cran: SAM | Projects | Ecosyste.ms: Papers

10.3389/fcell.2020.00242

Detection of Allosteric Effects of lncRNA Secondary Structures Altered by SNPs in Human Diseases
Cited by: 7
Author(s): Xiaoyan Lu, Yu Ding, Yu Bai, Jing Li, Guosi Zhang, Siyu Wang, Wenyan Gao, Liangde Xu, Hong Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-97879-z

Deep saliency models learn low-, mid-, and high-level features to predict scene attention
Cited by: 8
Author(s): Taylor R. Hayes, John M. Henderson
Software Mentions: 2
Published: about 5 years ago

10.18632/oncotarget.11931

A highly invasive subpopulation of MDA-MB-231 breast cancer cells shows accelerated growth, differential chemoresistance, features of apocrine tumors and reduced tumorigenicityin vivo
Cited by: 26
Author(s): Adriana Amaro, Giovanna Ángelini, Valentina Mirisola, Alba Esposito, Daniele Reverberi, Serena Matis, Massimo Maffei, Walter Giaretti, Maurizio Viale, Rosaria Gangemi, Laura Emionite, Simonetta Astigiano, Michele Cilli, Beatrice E. Bachmeier, Peter H. Killian, Adriana Albini, Ulrich Pfeffer
Software Mentions: 2
Published: about 10 years ago

10.1186/gb-2011-12-6-r55

Sniper: improved SNP discovery by multiply mapping deep sequenced reads
Cited by: 28
Author(s): Daniel F. Simola, Junhyong Kim
Software Mentions: 2
Published: over 15 years ago

10.1126/scisignal.abe1202

High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design
Cited by: 132
Author(s): Mónica Rosas‐Lemus, G. Minasov, L. Shuvalova, Nicole L. Inniss, O. Kiryukhina, J.S. Brunzelle, K.J.F. Satchell
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-7-114

Gene expression alterations in brains of mice infected with three strains of scrapie
Cited by: 81
Author(s): Pamela J. Skinner, H. Abbassi, Bruce Chesebro, Richard E. Race, Cavan Reilly, Ashley T. Haase
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2164-9-546

Transcriptional response of rat frontal cortex following acute In Vivo exposure to the pyrethroid insecticides permethrin and deltamethrin
Cited by: 18
Author(s): Joshua Harrill, Zhen Li, Fred A. Wright, Nicholas M. Radio, William R. Mundy, Rogelio Tornero‐Velez, Kevin M. Crofton
Software Mentions: 2
Published: almost 18 years ago

10.1155/2013/730210

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing
Cited by: 45
Author(s): Marisa Dolled‐Filhart, Michael Lee, Chih-wen Ou-Yang, Rajini Haraksingh, Jimmy C. Lin
Software Mentions: 2
Published: over 13 years ago

10.18632/oncotarget.11996

Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms
Cited by: 41
Author(s): Qingzhou Guan, Rou Chen, Haidan Yan, Hao Cai, You Guo, Mengyao Li, Xiangyu Li, Man‐Li Tong, Lu Ao, Hongdong Li, Hong Guan, Zheng Guo
Software Mentions: 2
Published: about 10 years ago

10.3389/fgene.2020.00113

FBXW4 Acts as a Protector of FOLFOX-Based Chemotherapy in Metastatic Colorectal Cancer Identified by Co-Expression Network Analysis
Cited by: 6
Author(s): Yiyi Zhang, Lijun Sun, Xiaojie Wang, Yanwu Sun, Ying Chen, Meifang Xu, Pan Chi, Xingrong Lu, Zongbin Xu
Software Mentions: 2
Published: over 6 years ago

10.2196/jmir.4233

Preventing Alcohol Abuse Through Social Networking Sites: A First Assessment of a Two-Year Ecological Approach
Cited by: 12
Author(s): Valentin Flaudias, Ingrid de Chazeron, Oulmann Zerhouni, Jordane Boudesseul, Laurent Bègue, Renaud Bouthier, Christel Lévrier, Pierre Michel Llorca, Georges Brousse
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0012770

