Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: SAM

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/SAM

Sparse Additive Modelling
9 versions
Latest release: over 3 years ago
4 dependent packages
341 downloads last month

Papers Mentioning SAM 4,566

10.3389/fnhum.2013.00076
BOLD Responses in Human Primary Visual Cortex are Insensitive to Substantial Changes in Neural Activity
Cited by: 32
Author(s): Jennifer B. Swettenham, Suresh Muthukumaraswamy, Krish Devi Singh
Software Mentions: 3
Published: about 12 years ago
10.3389/fimmu.2020.01475
Small RNA Deep Sequencing Identifies a Unique miRNA Signature Released in Serum Exosomes in a Mouse Model of Sjögren's Syndrome
Cited by: 8
Author(s): Shruti Singh Kakan, Srikanth Reddy Janga, Benjamin Cooperman, David W. Craig, Maria C. Edman, Curtis T. Okamoto, Sarah F. Hamm‐Alvarez
Software Mentions: 3
Published: over 4 years ago
10.3389/fgene.2015.00139
Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System
Cited by: 3
Author(s): Adam Blanchard, James A. Leigh, Sharon A. Egan, Richard D. Emes
Software Mentions: 3
Published: almost 10 years ago
10.1093/gigascience/giz040
Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls
Cited by: 41
Author(s): Brent S. Pedersen, Aaron R. Quinlan
Software Mentions: 3
Published: almost 6 years ago
10.1155/2021/7326853
Identification of Genes Universally Differentially Expressed in Gastric Cancer
Cited by: 6
Author(s): Yidan Shi, Lishuang Qi, Haifeng Chen, Jiahui Zhang, Qingzhou Guan, Jun He, Meifeng Li, Zheng Guo, Haidan Yan, Ping Li
Software Mentions: 3
Published: about 4 years ago
10.3389/fimmu.2018.00497
Overall Downregulation of mRNAs and Enrichment of H3K4me3 Change Near Genome-Wide Association Study Signals in Systemic Lupus Erythematosus: Cell-Specific Effects
Cited by: 11
Author(s): Zhe Zhang, Lei Shi, Li Song, Kelly Maurer, Michele A. Petri, Kathleen E. Sullivan
Software Mentions: 3
Published: almost 7 years ago
10.1186/s13062-016-0152-3
Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
Cited by: 14
Author(s): Suyan Tian, Howard H. Chang, Chi Wang
Software Mentions: 3
Published: over 8 years ago
10.1186/s12859-017-1705-x
An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
Cited by: 121
Author(s): Fatima Zare, Michelle Dow, Nicholas J. Monteleone, Abdelrahman Hosny, Sheida Nabavi
Software Mentions: 3
Published: over 7 years ago
10.3389/fgene.2021.622886
Familial Psychosis Associated With a Missense Mutation at MACF1 Gene Combined With the Rare Duplications DUP3p26.3 and DUP16q23.3, Affecting the CNTN6 and CDH13 Genes
Cited by: 3
Author(s): Josep Pol-Fuster, Francesca Cañellas, Laura Ruiz-Guerra, Aina Medina-Dols, Bàrbara Bisbal-Carrió, Víctor J. Asensio, Bernat Ortega-Vila, Diego M. Marzese, Carme Vidal, Carmen Sofia Pedro dos Santos, Jerònia Lladó, Gabriel Olmos, Damián Heine-Suñer, Konstantin Strauch, Antònia Flaquer, Cristòfol Vives-Bauzà
Software Mentions: 3
Published: almost 4 years ago
10.1093/bioinformatics/btu205
ReadXplorer—visualization and analysis of mapped sequences
Cited by: 94
Author(s): Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
Software Mentions: 3
Published: almost 11 years ago
10.1186/s40478-016-0338-z
A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association
Cited by: 54
Author(s): Michael J. Strong, Eugene Blanchard, Zhen Lin, Cindy A. Morris, Melody Baddoo, Christopher M. Taylor, Marcus L. Ware, Erik K. Flemington
Software Mentions: 3
Published: over 8 years ago
10.3389/fgene.2019.01260
Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases
Cited by: 8
