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

10.1371/journal.pone.0100250
Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
Cited by: 8
Author(s): Tzintzuni Garcia, Isa Matos, Yingjia Shen, Vagmita Pabuwal, M. M. Coelho, Yuko Wakamatsu, Manfred Schartl, Ronald B. Walter
Software Mentions: 4
Published: over 10 years ago
10.18632/aging.102754
The whole transcriptome regulation as a function of mitochondrial polymorphisms and aging in Caenorhabditis elegans
Cited by: 9
Author(s): Yuanjian Song, Yuechen Wang, Ying Liu, Liang Wang, WenDa Zhang, Jing Cheng, Yushan Zhu, Haoyu Zhang, Qiang Zhang, Haichen Niu, Yingwei Zheng, Mengyu Liang, Mengqiong Deng, Hao Shi, Hao Wang, Fang Zhang
Software Mentions: 4
Published: almost 5 years ago
10.3390/ijms21144865
Cytological and Gene Profile Expression Analysis Reveals Modification in Metabolic Pathways and Catalytic Activities Induce Resistance in Botrytis cinerea Against Iprodione Isolated From Tomato
Cited by: 4
Author(s): Ambreen Maqsood, Chaorong Wu, Sunny Ahmar, Haiyan Wu
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0126911
Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data
Cited by: 18
Author(s): David Wood, Kátia Nones, Anita L Steptoe, Angelika N. Christ, Ivon Harliwong, Felicity Newell, Timothy J. C. Bruxner, David Miller, Nicole Cloonan, Sean M. Grimmond
Software Mentions: 4
Published: over 9 years ago
10.1186/1471-2105-12-468
openBIS: a flexible framework for managing and analyzing complex data in biology research
Cited by: 105
Author(s): Angela Bauch, Izabela Adamczyk, Piotr Buczek, Franz-Josef Elmer, Kaloyan Enimanev, Pawel Glyzewski, Manuel Kohler, Tomasz Pylak, Andreas Quandt, Chandrasekhar Ramakrishnan, Christian Beisel, Lars Malmström, Ruedi Aebersold, Bernd Rinn
Software Mentions: 4
Published: almost 13 years ago
10.1186/1471-2105-15-198
CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
Cited by: 35
Author(s): Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes, Maud Silvain
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pone.0215465
FDG PET based prediction of response in head and neck cancer treatment: Assessment of new quantitative imaging features
Cited by: 18
Author(s): Reinhard Beichel, Ethan Ulrich, Brian J. Smith, Christian Bauer, Bruce P. Brown, Thomas L. Casavant, John Sunderland, Michael M. Graham, John M. Buatti
Software Mentions: 4
Published: over 5 years ago
10.1186/1471-2164-15-982
Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury
Cited by: 19
Author(s): Masayuki Yasuda, Yuji Tanaka, Koji M. Nishiguchi, Morin Ryu, S. Tsuda, Kouichi Maruyama, Toru Nakazawa
Software Mentions: 4
Published: about 10 years ago
10.1186/1471-2105-11-408
Comparison study of microarray meta-analysis methods
Cited by: 85
Author(s): Anna Campain, Jean Yee Hwa Yang
Software Mentions: 4
Published: over 14 years ago
10.1186/1471-2105-11-465
Parallel multiplicity and error discovery rate (EDR) in microarray experiments
Cited by: 4
Author(s): Wayne Xu, Clay J. Carter
Software Mentions: 4
Published: about 14 years ago
10.1371/journal.pone.0110134
Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer
Cited by: 20
Author(s): Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri
Software Mentions: 4
Published: about 10 years ago
10.1186/1471-2105-8-446
Novel definition files for human GeneChips based on GeneAnnot
Cited by: 110
Author(s): Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sérgio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato
Software Mentions: 4
Published: about 17 years ago
10.18632/oncotarget.7442
Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma
Cited by: 75