Distinct Transcriptome Expression of the Temporal Cortex of the Primate Microcebus murinus during Brain Aging versus Alzheimer's Disease-Like Pathology
Cited by: 30
Author(s): Ronza Abdel Rassoul, Sabine Alves, Véronique Pantesco, John De Vos, Bernard Michel, Martine Perret, Nadine Mestre‐Francés, Jean‐Michel Verdier, Gina Devau
Software Mentions: 2
Published: about 16 years ago

10.1155/2014/639142

RSSI-Based Smooth Localization for Indoor Environment
Cited by: 6
Author(s): Yujian Wang, Bin Zhao, Zhaohui Jiang
Software Mentions: 2
Published: over 12 years ago

10.1186/s40360-020-00402-9

Prospects of Indole derivatives as methyl transfer inhibitors: antimicrobial resistance managers
Cited by: 4
Author(s): Suprim Tha, Sapana Shakya, Rajani Malla, Pramod Aryal
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0237873

The EmojiGrid as a rating tool for the affective appraisal of touch
Cited by: 2
Author(s): Alexander Toet, J.B.F. van Erp
Software Mentions: 2
Published: about 6 years ago

10.3390/s101009026

Wearable Systems for Monitoring Mobility-Related Activities in Chronic Disease: A Systematic Review
Cited by: 105
Author(s): Lara Allet, Ruud H. Knols, Kei Shirato, Eling D. de Bruin
Software Mentions: 2
Published: almost 16 years ago

10.3390/s100807772

A Review of Accelerometry-Based Wearable Motion Detectors for Physical Activity Monitoring
Cited by: 837
Author(s): Chen-Chung Yang, Yeh‐Liang Hsu
Software Mentions: 2
Published: about 16 years ago

10.1186/gb-2010-11-11-r115

Constructing a fish metabolic network model
Cited by: 42
Author(s): Shuzhao Li, Alex Pozhitkov, Rachel A. Ryan, C. Steve Manning, Nancy J. Brown‐Peterson, Marius Brouwer
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0067142

Layered Signaling Regulatory Networks Analysis of Gene Expression Involved in Malignant Tumorigenesis of Non-Resolving Ulcerative Colitis via Integration of Cross-Study Microarray Profiles
Cited by: 13
Author(s): Shengjun Fan, Zhenyu Pan, Qiang Geng, Xin Li, Yefan Wang, Yu An, Yan Xu, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0100068

BRCA1 Haploinsufficiency Leads to Altered Expression of Genes Involved in Cellular Proliferation and Development
Cited by: 16
Author(s): Harriet Feilotter, Claire S. Michel, Paolo Uy, Lauren Bathurst, Scott Davey
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0103533

Effects of a Honeybee Sting on the Serum Free Amino Acid Profile in Humans
Cited by: 19
Author(s): Jan Matysiak, Paweł Dereziński, Agnieszka Klupczyńska, Joanna Matysiak, Elżbieta Kaczmarek, Zenon J. Kokot
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0149285

CD10-Equipped Melanoma Cells Acquire Highly Potent Tumorigenic Activity: A Plausible Explanation of Their Significance for a Poor Prognosis
Cited by: 8
Author(s): Junna Oba, Takeshi Nakahara, Akiko Hashimoto-Hachiya, Min Liu, Takeru Abe, Akihito Hagihara, Takehiko Yokomizo, Masutaka Furue
Software Mentions: 2
Published: over 10 years ago

10.1186/2049-2618-2-33

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples
Cited by: 185
Author(s): Changjin Hong, Solaiappan Manimaran, Ying Shen, Joseph Perez-Rogers, Allyson L. Byrd, Eduardo Castro-Nallar, Keith A. Crandall, W. Evan Johnson
Software Mentions: 2
Published: about 12 years ago

10.3390/s8053299

Hyperspectral Sensor Data Capability for Retrieving Complex Urban Land Cover in Comparison with Multispectral Data: Venice City Case Study (Italy)
Cited by: 54
Author(s): Rosa Maria Cavalli, Lorenzo Fusilli, Simone Pascucci, Stefano Pignatti, Federico Santini
Software Mentions: 2
Published: over 18 years ago

10.3390/s130506183

A Stratified Acoustic Model Accounting for Phase Shifts for Underwater Acoustic Networks
Cited by: 8
Author(s): Ping Wang, Lin Zhang, Victor O. K. Li
Software Mentions: 2
Published: over 13 years ago