Author(s): Beatriz Andrea Otálora‐Otálora, Mauro Florez, Liliana López‐Kleine, Alejandra Cañas Arboleda, Diana Urrego, Alejandra Rojas
Software Mentions: 3
Published: about 5 years ago
10.3389/fimmu.2020.595877
Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors
Cited by: 5
Author(s): Vladimir A. Veselovsky, Marina S. Dyachkova, Egor Menyailo, Polina S. Polyaeva, Evgenii I. Olekhnovich, Egor Shitikov, Dmitry Bespiatykh, Tatiana A. Semashko, Artem S. Kasianov, Elena N. Ilina, В Н Даниленко, Ksenia M. Klimina
Software Mentions: 3
Published: over 4 years ago
10.1186/1471-2105-13-42
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Cited by: 142
Author(s): Konstantinos Krampis, Tim Booth, Brad Chapman, Brijesh K. Tiwari, Mesude Bicak, Dawn Field, Karen E. Nelson
Software Mentions: 3
Published: almost 13 years ago
10.3389/fgene.2014.00031
Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
Cited by: 21
Author(s): James Hadfield, Matthew Eldridge
Software Mentions: 3
Published: about 11 years ago
10.1186/1471-2105-10-300
RCMAT: a regularized covariance matrix approach to testing gene sets
Cited by: 8
Author(s): Phillip D. Yates, Mark Reimers
Software Mentions: 3
Published: over 15 years ago
10.1186/1471-2164-14-471
Analysis and annotation of the hexaploid oat seed transcriptome
Cited by: 60
Author(s): Juan J. Gutiérrez-González, Zheng Jin Tu, David F. Garvin
Software Mentions: 3
Published: over 11 years ago
10.1093/bioinformatics/bty338
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs
Cited by: 49
Author(s): Matthew B. Stocks, Irina Mohorianu, Matthew Beckers, Claudia Paicu, Simon Moxon, Joshua Thody, Tamás Dalmay, Vincent Moulton
Software Mentions: 3
Published: almost 7 years ago
10.3389/fgene.2014.00043
Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models
Cited by: 12
Author(s): Andreia J. Amaral, Francisco Brito, Tamar Chobanyan, S. Yoshikawa, Takakazu Yokokura, David Van Vactor, Margarida Gama‐Carvalho
Software Mentions: 3
Published: almost 11 years ago
10.3389/fcimb.2017.00186
RegA Plays a Key Role in Oxygen-Dependent Establishment of Persistence and in Isocitrate Lyase Activity, a Critical Determinant of In vivo Brucella suis Pathogenicity
Cited by: 10
Author(s): Elias Abdou, María Pilar Jiménez de Bagüés, Ignacio Martínez-Abadía, Safia Ouahrani‐Bettache, Véronique Pantesco, Alessandra Occhialini, Sascha Al Dahouk, Stephan Köhler, Véronique Jubier-Maurin
Software Mentions: 3
Published: almost 8 years ago
10.1186/s12864-018-5017-y
Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves
Cited by: 6
Author(s): Zhixiong He, Albert J. Fischer, Yang Song, M.A. Steele, Le Luo Guan
Software Mentions: 3
Published: over 6 years ago
10.1093/bioinformatics/btab102
Genozip: a universal extensible genomic data compressor
Cited by: 15
Author(s): Divon Mordechai Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas
Software Mentions: 3
Published: about 4 years ago
10.3389/fgene.2019.01268
Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism
Cited by: 10
Author(s): Mette Juul Jacobsen, Jakob Hull Havgaard, Christian Anthon, Caroline M. Junker Mentzel, Susanna Cirera, Poula Maltha Krogh, Sachin Pundhir, Peter Karlskov-Mortensen, Camilla S. Bruun, Philippe Lesnik, Maryse Guérin, Jan Gorodkin, Claus B. Jørgensen, Merete Fredholm, Romain Barrès
Software Mentions: 3
Published: about 5 years ago
10.1093/bioinformatics/btaa707
The optimal discovery procedure for significance analysis of general gene expression studies
Cited by: 1
Author(s): Andrew J. Bass, J. Douglas Storey
Software Mentions: 3
Published: over 4 years ago
10.3389/fcvm.2021.693351