Author(s): Domenica Ronchetti, Luca Agnelli, Elisa Taìana, S. Galletti, Martina Manzoni, Katia Todoerti, Pellegrino Musto, Francesco Strozzi, Antonino Neri
Software Mentions: 4
Published: almost 9 years ago
10.1186/1471-2164-11-365
Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
Cited by: 39
Author(s): Jesper Ryge, Ole Winther, Jacob Wienecke, Albin Sandelin, Ann-Charlotte Westerdahl, Hans Hultborn, Ole Kiehn
Software Mentions: 4
Published: almost 15 years ago
10.1371/journal.pone.0038946
Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study
Cited by: 51
Author(s): Swanhild U. Meyer, Sebastian Kaiser, Carola Wagner, Christian Thirion, Michael W. Pfaffl
Software Mentions: 4
Published: over 12 years ago
10.1186/s12864-016-2524-6
Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants
Cited by: 16
Author(s): Julie Ferreira de Carvalho, Carla Oplaat, Nikolaos Pappas, Martijn F.L. Derks, Dick de Ridder, Koen J. F. Verhoeven
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pone.0137171
Discovery of a Novel Immune Gene Signature with Profound Prognostic Value in Colorectal Cancer: A Model of Cooperativity Disorientation Created in the Process from Development to Cancer
Cited by: 22
Author(s): Ning An, Xiaoyu Shi, Yueming Zhang, Ning Lv, Feng Li, Di Xia, Ning Han, Guiqi Wang, Shujun Cheng, Kaitai Zhang
Software Mentions: 4
Published: about 9 years ago
10.1371/journal.pone.0023581
Strategy to Find Molecular Signatures in a Small Series of Rare Cancers: Validation for Radiation-Induced Breast and Thyroid Tumors
Cited by: 16
Author(s): Nicolas Ugolin, Catherine Ory, Emilie Lefèvre, Nora Benhabilès, Paul Hofman, Martin Schlumberger, Sylvie Chevillard
Software Mentions: 4
Published: over 13 years ago
10.7554/eLife.51109
Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
Cited by: 47
Author(s): Sarah E Dremel, Neal A. DeLuca
Software Mentions: 4
Published: about 5 years ago
10.1186/1471-2164-15-218
Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses
Cited by: 60
Author(s): José F. Sánchez-Sevilla, Eduardo Cruz-Rus, Victoriano Valpuesta, Miguel A. Botella, Iraida Amaya
Software Mentions: 4
Published: over 10 years ago
10.7554/eLife.36666
Neolithic and medieval virus genomes reveal complex evolution of hepatitis B
Cited by: 94
Author(s): Ben Krause‐Kyora, Julian Susat, Felix M. Key, Denise Kühnert, Esther Bosse, Alexander Immel, Christoph Rinne, Sabin-Christin Kornell, Diego Yepes, Sören Franzenburg, Henrike O. Heyne, Thomas Meier, Sandra Lösch, Harald Meller, Susanne Friederich, Nicole Nicklisch, Kurt W. Alt, Stefan Schreiber, Andreas Tholey, Alexander Herbig, Almut Nebel, Johannes Krause
Software Mentions: 4
Published: over 6 years ago
10.7554/eLife.60833
Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules
Cited by: 9
Author(s): Patricia Giselle Cipriani, Olivia Bay, John Zinno, Michelle Gutwein, Hin Hark Gan, Vinay K. Mayya, George Chung, Jia‐Xuan Chen, Hala Fahs, Yu Guan, Thomas F. Duchaîne, Matthias Selbach, Fabio Piano, Kristin C. Gunsalus
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0223680
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Cited by: 51
Author(s): Xiaofang Jiang, Andrew Brantley Hall, Ramnik J. Xavier, Eric J. Alm
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pone.0013169
Gene Expression Signature-Based Screening Identifies New Broadly Effective Influenza A Antivirals
Cited by: 58
Author(s): Laurence Josset, Julien Textoris, Béatrice Loriod, Olivier Ferraris, Vincent Moulès, Bruno Lina, Catherine Nguyen, Jean‐Jacques Diaz, Manuel Rosa‐Calatrava
Software Mentions: 4
Published: about 14 years ago
10.1371/journal.pone.0198120
Spatial patterns of medium and large size mammal assemblages in várzea and terra firme forests, Central Amazonia, Brazil