10.12688/f1000research.21142.2

Falco: high-speed FastQC emulation for quality control of sequencing data
Cited by: 104
Author(s): Guilherme de Sena Brandine, Andrew D. Smith
Software Mentions: 2
Published: over 5 years ago

10.12688/f1000research.22954.3

QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing
Cited by: 3
Author(s): Frédéric Jarlier, Nicolas Joly, Nicolas Fedy, Thomas Magalhaes, Leonor Sirotti, Paul Paganiban, F. Elizabeth Martin, Michael T. McManus, Philippe Hupé
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpsyg.2018.00657

Physiological Response to Facial Expressions in Peripersonal Space Determines Interpersonal Distance in a Social Interaction Context
Cited by: 55
Author(s): Alice Cartaud, Gennaro Ruggiero, Laurent Ott, Tina Iachini, C. Yann
Software Mentions: 2
Published: over 8 years ago

10.1186/s12890-015-0142-8

A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis
Cited by: 36
Author(s): Yong Huang, Shwu Fan, Rekha Vij, Justin M. Oldham, Jose D. Herazo‐Maya, Steven M. Broderick, Mary E. Strek, Steven R. White, D. Kyle Hogarth, Nathan Sandbo, Yves A. Lussier, Kevin F. Gibson, Naftali Kaminski, Joe G.N. Garcia, Imre Noth
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13104-015-1382-7

cFinder: definition and quantification of multiple haplotypes in a mixed sample
Cited by: 6
Author(s): Norbert Niklas, Julia Hafenscher, Agnes Barna, Karin Wiesinger, Johannes Pröll, Stephan Dreiseitl, Sandra Preuner-Stix, Peter Valent, Thomas Lion, Christian Gabriel
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-018-5277-6

Constructing tissue-specific transcriptional regulatory networks via a Markov random field
Cited by: 6
Author(s): Shuping Ma, Tao Jiang, Rui Jiang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-015-1295-9

Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns
Cited by: 39
Author(s): Caitlyn Riedmann, Ye Ma, Manana Melikishvili, Steven Grason Godfrey, Zhou Zhang, Kuey Chu Chen, Eric C. Rouchka, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: over 11 years ago

10.1186/1756-0500-7-483

HMM-ModE: implementation, benchmarking and validation with HMMER3
Cited by: 11
Author(s): Swati Sinha, Andrew M. Lynn
Software Mentions: 2
Published: over 12 years ago

10.3390/s16020152

Spectral Similarity Assessment Based on a Spectrum Reflectance-Absorption Index and Simplified Curve Patterns for Hyperspectral Remote Sensing
Cited by: 11
Author(s): Di Ma, Jun Li, Jian Huang, Huali Li, Ping Liu, Huijuan Chen, Jing Qian
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0111581

MiRNA Expression May Account for Chronic but Not for Acute Regulation of mRNA Expression in Human Thyroid Tumor Models
Cited by: 9
Author(s): Sébastien Floor, Aline Hébrant, Jaime Miguel Gomes Pita, Manuel Saiselet, Christophe Trésallet, Frédérick Libert, Guy Andry, Jacques Emile Dumont, Wilma Van Staveren, Carine Maenhaut
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12984-017-0312-4

Adaptive hybrid robotic system for rehabilitation of reaching movement after a brain injury: a usability study
Cited by: 18
Author(s): Francisco Resquín, José González-Vargas, Jaime Ibáñez, F. Brunetti, I. Dimbwadyo, Laura Carrasco, Silas Franco dos Reis Alves, Carlos González-Alted, A. Gomez-Blanco, José L. Pons
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0093462

Arabidopsis Transcriptome Analysis Reveals Key Roles of Melatonin in Plant Defense Systems
Cited by: 262
Author(s): Sarah Weeda, Na Zhang, Xiaolei Zhao, Grace Ndip, Yang‐Dong Guo, Gregory A. Buck, Conggui Fu, Shuxin Ren
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0238231

Treatment outcome of Severe Acute Malnutrition and associated factors among under-five children in outpatient therapeutics unit in Gubalafto Wereda, North Wollo Zone, Ethiopia, 2019
Cited by: 14
Author(s): Biruk Beletew Abate, Befkad Deresse Tilahun, Ayelign Mengesha Kassie, Mesfin Wudu Kassaw
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0003474

