cran: SAM | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0031241

Genome-Wide Maps of Circulating miRNA Biomarkers for Ulcerative Colitis
Cited by: 92
Author(s): Radha Duttagupta, Sharon DiRienzo, Rong Jiang, Jessica Bowers, Jeremy Gollub, Jennifer L. Kao, Keith R. Kearney, David Rudolph, Noor Dawany, Michael K. Showe, Tom Stamato, Robert C. Getts, Keith Jones
Software Mentions: 2
Published: over 14 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: almost 5 years ago

10.1155/2012/373506

Detecting Cancer Outlier Genes with Potential Rearrangement Using Gene Expression Data and Biological Networks
Cited by: 12
Author(s): Mohammed Alshalalfa, Tarek A. Bismar, Reda Alhajj
Software Mentions: 2
Published: about 14 years ago

10.1111/1751-7915.12119

Polyphenols from olive mill waste affect biofilm formation and motility in <scp>E</scp>scherichia coli <scp>K</scp>‐12
Cited by: 37
Author(s): Lisa Carraro, Luca Fasolato, Filomena Montemurro, Maria Elena Martino, Stefania Balzan, Maurizio Servili, Enrico Novelli, Barbara Cardazzo
Software Mentions: 2
Published: over 12 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/s12859-019-2996-x

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
Cited by: 178
Author(s): Grzegorz M. Boratyn, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas Madden
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2105-7-538

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Cited by: 226
Author(s): Maureen A. Sartor, Craig R. Tomlinson, Scott C. Wesselkamper, Siva Sivaganesan, George D. Leikauf, Mario Medvedovic
Software Mentions: 2
Published: over 19 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

10.1186/s13058-021-01457-0

Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA
Cited by: 5
Author(s): Joseph P. Garay, Rebecca Smith, Kaylyn L. Devlin, Daniel P. Hollern, Tiera Liby, Moqing Liu, Shanta Boddapati, Spencer S. Watson, Amanda Esch, Ting Zheng, Wallace Thompson, Darcie Babcock, Sunjong Kwon, Koei Chin, Laura M. Heiser, Joe W. Gray, James E. Korkola
Software Mentions: 2
Published: almost 5 years ago

10.3390/microarrays5040024

OSAnalyzer: A Bioinformatics Tool for the Analysis of Gene Polymorphisms Enriched with Clinical Outcomes
Cited by: 14
Author(s): Giuseppe Agapito, Cirino Botta, PH Guzzi, Mariamena Arbitrio, Beniamino Di Martino, Pierfrancesco Tassone, Pierosandro Tagliaferri, Mario Cannataro
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0016345

Mayday SeaSight: Combined Analysis of Deep Sequencing and Microarray Data
Cited by: 20
Author(s): Florian Battke, Kay Nieselt
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-11-121

Mayday - integrative analytics for expression data
Cited by: 107
Author(s): Florian Battke, Stephan Symons, Kay Nieselt
Software Mentions: 2
Published: over 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

10.1371/journal.pone.0081123

ZODET: Software for the Identification, Analysis and Visualisation of Outlier Genes in Microarray Expression Data
Cited by: 5
Author(s): Daniel Roden, Gavin W. Sewell, Anna Lobley, Adam P. Levine, Andrew Smith, Anthony W. Segal
Software Mentions: 2
Published: over 12 years ago

10.1007/s11306-014-0662-x

Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach
Cited by: 22
Author(s): Lucille Stuani, Christophe Lechaplais, Aaro V. Salminen, Béatrice Segurens, Maxime Durot, Vanina Castelli, Agnès Pinet, Karine Labadie, Stéphane Cruveiller, Jean Weissenbach, Véronique de Berardinis, Marcel Salanoubat, Alain Perret
Software Mentions: 2
Published: about 12 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: almost 16 years ago

10.1186/1471-2105-9-214

M-BISON: Microarray-based integration of data sources using networks
Cited by: 9
Author(s): Bernie J. Daigle, Russ B. Altman
Software Mentions: 2
Published: over 18 years ago

10.3390/metabo11030143

Solanum lycopersicum Seedlings. Metabolic Responses Induced by the Alkamide Affinin
Cited by: 0
Author(s): Tonatiu Campos-García, Jorge Molina‐Torres
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0097255

Determinants of Spatial Distribution in a Bee Community: Nesting Resources, Flower Resources, and Body Size
Cited by: 74
Author(s): Anna Torné‐Noguera, Anselm Rodrigo, Xavier Arnán, Sergio Osorio, Helena Barril-Graells, Léo Correia da Rocha-Filho, Jordi Bosch
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0144428