Cited by: 31
Author(s): Guilherme Costa Alvarenga, Emiliano Esterci Ramalho, Fabrício Beggiato Baccaro, Daniel Gomes da Rocha, Jefferson Ferreira-Ferreira, Paulo Estefano Dineli Bobrowiec
Software Mentions: 4
Published: over 6 years ago
10.3390/s19081933
A Review of Remote Sensing Approaches for Monitoring Blue Carbon Ecosystems: Mangroves, Seagrassesand Salt Marshes during 2010–2018
Cited by: 83
Author(s): Tien Dat Pham, Junshi Xia, Nam Thang Ha, Dieu Tien Bui, Nga Nhu Le, Wataru Tekeuchi
Software Mentions: 4
Published: over 5 years ago
10.7554/eLife.21052
Embryonic origin of adult stem cells required for tissue homeostasis and regeneration
Cited by: 66
Author(s): Erin L. Davies, Kai Y. Lei, Christopher Seidel, Amanda E Kroesen, Sean A. McKinney, Longhua Guo, Sofia Robb, E. J. Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Software Mentions: 4
Published: almost 8 years ago
10.7554/eLife.46566
The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-021-91807-x
Amino acid-enriched plant-based RUTF treatment was not inferior to peanut-milk RUTF treatment in restoring plasma amino acid levels among patients with oedematous or non-oedematous malnutrition
Cited by: 3
Author(s): Wataru Sato, Chie Furuta, Peter Akomo, Paluku Bahwere, Steve Collins, Kate Sadler, Chrissy Banda, Elizabeth Maganga, Sylvester Kathumba, Hitoshi Murakami
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2105-5-197
Cited by: 43
Author(s): Sara Cheek, Yuan Qi, S. Sri Krishna, Lisa N. Kinch, Nick V. Grishin
Software Mentions: 4
Published: almost 21 years ago
10.1038/s41598-021-82731-1
Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan
Cited by: 0
Author(s): Ryōsuke Imai, Yoshiaki Tsuda, Atsushi Ebihara, Sadamu Matsumoto, Ayumi Tezuka, Atsushi J. Nagano, Ryo Ootsuki, Yasuyuki Watano
Software Mentions: 4
Published: almost 4 years ago
10.3390/ani11082300
Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand
Cited by: 5
Author(s): Karlette A. Fernandes, Erica K. Gee, Chris W. Rogers, Sandra Kittelmann, Patrick J. Biggs, Emma N. Bermingham, Charlotte F. Bolwell, David G. Thomas
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2164-13-619
Molecular characterisation of cell line models for triple-negative breast cancers
Cited by: 63
Author(s): Anita Grigoriadis, Alan Mackay, Elodie Noël, Pei Jun Wu, Rachael Natrajan, Jessica Frankum, Jorge S. Reis‐Filho, Andrew Tutt
Software Mentions: 4
Published: almost 13 years ago
10.1186/s12864-018-4709-7
Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts
Cited by: 20
Author(s): Marianne Elliott, Jennifer Yuzon, Mathu Malar C, Sucheta Tripathy, Mai Bui, Gary A. Chastagner, Katie Coats, David M. Rizzo, Matteo Garbelotto, Takao Kasuga
Software Mentions: 4
Published: over 6 years ago
10.1038/srep29434
Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Cited by: 13
Author(s): Dominic Pearce, Laura Arthur, Arran Turnbull, Lorna Renshaw, Victoria Sabine, Jeremy Thomas, John M.S. Bartlett, J. Michael Dixon, Andrew H. Sims
Software Mentions: 4
Published: over 8 years ago
10.1186/s12885-021-08218-4
MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker
Cited by: 5
Author(s): Sevan Omer Majed, Suhad Asad Mustafa
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-020-70757-w
Circadian regulation of chemotherapy-induced peripheral neuropathic pain and the underlying transcriptomic landscape
Cited by: 17
Author(s): Hee Kee Kim, Sun Yeul Lee, Nobuya Koike, Eunju Kim, Marvin Wirianto, Mark J. Burish, Kazuhiro Yagita, Hyun Kyoung Lee, Zheng Chen, Jin Mo Chung, Salahadin Abdi, Seung Hee Yoo
Software Mentions: 4
Published: over 4 years ago
10.1038/s41597-020-00642-8