Transcriptional and Functional Profiling of Human Embryonic Stem Cell-Derived Cardiomyocytes
Cited by: 211
Author(s): Feng Cao, Roger A. Wagner, Kitchener D. Wilson, Xiaoyan Xie, Ji-Dong Fu, Micha Drukker, Andrew Lee, Gary Tse, Sanjiv S. Gambhir, Irving L. Weissman, Robert C. Robbins, Joseph C. Wu
Software Mentions: 2
Published: almost 18 years ago

10.3390/s17051117

Characterization of Fine Metal Particles Derived from Shredded WEEE Using a Hyperspectral Image System: Preliminary Results
Cited by: 16
Author(s): Gabriele Candiani, Nicoletta Picone, L. Pompilio, Monica Pepe, Marcello Colledani
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0112971

Heart Mitochondrial Proteome Study Elucidates Changes in Cardiac Energy Metabolism and Antioxidant PRDX3 in Human Dilated Cardiomyopathy
Cited by: 16
Author(s): Esther Roselló‐Lletí, Estefanía Tarazón, María G. Barderas, Ana Ortega, Manuel Otero, Maria Micaela Molina‐Navarro, Francisca Lago, José Ramón González-Juanatey, Antonio Salvador, Manuel Portolés, Miguel Rivera
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0016208

A Day in the Life of Microcystis aeruginosa Strain PCC 7806 as Revealed by a Transcriptomic Analysis
Cited by: 86
Author(s): Cécile Straub, Philippe Quillardet, Julia Vergalli, Nicole Tandeau de Marsac, Jean‐François Humbert
Software Mentions: 2
Published: over 15 years ago

10.3389/fpsyg.2015.01232

Microtiming in Swing and Funk affects the body movement behavior of music expert listeners
Cited by: 34
Author(s): Lorenz Kilchenmann, Olivier Senn
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2164-15-1084

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature
Cited by: 72
Author(s): Derrick Coble, Damarius S. Fleming, Michael E. Persia, C. M. Ashwell, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0042161

Identification of Pluripotent and Adult Stem Cell Genes Unrelated to Cell Cycle and Associated with Poor Prognosis in Multiple Myeloma
Cited by: 18
Author(s): Alboukadel Kassambara, Dirk Hose, Jérôme Moreaux, Thierry Rème, Jennifer Torrent, Jean François Rossi, Hartmut Goldschmidt, Bernard Klein
Software Mentions: 2
Published: about 14 years ago

10.1186/s12974-020-01992-1

NFATc2-dependent epigenetic upregulation of CXCL14 is involved in the development of neuropathic pain induced by paclitaxel
Cited by: 13
Author(s): Meng Li, Subo Zhang, Yuxuan Luo, Yanling Yang, Xiangzhong Zhang, Bo Li, Yan Meng, Yuan-Jie Chen, Ruixian Guo, Yang Xiong, Wenjun Xin, Dai Li
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpsyg.2020.570761

Modeling Evaluations of Low-Level Sounds in Everyday Situations Using Linear Machine Learning for Variable Selection
Cited by: 2
Author(s): Siegbert Versümer, Jochen Steffens, Patrick Blättermann, Jörg Becker-Schweitzer
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12974-017-0937-z

Bioinformatics analysis of glial inflammatory responses to air pollution
Cited by: 0
Author(s): Chenyu Li, Wei Jiang, Nina Tang, Yan Xu
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0254098

Heart rate variability analysis for the assessment of immersive emotional arousal using virtual reality: Comparing real and virtual scenarios
Cited by: 9
Author(s): Javier Marín‐Morales, Juan Luis Higuera-Trujillo, Jaime Guixeres, Carmen Llinares, Mariano Alcañíz, Gaetano Valenza
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-10-196

Molecular profiles of Quadriceps muscle in myostatin-null mice reveal PI3K and apoptotic pathways as myostatin targets
Cited by: 78
Author(s): Ilham Chelh, Bruno Meunier, Brigitte Picard, Mark James Reecy, Catherine Chevalier, Jean-François Hocquette, Isabelle Cassar-Malek
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0101821

AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod
Cited by: 24
Author(s): María Quintela, Magnus Johansson, Bjarni K. Kristjánsson, Rodolfo Barreiro, Anssi Laurila
Software Mentions: 2
Published: about 12 years ago

10.3389/fgene.2020.603093

Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data
Cited by: 0
Author(s): Huijing Zhao, Shuang Wang, Xiguo Yuan
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0248192

Poor adherence to TB diagnosis guidelines among under-five children with severe acute malnutrition in central India: A missed window of opportunity?
Cited by: 3
Author(s): Akash Ranjan Singh, Arun Kumar, Hemant Deepak Shewade, Bhavna Dhingra
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0229075

miRNA profiling in renal carcinoma suggest the existence of a group of pro-angionenic tumors in localized clear cell renal carcinoma
Cited by: 6
Author(s): Lucía Trilla-Fuertes, Nahir Miranda, Daniel Castellano, Rocío López-Vacas, Carlos A. Farfán Tello, Guillermo Velasco, Felipe Villacampa, Elena López-Camacho, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Enrique Espinosa, Juan Ángel Fresno Vara, Álvaro Pinto, Angelo Gámez‐Pozo
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.12624

LncRNA profile study reveals four-lncRNA signature associated with the prognosis of patients with anaplastic gliomas
Cited by: 57
Author(s): Wen Wang, Fan Yang, Lu Zhang, Jing Chen, Zheng Zhao, Haoyuan Wang, Fan Wu, Tingyu Liang, Xiaoyan Yan, Jiye Li, Qing Lan, Jiangfei Wang, Jizong Zhao
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-9-580

Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata)
Cited by: 58
Author(s): Serena Ferraresso, Nicola Vitulo, Alba Nicoletta Mininni, Chiara Romualdi, Barbara Cardazzo, Enrico Negrisolo, Richard Reinhardt, Adelino V.M. Canário, Tomaso Patarnello, Luca Bargelloni
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0075402

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data
Cited by: 53
Author(s): Shunichi Kosugi, Satoshi Natsume, Kentaro Yoshida, Dan MacLean, Liliana Cano, Sophien Kamoun, Ryohei Terauchi
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0008003

Novel Rank-Based Statistical Methods Reveal MicroRNAs with Differential Expression in Multiple Cancer Types
Cited by: 153
Author(s): Roy Navon, Hui Wang, Israel Steinfeld, Anya Tsalenko, Amir Ben-Dor, Zohar Yakhini
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2210-8-16

Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in Atlantic salmon (Salmo salar L.)
Cited by: 23
Author(s): Pål A. Olsvik, Kai Kristoffer Lie, Eva Mykkeltvedt, Ole Bent Samuelsen, Kjell Petersen, Anne-Kristin Stavrum, Bjørn Tore Lunestad
Software Mentions: 2
Published: about 18 years ago

10.1186/s12864-017-3980-3

Mining sequence variations in representative polyploid sugarcane germplasm accessions
Cited by: 37
Author(s): Xiping Yang, Song Jiang, Qi You, Dev Paudel, Jisen Zhang, Jianping Wang
Software Mentions: 2
Published: about 9 years ago

10.3390/s19194079

Wearable-Based Affect Recognition—A Review
Cited by: 98
Author(s): Philip Schmidt, Attila Reiss, Robert Dürichen, Kristof Van Laerhoven
Software Mentions: 2
Published: almost 7 years ago

10.3390/s19224931

Physiological Responses During Hybrid BNCI Control of an Upper-Limb Exoskeleton
Cited by: 14
Author(s): Francisco J. Badesa, Jorge Díez, José Catalán, Emilio Trigili, Francesca Cordella, Marius Nann, Simona Crea, Surjo R. Soekadar, Loredana Zollo, Nicola Vitiello, Nicolás García-Aracil
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0070412

Detection of Deregulated Modules Using Deregulatory Linked Path
Cited by: 5
Author(s): Yuxuan Hu, Lin Gao, Kai Shi, David Chiu
Software Mentions: 2
Published: about 13 years ago

10.1186/bcr3586

Next generation sequencing-based expression profiling identifies signatures from benign stromal proliferations that define stromal components of breast cancer
Cited by: 15
Author(s): Xiangqian Guo, Shirley Zhu, Alayne Brunner, Matt van de Rijn, Robert B. West
Software Mentions: 2
Published: almost 13 years ago