Plasma Testosterone Levels and Atherosclerotic Plaque Gene Expression in Men With Advanced Atherosclerosis
Cited by: 3
Author(s): Floor Groepenhoff, Ernest Diez Benavente, Arjan Boltjes, Nathalie Timmerman, Farahnaz Waissi, Robin Hartman, N. Charlotte Onland‐Moret, Gérard Pasterkamp, Hester M. den Ruijter
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2105-8-195
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips
Cited by: 20
Author(s): Andrew Harrison, Caroline Johnston, Christine A. Orengo
Software Mentions: 3
Published: over 17 years ago
10.1186/s13040-016-0095-3
Visual programming for next-generation sequencing data analytics
Cited by: 13
Author(s): Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
Software Mentions: 3
Published: almost 9 years ago
10.1186/1471-2105-16-S7-S10
MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)
Cited by: 14
Author(s): Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, S. C. Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, Yingrui Li, Ruiqiang Li, Jun Wang, Xinhua Zhu, Shaoliang Peng, Tak Wah Lam
Software Mentions: 3
Published: almost 10 years ago
10.1186/1471-2164-13-355
Dose-dependent effects of small-molecule antagonists on the genomic landscape of androgen receptor binding
Cited by: 7
Author(s): Zhou Zhu, Minmin Shi, Wenyue Hu, Heather Estrella, Jon Engebretsen, Tim Nichols, David M. Briere, Natilie Hosea, Gerrit Los, Paul A. Rejto, Andrea Fanjul
Software Mentions: 3
Published: about 13 years ago
10.1186/1471-2202-9-93
Bioinformatic and statistical analysis of the optic nerve head in a primate model of ocular hypertension
Cited by: 40
Author(s): Kenneth S Kompass, Olga A. Agapova, Wenjun Li, Paul L. Kaufman, Carol A. Rasmussen, M. Rosario Hernandez
Software Mentions: 3
Published: over 16 years ago
10.1186/1471-2105-6-129
Considerations when using the significance analysis of microarrays (SAM) algorithm
Cited by: 110
Author(s): Ola Larsson, Claes Wahlestedt, James A. Timmons
Software Mentions: 3
Published: over 19 years ago
10.1038/srep32965
Predicting the synergy of multiple stress effects
Cited by: 157
Author(s): Matthias Liess, Kaarina Foit, Saskia Knillmann, Ralf B. Schäfer, Hans-Dieter Ließ
Software Mentions: 3
Published: over 8 years ago
10.1186/s12987-020-00207-2
Advancing brain barriers RNA sequencing: guidelines from experimental design to publication
Cited by: 14
Author(s): David Francisco, Luca Marchetti, Sabela Rodríguez‐Lorenzo, Eduardo Frías-Anaya, Ricardo Figueiredo, Marjolein Heymanns, Maxime Culot, Ana Raquel Santa-Maria, Mária A. Deli, Raoul Freitas Vale Germano, Benoît Vanhollebeke, Nikolaos Kakogiannos, Monica Giannotta, Elisabetta Dejana, Amaia Dominguez-Belloso, Stefan Liebner, Markus Schuster, Harm‐Anton Klok, Marie Wiatr, Horst Schroten, Tobias Tenenbaum, Gijs Kooij, Peter Winter, Ignacio A. Romero, Helga E. de Vries, Britta Engelhardt, Rémy Bruggmann
Software Mentions: 3
Published: over 4 years ago
10.1186/1471-2180-8-20
Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e σB regulon
Cited by: 135
Author(s): Torsten Hain, Hamid Hossain, Som Subhra Chatterjee, Silke Machata, Ute Volk, Sandra Wagner, Benedikt Brors, Stefan A. Haas, Carsten Kuenne, André Billion, Sonja Otten, Jan Pané‐Farré, Susanne Engelmann, Trinad Chakraborty
Software Mentions: 3
Published: about 17 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: over 19 years ago
10.1186/1471-2105-14-S9-S1
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Cited by: 84
Author(s): Xiao Xu, Yuanhao Zhang, Jennie L. Williams, Eric Antoniou, W. Richard McCombie, Song Wu, Wei Zhu, Nicholas O. Davidson, Paula Denoya, Ellen Li