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
Cited by: 65
Author(s): Solveig K. Sieberts, Thanneer M. Perumal, Minerva M. Carrasquillo, Mariet Allen, Joseph S. Reddy, Gabriel E. Hoffman, Kristen K. Dang, John N. Calley, Philip J. Ebert, James A. Eddy, X Wang, Anna K. Greenwood, Sara Mostafavi, Schahram Akbarian, Jaroslav Bendl, Michael S. Breen, Kristen J. Brennand, Leanne Brown, Andrew Browne, Joseph D. Buxbaum, Alex Charney, Andrew Chess, Lizette Couto, Greg Crawford, Olivia Devillers, Bernie Devlin, Amanda Dobbyn, Enrico Domenici, Michele Filosi, Elie Flatow, Nancy Francoeur, John F. Fullard, Sergio Espeso-Gil, Kiran Girdhar, Attila Gulyás-Kovács, Ruben C. Gur, Chang Gyu Hahn, Vahram Haroutunian, Mads E. Hauberg, Laura Huckins, Rivka Jacobov, Yonghua Jiang, Jessica Johnson, Bibi Kassim, Y Kim, Lambertus Klei, Robin Kramer, Mario Lauria, Thomas Lehner, David A. Lewis, Barbara K. Lipska, Kelsey S. Montgomery, Royce Park, Chaggai Rosenbluh, Panos Roussos, Douglas M. Ruderfer, Geetha Senthil, Hardik Shah, Laura Sloofman, Song Li, Eli Stahl, Patrick F. Sullivan, Roberto Visintainer, J Wang, Y C Wang, Jennifer Wiseman, Eva Xia, W Zhang, Elizabeth Zharovsky, Laura Addis, Sadiya N. Addo, David Airey, Matthias Arnold, David A. Bennett, Ying Bi, Knut Biber, Colette Blach, E Bradhsaw, Patrick McKinley Brennan, R Canet-Aviles, Shaolong Cao, A Cavalla, Yooree Chae, W W Chen, Joyce Cheng, David A. Collier, Jeffrey L. Dage, Eric B. Dammer, J Davis, J Davis, Derek Drake, Duc Duong, Brian J. Eastwood, Michelle E. Ehrlich, Benjamin M. Ellingson, Brett W. Engelmann, Sahar Esmaeeli-Nieh, Daniel Felsky, Cory C. Funk, Chris Gaiteri
Software Mentions: 4
Published: about 4 years ago
10.1186/s12864-017-4391-1
Profiling the onset of somatic embryogenesis in Arabidopsis
Cited by: 37
Author(s): Enrico Magnani, José M. Jiménez‐Gómez, Ludivine Soubigou‐Taconnat, Loïc Lepiniec, Elisa Fiume
Software Mentions: 4
Published: almost 7 years ago
10.1038/srep13364
Chimeric peptide constructs comprising linear B-cell epitopes: application to the serodiagnosis of infectious diseases
Cited by: 26
Author(s): Yao Lu, Zhong Li, Huan Teng, Hongke Xu, Songnan Qi, Jianan He, Dayong Gu, Qijun Chen, Hongwei Ma
Software Mentions: 4
Published: over 9 years ago
10.1186/s12864-015-1233-x
Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry
Cited by: 27
Author(s): Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj, Osama Alsmadi
Software Mentions: 4
Published: almost 10 years ago
10.1371/journal.pone.0103441
Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification
Cited by: 9
Author(s): Lőrinc Sándor Pongor, Roberto Vera, Balázs Ligeti
Software Mentions: 4
Published: over 10 years ago
10.1007/s13205-020-02291-5
ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa)
Cited by: 3
Author(s): Sathishkumar Natarajan, Mohammad Rashed Hossain, Hoy‐Taek Kim, Denison Michael Immanuel Jesse, Mostari Jahan Ferdous, Hee-Jeong Jung, Jong-In Park, Ill Sup Nou
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1007332
Genome-wide detection of conservative site-specific recombination in bacteria
Cited by: 37
Author(s): Ognjen Sekulović, Elizabeth M. Garrett, Jacob Bourgeois, Rita Tamayo, Aimee Shen, Andrew Camilli
Software Mentions: 4
Published: over 6 years ago
10.1038/srep26846
Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB
Cited by: 48
Author(s): Daniel Haustead, Andrew Stevenson, Vishal Saxena, Fiona Marriage, Martin J Firth, Robyn C Silla, Lisa W. Martin, Katharine F. Adcroft, Suzanne Rea, Philip J. Day, Phillip E. Melton, Fiona Wood, Mark W. Fear
Software Mentions: 4
Published: over 8 years ago
10.3390/s140101155