10.3389/fpsyg.2021.707809

The Effectiveness of Facial Expression Recognition in Detecting Emotional Responses to Sound Interventions in Older Adults With Dementia
Cited by: 4
Author(s): Ying Liu, Zixuan Wang, Ge Yu
Software Mentions: 2
Published: about 5 years ago

10.1186/2049-2618-2-19

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
Cited by: 204
Author(s): Agata Wesolowska-Andersen, Martin Iain Bahl, Vera Carvalho, Karsten Kristiansen, Thomas Sicheritz-Pontén, Ramneek Gupta, Tine Rask Licht
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0005662

Accumulating Progenitor Cells in the Luminal Epithelial Cell Layer Are Candidate Tumor Initiating Cells in a Pten Knockout Mouse Prostate Cancer Model
Cited by: 66
Author(s): Hanneke Korsten, Angelique Ziel-van der Made, Xiaoqian Ma, Theodorus H. van der Kwast, Jan Trapman
Software Mentions: 2
Published: over 17 years ago

10.1186/1743-8977-10-50

Label-free in vitro toxicity and uptake assessment of citrate stabilised gold nanoparticles in three cell lines
Cited by: 95
Author(s): Melissa Vetten, Nonhlanhla Tlotleng, Delia Tanner Rascher, Amanda Skepu, Frankline K. Keter, Kailen Boodhia, Leigh-Anne Koekemoer, Charlene Andraos, Robert Tshikhudo, Mary Gulumian
Software Mentions: 2
Published: almost 13 years ago

10.1111/pbi.13422

Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.)
Cited by: 52
Author(s): Pallavi Sinha, Vikas K. Singh, Rachit K. Saxena, Aamir W. Khan, Ragavendran Abbai, Annapurna Chitikineni, Aarthi Desai, Johiruddin Molla, Hari D. Upadhyaya, Arvind Kumar, Rajeev K. Varshney
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0014002

In Silico Ascription of Gene Expression Differences to Tumor and Stromal Cells in a Model to Study Impact on Breast Cancer Outcome
Cited by: 26
Author(s): Simen Myhre, Hayat Mohammed, Trine Tramm, Jan Alsner, Greg Finak, Morag Park, Jens Overgaard, Anne Lise Børresen-Dale, Arnoldo Frigessi, Thérese Sørlie
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0234323

Phenotype and molecular signature of CD8+ T cell subsets in T cell- mediated rejections after kidney transplantation
Cited by: 4
Author(s): Eun Jeong Ko, Jung Woo Seo, Kyoung Woon Kim, Bo Mi Kim, Jang Hee Cho, Chan Duck Kim, Junhee Seok, Chul Woo Yang, Sang Ho Lee, Byung Ha Chung
Software Mentions: 2
Published: over 6 years ago

10.3390/s20164551

CNN and LSTM-Based Emotion Charting Using Physiological Signals
Cited by: 50
Author(s): Muhammad Najam Dar, M. Usman Akram, Sajid Gul Khawaja, Amit N. Pujari
Software Mentions: 2
Published: about 6 years ago

10.1186/s13048-015-0176-9

Gene expression profiling of ovarian carcinomas and prognostic analysis of outcome
Cited by: 10
Author(s): Shengyun Cai, Tian Yang, Yu Chen, Jingwen Wang, L i Li, Man Xu
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0119166

The Role of Edaphic Environment and Climate in Structuring Phylogenetic Pattern in Seasonally Dry Tropical Plant Communities
Cited by: 48
Author(s): Marcelo Freire Moro, Igor Aurélio Silva, Francisca Soares de Araújo, Eimear Nic Lughadha, Thomas R. Meagher, Fernando Roberto Martins
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0134031

Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries
Cited by: 27
Author(s): Christopher Saski, Ranjana Bhattacharjee, Brian E. Scheffler, Robert Asiedu
Software Mentions: 2
Published: about 11 years ago

10.3389/fpsyg.2021.626118

Interindividual Variation Refuses to Go Away: A Bayesian Computer Model of Language Change in Communicative Networks
Cited by: 3
Author(s): Mathilde Josserand, Marc Allassonnière-Tang, François Pellegrino, Dan Dediu
Software Mentions: 2
Published: about 5 years ago