Software Mentions: 3
Published: over 11 years ago
10.3389/fbioe.2014.00064
Uncovering RNA Editing Sites in Long Non-Coding RNAs
Cited by: 41
Author(s): Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Antonio Montalvo, Graziano Pesole
Software Mentions: 3
Published: about 10 years ago
10.3389/fbioe.2019.00427
A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
Cited by: 1
Author(s): Liu Hui, Tiantongfei Jiang, Shuyuan Wang, Xiang Chen, Xiaoyan Jin, Qi Wang, Xinhui Li, Jiaqi Yin, Tingting Shao, Yongsheng Li, Juan Xu, Qiong Wu
Software Mentions: 3
Published: about 5 years ago
10.1186/s12911-020-1117-0
A machine learning framework for accurately recognizing circular RNAs for clinical decision-supporting
Cited by: 1
Author(s): Yidan Wang, Xuanping Zhang, Tao Wang, Jinchun Xing, Zhun Wu, Wei Li, Jiayin Wang
Software Mentions: 3
Published: over 4 years ago
10.1186/1755-8794-1-42
The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis
Cited by: 127
Author(s): Andrew H. Sims, Graeme J. Smethurst, Yvonne Hey, Michał Okoniewski, Stuart D Pepper, Anthony Howell, Crispin Miller, Robert B. Clarke
Software Mentions: 3
Published: over 16 years ago
10.1186/1755-8794-8-S2-S8
RCARE: RNA Sequence Comparison and Annotation for RNA Editing
Cited by: 12
Author(s): Soo-Youn Lee, Je Gun Joung, Chan Hee Park, Ji Hye Park, Ju Han Kim
Software Mentions: 3
Published: over 9 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: over 8 years ago
10.1186/1471-2180-11-39
Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis
Cited by: 44
Author(s): He Gao, Yiquan Zhang, Yanping Han, Lin Yang, Xia Liu, Zhaobiao Guo, Yafang Tan, Xinxiang Huang, Dongsheng Zhou, Ruifu Yang
Software Mentions: 3
Published: almost 14 years ago
10.1186/bcr3150
Relevance of PTEN loss in brain metastasis formation in breast cancer patients
Cited by: 87
Author(s): Harriet Wikman, Katrin Lamszus, Niclas Detels, Liubov Uslar, Michaela Wrage, Christian Benner, Ina Hohensee, Bauke Ylstra, Kathrin Eylmann, Marc Zapatka, Guido Sauter, Dirk Kemming, Markus Glatzel, Volkmar Müller, Manfred Westphal, Klaus Pantel
Software Mentions: 3
Published: almost 13 years ago
10.3389/fcvm.2021.658915
Common Variants Associated With OSMR Expression Contribute to Carotid Plaque Vulnerability, but Not to Cardiovascular Disease in Humans
Cited by: 3
Author(s): Daniëlle van Keulen, Ian D. van Koeverden, Arjan Boltjes, H.M.G. Princen, Alain J. van Gool, Gert J. de Borst, Folkert W. Asselbergs, Dennie Tempel, Gérard Pasterkamp, Sander W. van der Laan
Software Mentions: 3
Published: almost 4 years ago
10.3389/fpsyg.2021.622433
Understanding the Multidimensional and Dynamic Nature of Facial Expressions Based on Indicators for Appraisal Components as Basis for Measuring Drivers' Fear
Cited by: 2
Author(s): Meng Zhang, Klas Ihme, Uwe Drewitz, Meike Jipp
Software Mentions: 3
Published: almost 4 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: over 6 years ago
10.1186/s13059-021-02270-w
simATAC: a single-cell ATAC-seq simulation framework
Cited by: 12
Author(s): Zeinab Navidi, Lin Zhang, Bo Wang
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-018-31064-7
Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
Cited by: 33
Author(s): Johnny A. Sena, Giulia Galotto, Nico Devitt, Melanie C. Connick, Jennifer L. Jacobi, Pooja Umale, Luis Vidali, Callum J. Bell
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0177662
Network based stratification of major cancers by integrating somatic mutation and gene expression data
Cited by: 11