Schizophrenia-Associated MIR204 Regulates Noncoding RNAs and Affects Neurotransmitter and Ion Channel Gene Sets
Cited by: 11
Author(s): Sophia Cammaerts, Mojca Stražišar, Bart Smets, Sarah Weckhuysen, Annelie Nordin, Peter De Jonghe, Rolf Adolfsson, Peter De Rijk, Jurgen Del Favero
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-8-431

Comparative evaluation of gene-set analysis methods
Cited by: 94
Author(s): Qi Liu, Irina Dinu, Adeniyi J. Adewale, John D. Potter, Yutaka Yasui
Software Mentions: 2
Published: over 18 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

10.3390/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: about 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: about 13 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: almost 18 years ago

10.1371/journal.pone.0017163

Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue
Cited by: 136
Author(s): Lorenza Mittempergher, Jorma J. de Ronde, Marja Nieuwland, Ron Kerkhoven, Iris Simón, Emiel J. T. Rutgers, Lodewyk Wessels, Laura J. van’t Veer
Software Mentions: 2
Published: over 15 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: almost 6 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: about 6 years ago

10.1186/1471-2164-13-68

Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis
Cited by: 38
Author(s): Yang Wang, Chong Liu, Yīng Fāng, Xiaoli Liu, Wentao Li, Shuqing Liu, Yingyu Liu, Yuxi Liu, Catherine Charreyre, Jean-Christophe Audonnet, Pin Chen, Qigai He
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-11-47

Expression profiling of prospero in the Drosophila larval chemosensory organ: Between growth and outgrowth
Cited by: 10
Author(s): Laure Guenin, Mahatsangy Raharijaona, Rémi Houlgatte, Fawzia Baba‐Aïssa
Software Mentions: 2
Published: over 16 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: almost 16 years ago

10.1186/1471-2164-11-388

Expression of a retinoic acid signature in circulating CD34 cells from coronary artery disease patients
Cited by: 8
Author(s): Tineke C. T. M. van der Pouw Kraan, Stephan H. Schirmer, Joost O. Fledderus, Perry D. Moerland, Josefien M. Baggen, Thomas A. Leyen, A.M. van der Laan, Jan J. Piek, Niels van Royen, Anton J.G. Horrevoets
Software Mentions: 2
Published: over 16 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

10.1186/1471-2164-14-653

HANDS: a tool for genome-wide discovery of subgenome- specific base-identity in polyploids
Cited by: 9
Author(s): Aziz Mithani, Eric J. Belfield, C. Titus Brown, Caifu Jiang, Lindsey Leach, Nicholas P. Harberd
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0059190

Compression of FASTQ and SAM Format Sequencing Data
Cited by: 175
Author(s): James K. Bonfield, Matthew V. Mahoney
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-016-2778-z

Multiple adaptive routes of Salmonella enterica Typhimurium to biocide and antibiotic exposure
Cited by: 36
Author(s): Tânia Curião, Emmanuela Marchi, Denis Grandgirard, Ricardo León‐Sampedro, Carlo Viti, Stephen L. Leib, Fernando Baquero, Marco R. Oggioni, José Luis Martínez, Teresa M. Coque
Software Mentions: 2
Published: about 10 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: almost 10 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: almost 10 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: about 9 years ago

10.1186/1471-2229-10-273

Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees
Cited by: 37
Author(s): Caroline Côté, Francis Boileau, Vicky Roy, Mario Ouellet, Caroline Levasseur, Marie-Josée Morency, Janice E. K. Cooke, Armand Séguin, John Mackay
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: almost 7 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

10.1186/s12859-017-1827-1

VAliBS: a visual aligner for bisulfite sequences
Cited by: 2
Author(s): Min Li, Peijun Huang, Xiaodong Yan, Jianxin Wang, Yi Pan, Fang‐Xiang Wu
Software Mentions: 2
Published: almost 9 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

10.1186/1471-2105-12-S10-S3

Selecting a single model or combining multiple models for microarray-based classifier development? – A comparative analysis based on large and diverse datasets generated from the MAQC-II project
Cited by: 14
Author(s): Minjun Chen, Leming Shi, Reagan Kelly, Roger Perkins, Hong Fang, Weida Tong
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0005242

Short-Term Calorie Restriction in Male Mice Feminizes Gene Expression and Alters Key Regulators of Conserved Aging Regulatory Pathways
Cited by: 82
Author(s): Preston W. Estep, Jason Warner, Martha L. Bulyk
Software Mentions: 2
Published: over 17 years ago