10.1186/bcr3403

Embryonic mammary signature subsets are activated in Brca1 -/- and basal-like breast cancers
Cited by: 47
Author(s): Marketa Zvelebil, Erik Oliemuller, Qiong Gao, Olivia Wansbury, Alan Mackay, Howard Kendrick, Matthew J. Smalley, Jorge S. Reis‐Filho, Beatrice A. Howard
Software Mentions: 2
Published: over 13 years ago

10.3390/cancers13153755

Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma
Cited by: 6
Author(s): Laure Dutrieux, Yea-Lih Lin, Malik Lutzmann, Raphaël Rodriguez, Michel Cogné, Philippe Pasero, Jérôme Moreaux
Software Mentions: 2
Published: about 5 years ago

10.1111/ppl.12103

Long‐ and short‐distance signaling in the regulation of lateral plant growth
Cited by: 23
Author(s): Klaus Brackmann, Thomas Greb
Software Mentions: 2
Published: almost 13 years ago

10.3389/fgene.2021.634635

Research on the Mechanism of Soybean Resistance to Phytophthora Infection Using Machine Learning Methods
Cited by: 5
Author(s): Junxia Chi, Shizeng Song, Hao Zhang, Yuanning Liu, Hengyi Zhao, Liyan Dong
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers13010001

Incorporating the Patient Voice in Sarcoma Research: How Can We Assess Health-Related Quality of Life in This Heterogeneous Group of Patients? A Study Protocol
Cited by: 11
Author(s): Dide den Hollander, Marco Fiore, Javier Martin‐Broto, Bernd Kasper, Antonio Casado Herráez, Danijela Kuliš, Ioanna Nixon, Samantha Sodergren, Martin Eichler, Winan J. van Houdt, Ingrid M.E. Desar, Isabelle Ray‐Coquard, Claire Piccinin, Hanna Koseła-Paterczyk, Aisha Miah, Leopold Hentschel, Susanne Schnittger, Roger Wilson, Winette T.A. van der Graaf, Olga Husson
Software Mentions: 2
Published: over 5 years ago

10.3390/s21041138

Open-Design for a Smart Cover of a Night-Time Telescope for Day-Time Use
Cited by: 1
Author(s): R. Cedazo, Alberto Brunete, Hugo R. Albarracin, Esteban González
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12061355

The Possible Influence of Mediterranean Diet on Extracellular Vesicle miRNA Expression in Breast Cancer Survivors
Cited by: 8
Author(s): Yu‐Jin Kwon, Young-Eun Cho, A-Ra Cho, Won-Jun Choi, Sijung Yun, Hyunki Park, Hyung-Suk Kim, Ann K. Cashion, Jessica Gill, Hyangkyu Lee, Jiwon Lee
Software Mentions: 2
Published: over 6 years ago

10.3389/fcell.2021.715275

Identification of Somatic Mutation-Driven Immune Cells by Integrating Genomic and Transcriptome Data
Cited by: 2
Author(s): Ying Jiang, Buhong Zheng, Yang Yang, Xiangmei Li, Junwei Han
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2229-11-114

Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses
Cited by: 89
Author(s): G. Malacarne, Urška Vrhovšek, L. Zulini, Alessandro Cestaro, M. Stefanini, Fulvio Mattivi, Massimo Delledonne, Riccardo Velasco, C. Moser
Software Mentions: 2
Published: over 15 years ago

10.3390/s21051792

Learning Subject-Generalized Topographical EEG Embeddings Using Deep Variational Autoencoders and Domain-Adversarial Regularization
Cited by: 7
Author(s): Juan Lorenzo Hagad, Tsukasa Kimura, Kenichi Fukui, Masayuki Numao
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2431-13-17

Optimising Ankle Foot Orthoses for children with Cerebral Palsy walking with excessive knee flexion to improve their mobility and participation; protocol of the AFO-CP study
Cited by: 14
Author(s): Yvette L. Kerkum, Jaap Harlaar, Annemieke I. Buizer, Josien C. van den Noort, Jules G. Becher, Merel-Anne Brehm
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0099290