A Methodology to Assess the Accuracy with which Remote Data Characterize a Specific Surface, as a Function of Full Width at Half Maximum (FWHM): Application to Three Italian Coastal Waters
Cited by: 12
Author(s): Rosa Maria Cavalli, Mattia Betti, Alessandra Campanelli, Annalisa Di Cicco, Daniela Guglietta, Pierluigi Penna, Viviana Piermattei
Software Mentions: 4
Published: almost 11 years ago
10.1371/journal.pcbi.1009078
lra: A long read aligner for sequences and contigs
Cited by: 50
Author(s): Jimin Ren, Mark Chaisson
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2164-12-589
Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments
Cited by: 30
Author(s): Robert Kitchen, Victoria Sabine, Arthur A. Simen, JM Dixon, John M.S. Bartlett, Andrew H. Sims
Software Mentions: 4
Published: almost 13 years ago
10.1186/1471-2164-12-402
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
Cited by: 2,222
Author(s): Nabil-Fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour, Scott A. Beatson
Software Mentions: 4
Published: over 13 years ago
10.1186/1471-2164-14-494
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
Cited by: 6
Author(s): Quang Trinh, Fei-Yang Arthur Jen, Ziru Zhou, Kar Ming Chu, Marc D. Perry, Ellen Kephart, Sergio Contrino, Peter Ruzanov, Lincoln Stein
Software Mentions: 4
Published: over 11 years ago
10.1186/1471-2164-15-1081
Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator
Cited by: 137
Author(s): Laura M. Jones, Summaira Riaz, Abraham Morales‐Cruz, Katherine C. H. Amrine, Brianna McGuire, W. D. Gubler, Michael Walker, Dario Cantu
Software Mentions: 4
Published: almost 10 years ago
10.1007/s00251-014-0819-9
Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires
Cited by: 79
Author(s): Elin Bergseng, Siri Dørum, Magnus Ø. Arntzen, Morten Nielsen, Ståle Nygård, Søren Buus, Gustavo Souza, Ludvig M. Sollid
Software Mentions: 4
Published: almost 10 years ago
10.1186/gm551
Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia
Cited by: 28
Author(s): Miriam Sonnet, Rainer Claus, Natália Becker, Manuela Zucknick, Jana Petersen, Daniel B. Lipka, Christopher C. Oakes, Mindaugas Andrulis, Amelie Lier, Michael D. Milsom, Tania Witte, Lei Gu, Soo Zin Kim-Wanner, Peter Schirmacher, Michael Wulfert, Norbert Gattermann, Michael Lübbert, Frank Rosenbauer, Michael Rehli, Lars Bullinger, Dieter Weichenhan, Christoph Plass
Software Mentions: 4
Published: almost 11 years ago
10.1186/1471-2164-11-138
Escherichia coli infection induces distinct local and systemic transcriptome responses in the mammary gland
Cited by: 114
Author(s): Simone Mitterhuemer, Wolfram Petzl, Stefan Krebs, Daniel Mehne, Andrea Klanner, Eckhard Wolf, Holm Zerbe, Helmut Blum
Software Mentions: 4
Published: over 14 years ago
10.1186/s13073-014-0059-5
A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD
Cited by: 21
Author(s): Peter K. Davidsen, John Herbert, Philipp Antczak, Kim Clarke, Elisabet Ferrer, Víctor I. Peinado, C. González, Josep Roca, Stuart Egginton, Joan Albert Barberà, Francesco Falciani
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pgen.0030087
Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Cited by: 414
Author(s): Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, King-Wah Chiu, Leonard Lipovich, Daniel H. Barnett, Fabio Stossi, A. Yeo, Joshy George, Vladimir A. Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D. Miller, Edwin Cheung, Benita S. Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia Lin Wei, Edison T. Liu
Software Mentions: 4
Published: over 17 years ago
10.1186/1471-2105-12-29
Investigating the effect of paralogs on microarray gene-set analysis
Cited by: 0
Author(s): Aline Faure, Cathal Seoighe, Nicola Mulder