10.1186/1752-0509-4-134

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche
Cited by: 58
Author(s): Eugenio Azpeitia, Mariana Benítez, Iliusi Vega, Cuauhtémoc Calderón Villarreal, Elena Alvarez–Buylla
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0091894

A Systematic In Silico Mining of the Mechanistic Implications and Therapeutic Potentials of Estrogen Receptor (ER)-α in Breast Cancer
Cited by: 5
Author(s): Xin Li, Rong Sun, Wanpeng Chen, Bangmin Lu, Xiaoyu Li, Zijie Wang, Ji Bao
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0015271

The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe
Cited by: 52
Author(s): Ting Ni, Kang Tu, Zhong Wang, Shen Song, Han Wu, Bin Xie, Kristin C. Scott, Shiv I. S. Grewal, Yuan Gao, Jun Zhu
Software Mentions: 2
Published: over 15 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: over 10 years ago

10.1186/s12859-020-03751-8

SequelTools: a suite of tools for working with PacBio Sequel raw sequence data
Cited by: 16
Author(s): David E. Hufnagel, Matthew B. Hufford, Arun S. Seetharam
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-10-295

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus
Cited by: 20
Author(s): Christian Obermeier, Bashir Hosseini, W. Friedt, Rod J. Snowdon
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-9-478

Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma
Cited by: 19
Author(s): Mary H. Estler, Goran Bošković, James Denvir, Sarah Miles, Donald A. Primerano, Richard M. Niles
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0087836

Deciphering the Adjustment between Environment and Life History in Annuals: Lessons from a Geographically-Explicit Approach in Arabidopsis thaliana
Cited by: 53
Author(s): Esperanza Manzano-Piedras, Arnald Marcer, Carlos Alonso‐Blanco, F. Xavier Picó
Software Mentions: 2
Published: over 12 years ago

10.1111/anec.12840

Young and early‐onset dilated cardiomyopathy with malignant ventricular arrhythmia and sudden cardiac death induced by the heterozygous LDB3, MYH6, and SYNE1 missense mutations
Cited by: 9
Author(s): Ting Zhao, Yuting Ma, Zuoquan Zhang, Jing Xian, Xiaojing Geng, Feng Wang, Jiana Huang, Zhe Yang, Yi Luo, Yenn‐Jiang Lin
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0036540

Algebraic Comparison of Partial Lists in Bioinformatics
Cited by: 21
Author(s): Giuseppe Jurman, Samantha Riccadonna, Roberto Visintainer, Cesare Furlanello
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0173427

Five decades on: Use of historical weaning size data reveals that a decrease in maternal foraging success underpins the long-term decline in population of southern elephant seals (Mirounga leonina)
Cited by: 15
Author(s): Ella Clausius, Clive R. McMahon, Mark A. Hindell
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0189999

HIV-1 envelope sequence-based diversity measures for identifying recent infections
Cited by: 8
Author(s): Alexis Kafando, Éric Fournier, Bouchra Serhir, Christine Martineau, Florence Doualla-Bell, Mohamed N'dongo Sangaré, Mohamed Sylla, Annie Chamberland, Mohamed El-Far, Hugues Charest, Cécile Tremblay
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-14-337

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data
Cited by: 7
Author(s): Changjin Hong, Nathan Clement, Spencer C. Clement, Saher Sue Hammoud, Douglas T. Carrell, Bradley R. Cairns, Quinn Snell, Mark J. Clement, W. Evan Johnson
Software Mentions: 2
Published: over 12 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: over 6 years ago

10.1186/1471-2164-15-1115

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo
Cited by: 47
Author(s): Kenji Nakahigashi, Yuki Takai, Yuh Shiwa, Masahiko Wada, Masayuki Honma, Hideki Yoshikawa, Masaru Tomita, Akio Kanai, Hirotada Mori
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-15-827

Genome-wide characterization, expression and functional analysis of CLV3/ESR gene family in tomato
Cited by: 37
Author(s): Yu Zhang, Shaohui Yang, Yingjin Song, Jiehua Wang
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0152468

Disentangling the Role of Climate, Topography and Vegetation in Species Richness Gradients
Cited by: 60
Author(s): Mario R. Moura, Fabricio Villalobos, Gabriel C. Costa, Paulo Christiano de Anchieta Garcia
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0084646

Using Expression Profiling to Understand the Effects of Chronic Cadmium Exposure on MCF-7 Breast Cancer Cells
Cited by: 15
Author(s): Zelmina Lubovac-Pilav, Daniel Borràs, Esmeralda Ponce, Maggie C. Louie
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-15-264