Direct Amplification, Sequencing and Profiling of Chlamydia trachomatis Strains in Single and Mixed Infection Clinical Samples
Cited by: 24
Author(s): Sandeep J. Joseph, Ben Li, Tanvi Ghonasgi, Chad P. Haase, Zhaohui S. Qin, Deborah Dean, Timothy D. Read
Software Mentions: 2
Published: about 12 years ago

10.1186/s13071-020-04047-9

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection
Cited by: 11
Author(s): Xian-Cheng Fan, Ting-Li Liu, Yi Wang, Xuemei Wu, Yuxin Wang, Lai Peng, Jun-Ke Song, Guang‐Hui Zhao
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-021-02970-2

BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon
Cited by: 7
Author(s): Kaori Sakai, Sylvie Citerne, Sébastien Antelme, Philippe Le Bris, Sylviane Daniel, Axelle Bouder, Angélina D’Orlando, Amy Cartwright, Frédérique Tellier, Stéphanie Pateyron, Étienne Delannoy, Debbie Laudencia‐Chingcuanco, Grégory Mouille, Jean-Christophe Palauqui, John P. Vogel, Richard Sibout
Software Mentions: 2
Published: over 5 years ago

10.3390/ph4010007

GPCR Conformations: Implications for Rational Drug Design
Cited by: 16
Author(s): Abby L. Parrill, Debra L. Bautista
Software Mentions: 2
Published: over 15 years ago

10.3390/s21165279

Rapid Foreign Object Detection System on Seaweed Using VNIR Hyperspectral Imaging
Cited by: 6
Author(s): Donghoon Kwak, Guk-Jin Son, Mi‐Kyung Park, Young-Duk Kim
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0019651

Platelets Alter Gene Expression Profile in Human Brain Endothelial Cells in an In Vitro Model of Cerebral Malaria
Cited by: 35
Author(s): Mathieu Barbier, Dorothée Faille, Béatrice Loriod, Julien Textoris, Claire Camus, Denis Puthier, Laurence Flori, Samuel C. Wassmer, Geneviève Victoréro, Marie‐Christine Alessi, Thierry Fusaı̈, Catherine Nguyen, Georges E. Grau, Pascal Rihet
Software Mentions: 2
Published: over 15 years ago

10.3390/medicina55090531

The Extent of Extemporaneous Preparation and Regulatory Framework of Extemporaneous Compounding in Latvia
Cited by: 3
Author(s): Olga Kiseļova, Baiba Mauriņa, Venta Šidlovska, Jānis Zvejnieks
Software Mentions: 2
Published: about 7 years ago

10.3389/fgene.2019.01190

Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations
Cited by: 6
Author(s): Haile Berihulay, Yefang Li, Berihu Gebrekidan, Gebremedhin Gebreselassie, Xuexue Liu, Lin Jiang, Yue Ma
Software Mentions: 2
Published: almost 7 years ago

10.1186/1758-907X-2-2

Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
Cited by: 83
Author(s): Kevin McCormick, Matthew R. Willmann, Blake C. Meyers
Software Mentions: 2
Published: over 15 years ago

10.3389/fgene.2019.00296

Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice
Cited by: 7
Author(s): Hao Zhang, Sifei Liu, Haowu Chang, Mengping Zhan, Qing‐Ming Qin, Borui Zhang, Zhi Li, Yuanning Liu
Software Mentions: 2
Published: over 7 years ago

10.1186/1751-0473-7-6

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
Cited by: 63
Author(s): Ricardo H. Ramírez-González, Raoul Jean Pierre Bonnal, Mario Cáccamo, Dan MacLean
Software Mentions: 2
Published: over 14 years ago

10.7717/peerj.1784

Ade novotranscriptome of the Malpighian tubules in non-blood-fed and blood-fed Asian tiger mosquitoesAedes albopictus: insights into diuresis, detoxification, and blood meal processing
Cited by: 45
Author(s): Carlos J. Esquivel, Bryan J. Cassone, Peter M. Piermarini
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.7604

Gene expression analyses of primary melanomas reveal CTHRC1 as an important player in melanoma progression
Cited by: 31
Author(s): Johanna Eriksson, Vadim Le Joncour, Pirjo Nummela, Tiina Jahkola, Susanna Virolainen, Pirjo Laakkonen, Olli Saksela, Erkki Hölttä
Software Mentions: 2
Published: over 10 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566