Software Mentions: 4
Published: almost 14 years ago
10.1371/journal.pcbi.1004884
A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells
Cited by: 5
Author(s): Víctor Treviño, Alberto Cassese, Zsuzsanna Nagy, Xiaodong Zhuang, John Herbert, Philipp Antzack, Kim Clarke, Nick Davies, Ayesha Rahman, Moray J. Campbell, Michele Guindani, Roy Bicknell, Marina Vannucci, Francesco Falciani
Software Mentions: 4
Published: over 8 years ago
10.1111/imb.12688
Jekyll or Hyde? The genome (and more) of <i>Nesidiocoris tenuis</i>, a zoophytophagous predatory bug that is both a biological control agent and a pest
Cited by: 11
Author(s): Kim Ferguson, Sako Visser, Martina Dalíková, Irena Provazníková, Alberto Urbaneja, František Marec, John H. Werren, Bas J. Zwaan, Bart A. Pannebakker, Eveline C. Verhulst
Software Mentions: 4
Published: almost 4 years ago
10.3390/plants9101355
Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review
Cited by: 36
Author(s): Parmeshwar K. Sahu, Richa Sao, Suvendu Mondal, Gautam Vishwakarma, Sudhir Kumar Gupta, Vinay Kumar, Sudhir Singh, Deepak Sharma, Bikram Das
Software Mentions: 4
Published: about 4 years ago
10.3390/plants10020364
A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants
Cited by: 5
Author(s): Rachel M. McCoy, Russell Julian, Shoban R V Kumar, Rajeev Ranjan, Kranthi Varala, Ying Liu
Software Mentions: 4
Published: almost 4 years ago
10.1186/s13059-021-02375-2
Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation
Cited by: 8
Author(s): Nisha Padmanabhan, Kie Kyon Huang, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, Hyung-O K Lee, Vineeth T. Mukundan, Charlene Chan, Yarn Kit Chan, Xuewen Ong, Jason J. Pitt, Zul Fazreen Adam Isa, Manjie Xing, Ming Hui Lee, Angie Lay Keng Tan, Shamaine Ho Wei Ting, Micah A. Luftig, Dennis Kappei, Warren D. Kruger, Jun Bian, Ying Swan Ho, Ming Teh, Steve Rozen, Patrick Tan
Software Mentions: 4
Published: over 3 years ago
10.1186/s12859-017-1816-4
mmquant: how to count multi-mapping reads?
Cited by: 29
Author(s): Matthias Zytnicki
Software Mentions: 4
Published: about 7 years ago
10.1186/1471-2164-12-5
The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits
Cited by: 23
Author(s): Isabelle Privat, Amélie Bardil, Aureliano Bombarely, Dany Séverac, Christelle Le Dantec, Ivanna Fuentes, Lukas A. Mueller, Thierry Joët, David Pot, Séverine Foucrier, Stéphane Dussert, Thierry Leroy, Laurent Journot, Alexandre de Kochko, Claudine Campa, Marie‐Christine Combes, Philippe Lebailly, Benoît Bertrand
Software Mentions: 4
Published: almost 14 years ago
10.1186/s13059-017-1290-3
A tandem simulation framework for predicting mapping quality
Cited by: 14
Author(s): Ben Langmead
Software Mentions: 4
Published: over 7 years ago
10.1186/1471-2164-14-425
Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing
Cited by: 47
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith, Thomas Messina, Huiying Fan, Edward P. Jaeger, S. A. Stephens
Software Mentions: 4
Published: almost 12 years ago
10.7717/peerj.2681
RGFA: powerful and convenient handling of assembly graphs
Cited by: 5
Author(s): Giorgio Gonnella, Stefan Kurtz
Software Mentions: 4
Published: about 8 years ago
10.7717/peerj.2478
Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
Cited by: 13
Author(s): Chien-Hung Huang, Jin-Shuei Ciou, Shun-Tsung Chen, Victor C. Kok, Yuan‐Chiang Chung, Jeffrey J. P. Tsai, Nilubon Kurubanjerdjit, Chi-Ying F. Huang, Ka-Lok Ng
Software Mentions: 4
Published: about 8 years ago
10.1186/gb-2013-14-11-r125
Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts
Cited by: 176
