mentions: 3
Published: over 19 years ago

10.1371/journal.pone.0136653

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq
Cited by: 42
Author(s): Yafang Li, Xiayu Rao, William Mattox, Christopher I. Amos, Bin Liu
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0015617

A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology
Cited by: 61
Author(s): Martin Blythe, Damian Kao, Sunir Malla, Joanna Rowsell, Reginald H. Wilson, Deborah Evans, Jamie Jowett, Amy Hall, Virginie Lemay, Sabrina Lam, A. Aziz Aboobaker
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2407-7-61

Identification of a robust gene signature that predicts breast cancer outcome in independent data sets
Cited by: 37
Author(s): James E. Korkola, Ekaterini Blaveri, Sandy DeVries, Dan H. Moore, E. Shelley Hwang, Yunn Yi Chen, Anne L. Estep, Karen Chew, Ronald H. Jensen, Frederic M. Waldman
Software Mentions: 3
Published: over 19 years ago

10.1186/1471-2105-16-S7-S5

Heterozygous genome assembly via binary classification of homologous sequence
Cited by: 13
Author(s): Paul Bodily, Mao Fujimoto, Cameron Ortega, Nozomu Okuda, Joseph Price, Mark J. Clement, Quinn Snell
Software Mentions: 3
Published: over 11 years ago

10.18632/oncotarget.15604

NUSAP1 promotes invasion and metastasis of prostate cancer
Cited by: 49
Author(s): Catherine A. Gordon, Xue Gong, Durga Ganesh, James D. Brooks
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0239627

Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel
Cited by: 5
Author(s): Gabriel Schneebauer, Constantin Lindemann, Victoria Drechsel, Lasse Marohn, Klaus Wysujack, Elena Santidrian, Ron P. Dirks, Reinhold Hanel, Bernd Pelster
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-15-969

MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence
Cited by: 9
Author(s): Turki Turki, Usman Roshan
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0160168

New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction
Cited by: 14
Author(s): Ana Ortega, Carolina Gil-Cayuela, Estefanía Tarazón, María García‐Manzanares, José Montero, Juan Cinca, Manuel Portolés, Miguel Rivera, Esther Roselló‐Lletí
Software Mentions: 3
Published: about 10 years ago

10.18632/oncotarget.10947

Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Cited by: 22
Author(s): Zhiming Li, Zaozao Zheng, Jun Ruan, Zhi Li, Xuan Zhuang, Chi-Meng Tzeng
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0028275

The Global Transcriptional Response of Fission Yeast to Hydrogen Sulfide
Cited by: 8
Author(s): Jianmin Xu, Weizhi He, Alastair I. H. Murchie, Dongrong Chen
Software Mentions: 3
Published: almost 15 years ago

10.1186/1471-2164-10-420

Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation
Cited by: 13
Author(s): Tamara Aid-Pavlidis, Pavlos Pavlidis, Tõnis Timmusk
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-13-S14-S5

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0102185

Embryonic miRNA Profiles of Normal and Ectopic Pregnancies
Cited by: 30
Author(s): Francisco Domı́nguez, Juan Manuel Moreno-Moya, Teresa Lozoya, Ainhoa Romero, Sebastián Martínez, Mercedes Monterde, Marta Gurrea, Blanca Ferri, Marı́a José Núñez, Carlos Simón, António Pellicer
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0219551

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes
Cited by: 16
Author(s): Han-Ming Liu, Dan Yang, Zhao-Fa Liu, Shengzhou Hu, Yan Shen-hai, Xian-Wen He
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-11-13

Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos
Cited by: 55
Author(s): Shaobing O. Zhang, Sachin Mathur, Gaye Hattem, Olivier Tassy
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2105-6-173

Normal uniform mixture differential gene expression detection for cDNA microarrays
Cited by: 74
Author(s): Nema Dean, Adrian E. Raftery
Software Mentions: 3
Published: about 21 years ago

10.1186/s12885-016-2453-4

Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes
Cited by: 26
Author(s): Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xiaoting Ke, Anne Margrete Øyan, Karl H. Kalland
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-8-428

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
Cited by: 226
Author(s): S. Pilati, Michele Perazzolli, A. Malossini, Alessandro Cestaro, L. Dematté, Paolo Fontana, A. Dal Rì, Roberto Viola, Riccardo Velasco, C. Moser
Software Mentions: 3
Published: almost 19 years ago

10.1371/journal.pone.0191932

Integrated micro/messenger RNA regulatory networks in essential thrombocytosis
Cited by: 8
Author(s): Lu Zhao, Song Wu, Erya Huang, Dimitri Gnatenko, Wadie F. Bahou, Wei Zhu
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-14-666

Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Cited by: 62
Author(s): Pablo Cingolani, Xiaoyi Cao, Radhika S. Khetani, Chieh Chun Chen, Melissa Coon, Alya’a Sammak, Aliccia Bollig‐Fischer, Susan Land, Yun Huang, Matthew E. Hudson, Mark D. Garfinkel, Sheng Zhong, Gene E. Robinson, Douglas M. Ruden
Software Mentions: 3
Published: almost 13 years ago