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data
Cited by: 80
Author(s): Ségolène Caboche, Christophe Audebert, Yves Lemoine, David Hot
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-015-2129-5

iRDA: a new filter towards predictive, stable, and enriched candidate genes
Cited by: 1
Author(s): Hung-Ming Lai, Andreas Albrecht, Kathleen Steinhöfel
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0034291

Characterisation of Bovine Leukocyte Ig-like Receptors
Cited by: 19
Author(s): Louise E. Hogan, Sabin Bhuju, Des C. Jones, Ken Laing, John Trowsdale, Philip D. Butcher, Mahavir Singh, Martin Vordermeier, Rachel Allen
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0213040

Metabolic and physiological changes induced by plant growth regulators and plant growth promoting rhizobacteria and their impact on drought tolerance in Cicer arietinum L.
Cited by: 72
Author(s): Naeem Khan, Asghari Bano, Ali Babar
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-11-267

A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes
Cited by: 13
Author(s): Guofeng Meng, Axel Mosig, Martin Vingron
Software Mentions: 2
Published: about 16 years ago

10.1186/s12864-015-1761-4

Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks
Cited by: 31
Author(s): Shawn J. Cokus, Paul F. Gugger, Victoria L. Sork
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0022585

Epigenetic Silencing of Nucleolar rRNA Genes in Alzheimer's Disease
Cited by: 122
Author(s): Maciej Pietrzak, Grzegorz A. Rempała, Peter T. Nelson, Jing-Juan Zheng, Michał Hetman
Software Mentions: 2
Published: about 15 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: about 15 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.0089330

Evidence of a Critical Role for Cellodextrin Transporte 2 (CDT-2) in Both Cellulose and Hemicellulose Degradation and Utilization in Neurospora crassa
Cited by: 30
Author(s): Pengli Cai, Ruimeng Gu, Bang Wang, Jingen Li, Li Wan, Chaoguang Tian, Yanhe Ma
Software Mentions: 2
Published: over 12 years ago

10.1186/s12918-018-0653-z

Reframing gene essentiality in terms of adaptive flexibility
Cited by: 11
Author(s): Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard Ø. Palsson, Adam M. Feist
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2229-10-14

SoyDB: a knowledge database of soybean transcription factors
Cited by: 105
Author(s): Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng
Software Mentions: 2
Published: over 16 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/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

10.1186/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: almost 9 years ago

10.1186/s12870-018-1585-x

Comparative transcriptomics identifies patterns of selection in roses
Cited by: 13
Author(s): Shubin Li, Mingyu Zhong, Xue Dong, Xiaoling Jiang, Yuxing Xu, Yibo Sun, Fang Cheng, Li D, Kaixue Tang, Wang Si-qing, Silan Dai, Jin‐Yong Hu
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-5-203

Cited by: 94
Author(s): Norman Pavelka, Mattia Pelizzola, Caterina Vizzardelli, Monica Capozzoli, Andrea Splendiani, Francesca Granucci, Paola Ricciardi‐Castagnoli
Software Mentions: 2
Published: over 22 years ago

10.1186/1752-0509-7-14

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
Cited by: 51
Author(s): Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0023900

B Cell Signature during Inactive Systemic Lupus Is Heterogeneous: Toward a Biological Dissection of Lupus
Cited by: 48
Author(s): Jean-Claude Garaud, Jean-Nicolas Schickel, G. Blaison, Anne‐Marie Knapp, Doulaye Dembélé, Julie Ruer-Laventie, Anne‐Sophie Korganow, Thierry Martin, Pauline Soulas-Sprauel, Jean‐Louis Pasquali
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0247258

Prospective observational study and serosurvey of SARS-CoV-2 infection in asymptomatic healthcare workers at a Canadian tertiary care center
Cited by: 12
Author(s): Victor H Ferreira, Andrzej Chruscinski, Vathany Kulasingam, Trevor J. Pugh, Tamara Dus, Brad Wouters, Amit M. Oza, Matthew Ierullo, Terrance Ku, Beata Majchrzak-Kita, Sonika T. Humar, Ilona Bahinskaya, Natalia Pinzon, Jianhua Zhang, Lawrence E. Heisler, Paul M. Krzyzanowski, Bernard Lam, Ilinca M. Lungu, Dorin Manase, Krista Pace, Pouria Mashouri, Michael Brudno, Michael Garrels, Tony Mazzulli, Myron I. Cybulsky, Atul Humar, Deepali Kumar
Software Mentions: 2
Published: over 5 years ago