Author(s): Adam D. Pfefferle, Jason I. Herschkowitz, Jerry Usary, J. Chuck Harrell, Benjamin T. Spike, Jessica R. Adams, Maria I. Torres-Arzayus, Myles Brown, Sean E. Egan, Geoffrey M. Wahl, Jeffrey M. Rosen, Charles M. Perou
Software Mentions: 4
Published: almost 12 years ago
10.1186/gb-2014-15-1-r4
Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein
Cited by: 93
Author(s): Li-Nan Chen, Jason G Dumelie, Xiao Li, Matthew Hong Kei Cheng, Zhiyong Yang, John Laver, Najeeb U. Siddiqui, J. Timothy Westwood, Quaid Morris, Howard D. Lipshitz, Craig Smibert
Software Mentions: 4
Published: almost 11 years ago
10.1186/gb-2014-15-1-r11
dCLIP: a computational approach for comparative CLIP-seq analyses
Cited by: 46
Author(s): Tao Wang, Yang Xie, Guanghua Xiao
Software Mentions: 4
Published: almost 11 years ago
10.1186/s12711-016-0257-2
Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Cited by: 31
Author(s): Harald Olsen, Tim Martin Knutsen, Anna Lewandowska-Sabat, Harald Grove, Torfinn Nome, Mathias Tiedemann Svendsen, Mariann Árnyasi, Marte Sodeland, Kristil Kindem Sundsaasen, Sandra Rinne Dahl, B. Heringstad, Hanne Hellerud Hansen, I. Olsaker, Matthew Kent, Sigbjørn Lien
Software Mentions: 4
Published: about 8 years ago
10.1186/s12864-015-1635-9
Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection
Cited by: 72
Author(s): James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Igseo Choi, Hua Bao, Arun Kommadath, Nick V. L. Serão, Nicholas Boddicker, Samuel M. Abrams, Martine Schroyen, Hyelee Loyd, Christopher K. Tuggle, Graham Plastow, Leluo Guan, Paul Stothard, Joan K. Lunney, Peng Liu, Susan Carpenter, Raymond R. R. Rowland, Jack C. M. Dekkers, James M. Reecy
Software Mentions: 4
Published: over 9 years ago
10.1186/gb-2005-6-6-r54
Cited by: 148
Author(s): Nils Rostoks, Justin O. Borevitz, Pete E. Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David Marshall, Robbie Waugh
Software Mentions: 4
Published: almost 20 years ago
10.1186/1471-2105-9-548
GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Cited by: 34
Author(s): Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J. Butte
Software Mentions: 4
Published: almost 16 years ago
10.1186/s12859-015-0795-6
TOGGLE: toolbox for generic NGS analyses
Cited by: 20
Author(s): Cécile Monat, Christine Tranchant‐Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela, Marilyne Summo, François Sabot
Software Mentions: 4
Published: about 9 years ago
10.1186/1471-2105-7-359
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
Cited by: 321
Author(s): Ian B. Jeffery, Desmond G. Higgins, Aedín C. Culhane
Software Mentions: 4
Published: over 18 years ago
10.7717/peerj.5551
BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments
Cited by: 11
Author(s): Maria Luiza Mondelli, Thiago Tavares Magalhães, Guilherme Loss, Michael Wilde, Ian Foster, Marta Mattoso, Daniel S. Katz, Hélio J. C. Barbosa, Ana Tereza Ribeiro de Vasconcelos, Kary Ocaña, Luiz M. R. Gadelha
Software Mentions: 4
Published: about 6 years ago
10.1186/s12859-017-1849-8
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics
Cited by: 11
Author(s): Peng Zhai, Longshu Yang, Xiao Guo, Zhe Wang, Jiangtao Guo, Xiaoqi Wang, Huaiqiu Zhu
Software Mentions: 4
Published: about 7 years ago
10.1186/s13059-014-0555-3
Determining the quality and complexity of next-generation sequencing data without a reference genome
Cited by: 27
Author(s): Seyed Yahya Anvar, Lusine Khachatryan, Martijn Vermaat, M.A. van Galen, Irina Pulyakhina, Yavuz Ariyürek, Ken Kraaijeveld, Johan T. den Dunnen, Peter de Knijff, Peter A C ‘t Hoen, Jeroen F. J. Laros
Software Mentions: 4
Published: almost 10 years ago
10.1534/g3.117.300550
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (<i>Lolium perenne</i> L.)