10.3390/ani11092557

Identification of Circular RNAs in the Anterior Pituitary in Rats Treated with GnRH
Cited by: 3
Author(s): Haixiang Guo, Bao Yuan, Meng-Ting Su, Yi Zheng, Jinyu Zhang, Dong-Xu Han, Hao-Qi Wang, Yongping Huang, Hao Jiang, Jiabao Zhang
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0173094

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response
Cited by: 6
Author(s): Alex Yi‐Lin Tsai, Kin Chan, Chi-Yip Ho, Thomas Canam, Resmi Capron, Emma R. Master, Katharina Bräutigam
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0201851

Small RNAs detected in exosomes derived from the MH7A synovial fibroblast cell line with TNF-α stimulation
Cited by: 19
Author(s): Yosuke Takamura, Wataru Aoki, Atsushi Satomura, Seiji Shibasaki
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0238907

A new advanced in silico drug discovery method for novel coronavirus (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction
Cited by: 33
Author(s): Y-h. Taguchi, Turki Turki
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-11-592

Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray
Cited by: 55
Author(s): Stéphane Fénart, Yves-Placide Assoumou Ndong, Jorge Duarte, Nathalie Rivière, Jeroen Wilmer, Olivier Van Wuytswinkel, Anca Lucau, Emmanuelle Cariou, Godfrey Neutelings, Laurent Gutierrez, Brigitte Chabbert, Xavier Guillot, Reynald Tavernier, Simon Hawkins, Brigitte Thomasset
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12864-021-07505-5

Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle
Cited by: 12
Author(s): Paulina G. Eusebi, Natalia Sevane, Thomas O’Rourke, Manuel Pizarro, Cédric Boeckx, S. Dunner
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-9-131

The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
Cited by: 127
Author(s): Kirstin Replogle, Arthur P. Arnold, Gregory F. Ball, Mark Band, Staffan Bensch, Eliot A. Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M. George, George Gong, Dennis Hasselquist, Álvaro Gonzalez Hernández, Ryan Kim, Harris A. Lewin, Lei Liu, Peter V. Lovell, Claudio V. Mello, Sara Naurin, Sandra L. Rodriguez-Zas, Jyothi Thimmapuram, Juli Wade, David F. Clayton
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pone.0132642

Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage
Cited by: 12
Author(s): Richard John Puxty, Blanca Perez-Sepulveda, Branko Rihtman, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-10-98

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data
Cited by: 26
Author(s): Adriane Menßen, Götz Edinger, Joachim R. Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, G.-R. Burmester, Thomas Häupl
Software Mentions: 3
Published: over 17 years ago

10.1371/journal.pone.0063946

Predicting Species Cover of Marine Macrophyte and Invertebrate Species Combining Hyperspectral Remote Sensing, Machine Learning and Regression Techniques
Cited by: 26
Author(s): Jonne Kotta, Tiit Kutser, Karolin Teeveer, Ele Vahtmäe, Merli Pärnoja
Software Mentions: 3
Published: over 13 years ago

10.18632/oncotarget.18162

Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma
Cited by: 53
Author(s): Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0040194

Microarray-Based Sketches of the HERV Transcriptome Landscape
Cited by: 46
Author(s): Philippe Pérot, Nathalie Mugnier, Cécile Montgiraud, Juliette Gimenez, Magali Jaillard, Bertrand Bonnaud, François Mallet
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0151522

Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Cited by: 25
Author(s): Paul Pavlidis, Vignesh Dhandapani, Jana Jeevan Rameneni, Xiaonan Li, Ganesan Sivanandhan, Su Ryun Choi, Wenxing Pang, Subin Im, Yong Pyo Lim
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0087499

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress
Cited by: 80
Author(s): Henry D. Priest, Samuel E. Fox, Erik R. Rowley, Jessica R. Murray, Todd P. Michael, Todd C. Mockler
Software Mentions: 3
Published: over 12 years ago

10.18632/oncotarget.19733

Overexpression of COL3A1 confers a poor prognosis in human bladder cancer identified by co-expression analysis
Cited by: 59
Author(s): Lushun Yuan, Bo Shu, Changhong Liang, Kaiyu Qian, Yongzhi Wang, Guofeng Qian, Yuan Zhu, Xinyue Cao, Conghua Xie, Yu Xiao, Xinghuan Wang
Software Mentions: 3
Published: about 9 years ago

10.3390/ijms22179246

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus
Cited by: 8
Author(s): Nesma Shalby, Ibrahim A. A. Mohamed, Jie Xiong, Kaining Hu, Yuting Yang, Elsayed Nishawy, Bin Yi, Jing Wen, Chaozhi Ma, Tingdong Fu, Jinxing Tu
Software Mentions: 3
Published: about 5 years ago

10.1186/s12974-017-0858-x

Toll-like receptor 4 in glial inflammatory responses to air pollution in vitro and in vivo
Cited by: 99
Author(s): Nick Woodward, Morgan C. Levine, Amin Haghani, Farimah Shirmohammadi, Arian Saffari, Constantinos Sioutas, Todd E. Morgan, Caleb E. Finch
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0085583