Author(s): Zongzhen He, Junying Zhang, Xiguo Yuan, Zhaowen Liu, Baobao Liu, Shouheng Tuo, Yajun Liu
Software Mentions: 3
Published: almost 8 years ago
10.1120/jacmp.v17i3.6370
2016 AAPM Spring Clinical Meeting - Abstracts
Cited by: 0
Author(s):
Software Mentions: 3
Published: almost 9 years ago
10.1007/s13361-016-1544-4
Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging
Cited by: 37
Author(s): Sha Lou, Benjamin Balluff, Arjen H.G. Cleven, Judith V.M.G. Bovée, Liam A. McDonnell
Software Mentions: 3
Published: about 8 years ago
10.1029/2020MS002138
Clouds and Convective Self‐Aggregation in a Multimodel Ensemble of Radiative‐Convective Equilibrium Simulations
Cited by: 69
Author(s): Allison A. Wing, Catherine L. Stauffer, Tobias Becker, Kevin A. Reed, Min‐Seop Ahn, Nathan Arnold, Sandrine Bony, Mark Branson, G. H. Bryan, Jean‐Pierre Chaboureau, Stephan R. de Roode, Gayatri Kulkarni, Cathy Hohenegger, I‐Kuan Hu, Fredrik Jansson, Todd R. Jones, Marat Khairoutdinov, Dae Hyun Kim, Zane Martin, Shuhei Matsugishi, Brian Medeiros, Hiroaki Miura, Yumin Moon, Sebastian K. Müller, Tomoki Ohno, Max Popp, Thara Prabhakaran, David A. Randall, Rosimar Ríos-Berríos, Nicolas Rochetin, Romain Roehrig, David M. Romps, James H. Ruppert, Masaki Satoh, Levi G. Silvers, Martin S. Singh, Björn Stevens, Lorenzo Tomassini, Chiel C. van Heerwaarden, Shuguang Wang, Ming Zhao
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-018-31093-2
Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing
Cited by: 23
Author(s): David Jebb, Nicole M. Foley, Conor V. Whelan, Frédéric Touzalin, Sébastien J. Puechmaille, Emma C. Teeling
Software Mentions: 3
Published: over 6 years ago
10.1186/1479-5876-9-155
SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools - a compass in the land of biomarker discovery
Cited by: 26
Author(s): Davide Bedognetti, James M Balwit, Ena Wang, Mary L. Disis, Cedrik M. Britten, Lucia Gemma Delogu, Sara Tomei, Bernard A. Fox, Thomas F. Gajewski, Francesco M. Marincola, Lisa H. Butterfield
Software Mentions: 3
Published: over 13 years ago
10.1186/1756-0500-1-80
Advanced spot quality analysis in two-colour microarray experiments
Cited by: 10
Author(s): Mikalai M. Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich
Software Mentions: 3
Published: about 17 years ago
10.3389/fpsyg.2020.00953
Global Image Properties Predict Ratings of Affective Pictures
Cited by: 17
Author(s): Christoph Redies, Maria Grebenkina, Mahdi Mohseni, Ali Kaduhm, Christian Dobel
Software Mentions: 3
Published: almost 5 years ago
10.3389/fpsyt.2021.685656
Metabolic Profiling Indicates Diversity in the Metabolic Physiologies Associated With Maternal Postpartum Depressive Symptoms
Cited by: 4
Author(s): Emma Bränn, Christina J. Malavaki, Emma Fransson, Maria-Konstantina Ioannidi, Hanna Henriksson, Fotios C. Papadopoulos, George P. Chrousos, Maria I. Klapa, Alkistis Skalkidou
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0084231
Identification of the Third Binding Site of Arsenic in Human Arsenic (III) Methyltransferase
Cited by: 12
Author(s): Xiangli Li, Zhirong Geng, Jiayin Chang, Shuping Wang, Xiaoli Song, Xin Hu, Zhilin Wang
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pone.0036504
Transcript Profiling Identifies Dynamic Gene Expression Patterns and an Important Role for Nrf2/Keap1 Pathway in the Developing Mouse Esophagus
Cited by: 27
Author(s): Hao Chen, Jianying Li, Haiyan Li, Yuhui Hu, Whitney Tevebaugh, Masayuki Yamamoto, Jianwen Que, Xiaoxin Chen
Software Mentions: 3
Published: almost 13 years ago
10.1038/s41598-019-39880-1
MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: almost 6 years ago
10.7554/eLife.27529
A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection
Cited by: 55
Author(s): Shanshan Zhao, Wei Hong, Jiang Wu, Yu Wang, Shaoyi Ji, Shuyi Zhu, Chunhong Wei, Jinsong Zhang, Yang Li
Software Mentions: 3
Published: over 7 years ago
10.3389/fpls.2019.01624
Gene Expression Profiling of the Shoot Meristematic Tissues in Woodland Strawberry Fragaria vesca
Cited by: 8
Author(s): Yongping Li, Jia Feng, Laichao Cheng, Cheng Dai, Qi Gao, Zhongchi Liu, Chunying Kang
Software Mentions: 3
Published: about 5 years ago
10.3389/fpls.2016.01020
Low Temperature and Short-Term High-CO2 Treatment in Postharvest Storage of Table Grapes at Two Maturity Stages: Effects on Transcriptome Profiling
Cited by: 30
Author(s): Raquel Rosales, Irene Romero, Carlos Fernández-Caballero, M. Isabel Escribano, Carmen Merodio, Marı́a T. Sanchez-Ballesta
Software Mentions: 3
Published: over 8 years ago
10.1186/1756-0500-3-298
KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data
Cited by: 22
Author(s): Jorma J. de Ronde, Christiaan Klijn, Arno Velds, Henne Holstege, Marcel J. T. Reinders, Jos Jonkers, Lodewyk Wessels
Software Mentions: 3
Published: over 14 years ago
10.7554/eLife.22345
Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition
Cited by: 83
Author(s): Yun Huang, Jong Kim, Dang Vinh, Caroline Lee, Christopher A. Penfold, J. Ż̷ylicz, John C. Marioni, Jim Hackett, M. Azim Surani
Software Mentions: 3
Published: almost 8 years ago
10.3389/fpls.2018.01962
Early Detection of Magnaporthe oryzae-Infected Barley Leaves and Lesion Visualization Based on Hyperspectral Imaging
Cited by: 23
Author(s): Ruiqing Zhou, Juanjuan Jin, Qing-Mian Li, Zhen-Zhu Su, Xinjie Yu, Yu Tang, Shaoming Luo, Yong He, Yuanyuan Liu
Software Mentions: 3
Published: about 6 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: almost 18 years ago
10.7150/ijms.51743
Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland
Cited by: 5
Author(s): Yi Zheng, Hao Jiang, Hao-Qi Wang, Haixiang Guo, Dong-Xu Han, Yongping Huang, Yan Gao, Bao Yuan
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-019-41625-z
Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data
Cited by: 12
Author(s): Lázaro Betancourt, Krzysztof Pawłowski, Jonatan Eriksson, Attila Marcell Szász, Shamik Mitra, Indira Pla, Charlotte Welinder, Henrik Ekedahl, Per Broberg, Roger Appelqvist, Maria Yakovleva, Y. Sugita, Kenichi Miharada, Christian Ingvar, Lotta Lundgren, Bo Baldetorp, Håkan Olsson, Melinda Rezeli, Elisabet Wieslander, Péter Horvatovich, Johan Malm, Göran Jönsson, György Markó-Varga
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-019-43141-6
CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
Cited by: 62
Author(s): Joshua K. Young, Gina Zastrow-Hayes, Stéphane Deschamps, Sergei Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris Schwartz, Vesna Djukanovic, Brian Lenderts, Lanie Feigenbutz, Limin Wang, Clara M. Alarcon, Virginijus Šikšnys, Gregory D. May, N. Doane Chilcoat, Sandeep Kumar
Software Mentions: 3
Published: almost 6 years ago
10.1186/1476-4598-12-140
Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Cited by: 53
Author(s): Ângela Aguirres Fachel, Ana Carolina Tahira, Santiago A. Vilella-Arias, Vinicius Maracaja‐Coutinho, Etel Rp Gimba, Giselle Maria Vignal, Franz Campos, Eduardo M. Reis, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: over 11 years ago
10.3389/fpls.2016.01528
Invasive Shrub Mapping in an Urban Environment from Hyperspectral and LiDAR-Derived Attributes
Cited by: 29