10.1186/1752-0509-4-136

Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks
Cited by: 77
Author(s): Monika Ray, Weixiong Zhang
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2164-9-S1-S8

HMMEditor: a visual editing tool for profile hidden Markov model
Cited by: 14
Author(s): Jianyong Dai, Jianlin Cheng
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0240277

The School Attachment Monitor—A novel computational tool for assessment of attachment in middle childhood
Cited by: 1
Author(s): Maki Rooksby, Simona Di Folco, Mohammad Tayarani, Dong-Bach Vo, Rui Huan, Alessandro Vinciarelli, Stephen Brewster, Helen Minnis
Software Mentions: 2
Published: about 5 years ago

10.1155/2008/892927

Bayesian Mixture Model Analysis for Detecting Differentially Expressed Genes
Cited by: 4
Author(s): Zhenyu Jia, Shizhong Xu
Software Mentions: 2
Published: over 18 years ago

10.1155/2012/831460

SNP Discovery through Next-Generation Sequencing and Its Applications
Cited by: 211
Author(s): Santosh Kumar, Travis Banks, Sylvie Cloutier
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0074599

Specific Extracellular Matrix Remodeling Signature of Colon Hepatic Metastases
Cited by: 42
Author(s): Maguy Del Rio, Caroline Mollévi, Nadia Vezzio-Vié, Fréderic Bibeau, Marc Ychou, Pierre Martineau
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-016-3374-y

Potential immunosuppressive effects of Escherichia coli O157:H7 experimental infection on the bovine host
Cited by: 11
Author(s): Evelien Kieckens, Joanna Rybarczyk, RW Li, Daisy Vanrompay, Eric Cox
Software Mentions: 2
Published: over 9 years ago

10.1186/2041-2223-5-9

Validation of high throughput sequencing and microbial forensics applications
Cited by: 56
Author(s): Bruce Budowle, Nancy Connell, Anna Bielecka-Oder, Rita R. Colwell, Cindi R. Corbett, Jacqueline Fletcher, Mats Forsman, Dana R Kadavy, Alemka Markotić, Stephen Morse, Randall S. Murch, Antti Sajantila, Sarah E. Schmedes, Krista Ternus, Stephen D. Turner, Samuel S. Minot
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0097842

Impact of Gene Dosage on Gene Expression, Biological Processes and Survival in Cervical Cancer: A Genome-Wide Follow-Up Study
Cited by: 40
Author(s): Ingrid Medina-Martínez, Valeria Barrón, Edgar Román-Bassaure, Eligia Juárez-Torres, Mariano Guardado-Estrada, Ana Espinosa, Miriam Bermúdez, Fernando Fernández, Carlos Venegas-Vega, Lorena Orozco, Edgar Zenteno, Susana Kofman, Jaime Berumen
Software Mentions: 2
Published: about 12 years ago

10.1002/acn3.51119

Using urine to diagnose large‐scale mtDNA deletions in adult patients
Cited by: 10
Author(s): Kristin Nielsen Varhaug, Gonzalo S. Nido, I.F.M. de Coo, Pirjo Isohanni, Anu Suomalainen, Charalampos Tzoulis, Per M. Knappskog, Laurence A. Bindoff
Software Mentions: 2
Published: about 6 years ago

10.1186/bcr1608

Gene expression signatures of morphologically normal breast tissue identify basal-like tumors
Cited by: 121
Author(s): Greg Finak, Svetlana Sadekova, François Pépin, Michael Hallett, Sarkis Meterissian, Fawaz Halwani, Karim Khetani, Margarita Souleimanova, Brent Zabolotny, Atilla Ömeroğlu, Morag Park
Software Mentions: 2
Published: almost 20 years ago

10.1186/s12870-016-0831-3

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways
Cited by: 54
Author(s): Stephen Pearce, Néstor Kippes, Andrew Chen, Juan M. Debernardi, Jorge Dubcovsky
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0126852

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads
Cited by: 6
Author(s): Jovan David Rebolledo-Mendez, Matthew S. Hestand, Stephen J. Coleman, Zheng Zeng, Ludovic Orlando, James N. MacLeod, Theodore S. Kalbfleisch
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-016-2772-5

Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations
Cited by: 10
Author(s): Cristina Gómez‐Aix, Laura Pascual, Joaquı́n Cañizares, M. Amelia Sánchez-Pina, Miguel A. Aranda
Software Mentions: 2
Published: about 10 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566