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming
Cited by: 36
Author(s): Thomas P. van Gurp, Lauren M. McIntyre, Koen J. F. Verhoeven
Software Mentions: 3
Published: over 12 years ago

10.3390/ijms22169081

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
Cited by: 10
Author(s): Aljaž Gaber, Miha Pavšič
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-10-342

Gene expression profile of rat left ventricles reveals persisting changes following chronic mild exercise protocol: implications for cardioprotection
Cited by: 23
Author(s): Betti Giusti, Marina Marini, Luciana Rossi, Ilaria Lapini, Alberto Magi, Andrea Capalbo, Rosa Lapalombella, Simona di Tullio, Michele Samaja, Fabio Esposito, V. Margonato, Maria Boddi, Rosanna Abbate, Arsenio Veicsteinas
Software Mentions: 3
Published: over 17 years ago

10.1186/s12915-021-01108-y

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
Cited by: 14
Author(s): Nicole Gruenheit, Amy Baldwin, Balint Stewart, Sarah Jaques, Thomas Keller, Katie Parkinson, William Salvidge, Robert Baines, Chris Brimson, Jason B. Wolf, Rex L. Chisholm, Adrian J. Harwood, Christopher Thompson
Software Mentions: 3
Published: about 5 years ago

10.1186/s12915-021-01114-0

Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species
Cited by: 7
Author(s): Lianggang Huang, Xuejie Li, Lü Dong, Bin Wang, Li Pan
Software Mentions: 3
Published: about 5 years ago

10.1186/s13007-020-00588-3

In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing
Cited by: 2
Author(s): Narinder Singh, John Raupp, Dal‐Hoe Koo, Bernd Friebe, Bikram S. Gill, Jesse Poland
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1005096

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
Cited by: 10
Author(s): Qi Zheng, Elizabeth A. Grice
Software Mentions: 3
Published: almost 10 years ago

10.3390/ijms20010016

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools
Cited by: 34
Author(s): Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Shantharam Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, Mehdi Mirzaei
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-015-0775-x

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
Cited by: 21
Author(s): Jilong Li, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.1007543

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Cited by: 6
Author(s): Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pbio.0050057

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs
Cited by: 501
Author(s): Kristin D. Kasschau, Noah Fahlgren, Elisabeth J. Chapman, Christopher Sullivan, Jason S. Cumbie, Scott A. Givan, James C. Carrington
Software Mentions: 3
Published: over 19 years ago

10.3390/ijms16035975

RNA-Seq Transcriptome Analysis of Maize Inbred Carrying Nicosulfuron-Tolerant and Nicosulfuron-Susceptible Alleles
Cited by: 26
Author(s): Xiaomin Liu, Xiaogang Xu, Binghua Li, Xueqing Wang, Guiqi Wang, Yaqian Li
Software Mentions: 3
Published: over 11 years ago

10.3390/ijms20235922

Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies
Cited by: 10
Author(s): Xiaoxiang Zhang, Juan Zhou, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Chen Chen, Yin Su, Jianhua Ju, Guichun Dong, Yong Zhou, Zefeng Yang, Aihong Li, Yulong Wang, Jianye Huang, Youli Yao
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms22041837

Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer
Cited by: 5
Author(s): Diamanto Skopelitou, Benchun Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuswick, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-1860-2

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data
Cited by: 115
Author(s): Jane Hawkey, Mohammad Hamidian, Ryan R. Wick, D.J. Edwards, Helen Billman‐Jacobe, Ruth M. Hall, Kathryn E. Holt
Software Mentions: 3
Published: about 11 years ago

10.1038/s41396-018-0332-5

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
Cited by: 55
Author(s): Adrian‐Ştefan Andrei, Michaela M. Salcher, Maliheh Mehrshad, Pavel Rychtecký, Petr Znachor, Rohit Ghai
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-8-123

STATc is a key regulator of the transcriptional response to hyperosmotic shock
Cited by: 32
Author(s): Jianbo Na, Budi Tunggal, Ludwig M. Eichinger
Software Mentions: 3
Published: over 19 years ago

10.1101/2021.07.09.21260221

Genetic regulation of<i>OAS1</i>nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: about 5 years ago

10.1186/s40246-019-0194-6

vi-HMM: a novel HMM-based method for sequence variant identification in short-read data
Cited by: 1
Author(s): Man Lai Tang, Mohammad Shabbir Hasan, Hongxiao Zhu, Liqing Zhang, Xiaowei Wu
Software Mentions: 3
Published: over 7 years ago

10.1155/2013/924971

Gene Expression Profile Analysis of T1 and T2 Breast Cancer Reveals Different Activation Pathways
Cited by: 3
Author(s): Margit Riis, Xi Zhao, Fatemeh Kaveh, Hilde Synnøve Vollan, Anne-Jorunn Nesbakken, Hiroko Kato Solvang, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen
Software Mentions: 3
Published: over 13 years ago