Author(s): Curtis M. Chance, Nicholas C. Coops, Andrew Plowright, Thoreau Rory Tooke, Andreas Christen, Neal W. Aven
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0065632
SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner
Cited by: 111
Author(s): Ruibang Luo, Thomas K. F. Wong, Jian-Qiao Zhu, Chi-Man Liu, Xinhua Zhu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Shaoliang Peng, Chang Yu, Yingrui Li, Ruiqiang Li, Tak Wah Lam
Software Mentions: 3
Published: over 11 years ago
10.3389/fphar.2019.01690
SAMbinder: A Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
Cited by: 3
Author(s): Piyush Agrawal, Gaurav Mishra, Gajendra P. S. Raghava
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pone.0230404
A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze
Cited by: 7
Author(s): Pedro Italo T. Silva, Orzenil B. Silva‐Junior, Lucileide Vilela Resende, V. A. de Sousa, A. V. de Aguiar, Dário Grattapaglia
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-019-43512-z
Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: almost 6 years ago
10.1155/2020/3158108
Danhong Injection Alleviates Cardiac Fibrosis via Preventing the Hypermethylation of Rasal1 and Rassf1 in TAC Mice
Cited by: 7
Author(s): Sinai Li, Ping Li, Weihong Liu, Juju Shang, Sheng-Lei Qiu, Xiang Li, Wei Liu, Haoyue Shi, Mingxue Zhou, Hongxu Liu
Software Mentions: 3
Published: about 4 years ago
10.1002/ece3.498
New-old hemoglobin-like proteins of symbiotic dinoflagellates
Cited by: 11
Author(s): Nedeljka Rosic, William Leggat, Paulina Kaniewska, Sophie Dove, Ove Hoegh‐Guldberg
Software Mentions: 3
Published: almost 12 years ago
10.1002/ece3.2213
Is individual consistency in body mass and reproductive decisions linked to individual specialization in foraging behavior in a long‐lived seabird?
Cited by: 13
Author(s): Nina Dehnhard, Marcel Eens, Nicolas Sturaro, Gilles Lepoint, Laurent Demongin, Petra Quillfeldt, Maud Poisbleau
Software Mentions: 3
Published: over 8 years ago
10.1038/s41598-019-45898-2
Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: over 5 years ago
10.7554/eLife.29736
CDK9-dependent RNA polymerase II pausing controls transcription initiation
Cited by: 157
Author(s): Saskia Gressel, Björn Schwalb, Tim-Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer
Software Mentions: 3
Published: over 7 years ago
10.3390/v11010033
A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium
Cited by: 5
Author(s): Wei Zou, Min Xiong, Xuefeng Deng, John F. Engelhardt, Ziying Yan, Jianming Qiu
Software Mentions: 3
Published: about 6 years ago
10.1002/ece3.4504
Methylation divergence of invasive<i>Ciona</i>ascidians: Significant population structure and local environmental influence
Cited by: 17
Author(s): Ping Ni, Shiguo Li, Ya‐Ping Lin, Wei Xiong, Xuena Huang, Aibin Zhan
Software Mentions: 3
Published: over 6 years ago
10.1002/ece3.646
Environmental effects on molecular and phenotypic variation in populations of<i>Eruca sativa</i>across a steep climatic gradient
Cited by: 31
Author(s): Erik Westberg, Shachar Ohali, Anatoly Shevelevich, Pinchas Fine, Oz Barazani
Software Mentions: 3
Published: over 11 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: over 5 years ago
10.1371/journal.pone.0142864
Evolutionary Quantitative Genomics of Populus trichocarpa
Cited by: 24
Author(s): Ilga Porth, Jaroslav Klápště, Athena D. McKown, Jonathan La Mantia, Robert D. Guy, Pär K. Ingvarsson, Richard Hamelin, Shawn D. Mansfield, Jürgen Ehlting, Carl J. Douglas, Yousry A. El‐Kassaby
Software Mentions: 3
Published: about 9 years ago
10.1002/ece3.8075
High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed <i>Mikania micrantha</i>
Cited by: 5
Author(s): Yingjuan Su, Qiqi Huang, Zhen Wang, Ting Wang
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0037108
Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation
Cited by: 10
Author(s): Jamie Bates, Julia Salzman, Damon May, Patty B. Garcia, Gregory J. Hogan, Martin W. McIntosh, Mark S. Schlissel, Pat Brown
Software Mentions: 3
Published: over 12 years ago
10.3390/jpm11040262
A Novel Low-Risk Germline Variant in the SH2 Domain of the SRC Gene Affects Multiple Pathways in Familial Colorectal Cancer
Cited by: 0
Author(s): Diamanto Skopelitou, Benchun Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuświk, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: almost 4 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: about 13 years ago
10.1371/journal.pone.0173664
The miR-200 family is increased in dysplastic lesions in ulcerative colitis patients
Cited by: 14
Author(s): Amy Lewis, Carla Felice, Tomoko Kumagai, Claudia K. Y. Lai, Kriti Singh, Rosemary Jeffery, Roger Feakins, Eleni Giannoulatou, Alessandro Armuzzi, Noor Jawad, James O. Lindsay, Andrew Silver
Software Mentions: 3
Published: almost 8 years ago
10.1186/s13637-015-0034-5
Gene expression analysis supports tumor threshold over 2.0 cm for T-category breast cancer
Cited by: 2
Author(s): Hiroko Kato Solvang, Arnoldo Frigessi, Fatemeh Kaveh, Margit Riis, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen, Bettina Kulle Andreassen
Software Mentions: 3
Published: about 9 years ago
10.1016/j.mcpro.2021.100125
Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network
Cited by: 6
Author(s): Cristian V. A. Munteanu, Gabriela Chirițoiu, Marioara Chirițoiu, Simona Ghenea, Andrei-José Petrescu, Ștefana M. Petrescu
Software Mentions: 3
Published: about 4 years ago
10.7554/eLife.17903
A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Cited by: 32
Author(s): Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates, Péter L. Nagy, Liang Tong, Songtao Jia
Software Mentions: 3
Published: over 8 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: about 7 years ago
10.15252/emmm.202013901
Glycolysis downregulation is a hallmark of HIV‐1 latency and sensitizes infected cells to oxidative stress
Cited by: 23
Author(s): Iart Luca Shytaj, Francesco A. Procopio, Mohammad Tarek, Irene Carlón-Andrés, Hsin‐Yao Tang, Aaron R. Goldman, MohamedHusen Munshi, Virender Kumar Pal, Mattia Forcato, Sheetal Sreeram, Konstantin Leskov, Fengchun Ye, Bojana Lucic, Nicolly Cruz, Lishomwa C. Ndhlovu, Silvio Bicciato, Sergi Padilla‐Parra, Ricardo Sobhie Diaz, Amit Singh, Marina Lušić, Jonathan Karn, David Alvarez-Carbonell, Andrea Savarino
Software Mentions: 3
Published: over 3 years ago
10.3390/v12070782
High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
Cited by: 4
Author(s): Sílvia Inês Sardi, Renata Carvalho, Luis Gustavo Carvalho Pacheco, João Fernando Lourenço de Almeida, Emilia M M D A Belitardo, Carina S. Pinheiro, Gúbio Soares Campos, Eric Roberto Guimarães Rocha Aguiar
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0059128
Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies
Cited by: 133
Author(s): Junbo Duan, Jigang Zhang, Hong‐Wen Deng, Yuping Wang
Software Mentions: 3
Published: almost 12 years ago
10.3390/molecules24030631
Stratification of Breast Cancer by Integrating Gene Expression Data and Clinical Variables
Cited by: 8
Author(s): Zongzhen He, Junying Zhang, Xiguo Yuan, Jianing Xi, Zhaowen Liu, Yuanyuan Zhang
Software Mentions: 3
Published: about 6 years ago