Cited by: 8
Author(s): Rachel F. Begheyn, Steven Yates, Timothy Sykes, Bruno Studer
Software Mentions: 4
Published: over 6 years ago
10.1534/g3.119.400777
<i>rmtA</i>-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence in<i>Aspergillus flavus</i>
Cited by: 5
Author(s): Timothy Satterlee, Sarah Entwistle, Yanbin Yin, J. W. Cary, Matthew D. Lebar, Liliana Losada, Ana M. Calvo
Software Mentions: 4
Published: almost 5 years ago
10.1186/1471-2105-12-139
PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Cited by: 146
Author(s): Xin Feng, Robert L. Grossman, Lincoln Stein
Software Mentions: 4
Published: over 13 years ago
10.1534/g3.116.026914
Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in<i>Glycine soja</i>, the Wild Progenitor of Cultivated Soybeans
Cited by: 39
Author(s): Justin Anderson, Thomas J. Y. Kono, Robert M. Stupar, Michael B. Kantar, Peter L. Morrell
Software Mentions: 4
Published: over 8 years ago
10.3390/genes9040180
Non-Pleiotropic Coupling of Daily and Seasonal Temporal Isolation in the European Corn Borer
Cited by: 29
Author(s): Rebecca C. Levy, Genevieve M. Kozak, Erik B. Dopman
Software Mentions: 4
Published: over 6 years ago
10.1186/s12859-017-1897-0
Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: almost 7 years ago
10.1186/s12944-018-0915-1
Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: almost 6 years ago
10.1186/1471-2164-13-131
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
Cited by: 31
Author(s): Elena S. Peterson, Lee Ann McCue, Alexandra C. Schrimpe‐Rutledge, Jeffrey L. Jensen, Hyunjoo Walker, Markus A. Kobold, Samantha R Webb, Samuel H. Payne, Charles Ansong, Joshua N. Adkins, W. Roger Cannon, Bobbie-Jo M. Webb-Robertson
Software Mentions: 4
Published: over 12 years ago
10.3390/genes10070554
Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
Cited by: 17
Author(s): Guoliang Li, Tongkai Sun, Huidan Chang, Liuyang Cai, Hong Pan, Qiangwei Zhou
Software Mentions: 4
Published: over 5 years ago
10.3390/life11080862
Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
Cited by: 6
Author(s): Zulema Udaondo, Kanchana Sittikankaew, Tanaporn Uengwetwanit, Thidathip Wongsurawat, Chutima Sonthirod, Piroon Jenjaroenpun, Wirulda Pootakham, Nitsara Karoonuthaisiri, Intawat Nookaew
Software Mentions: 4
Published: about 3 years ago
10.1093/bib/bbw020
A review of bioinformatic pipeline frameworks
Cited by: 155
Author(s): Jeremy Leipzig
Software Mentions: 4
Published: over 8 years ago
10.1155/2013/270362
A Case Report and Genetic Characterization of a Massive Acinic Cell Carcinoma of the Parotid with Delayed Distant Metastases
Cited by: 5
Author(s): Anthony C. Nichols, Michelle Chan-Seng-Yue, John Yoo, Sumit Agrawal, Maud H.W. Starmans, Daryl Waggott, Nicholas J. Harding, Samuel Dowthwaite, David A. Palma, Kevin Fung, Bret Wehrli, Danielle MacNeil, Philippe Lambin, Eric Winquist, James Koropatnick, Joe S. Mymryk, Paul C. Boutros, John W. Barrett
Software Mentions: 4
Published: almost 12 years ago
10.1186/1471-2164-11-23
Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development
Cited by: 37
Author(s): Wen Huang, Brian S. Yandell, Hasan Khatib
Software Mentions: 4
Published: almost 15 years ago
10.1186/s13058-019-1159-3
On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer
Cited by: 32
Author(s): Richard J. Bownes, Arran Turnbull, Carlos Martínez-Pérez, David Cameron, Andrew H. Sims, Olga Oikonomidou
Software Mentions: 4
Published: over 5 years ago
10.3389/fgene.2018.00328
Co-expression Network Analysis of Biomarkers for Adrenocortical Carcinoma
Cited by: 37
Author(s): Lushun Yuan, Guofeng Qian, Liang Chen, Chin‐Lee Wu, Dong Han, Yu Xiao, Xinghuan Wang
Software Mentions: 4
Published: over 6 years ago
10.1002/ece3.5604
Contribution of rare and common species to subterranean species richness patterns
Cited by: 28
Author(s): Petra Bregović, Cene Fišer, Maja Zagmajster
Software Mentions: 4
Published: about 5 years ago
10.1093/biostatistics/kxu038
Joint analysis of differential gene expression in multiple studies using correlation motifs
Cited by: 29
Author(s): Yingying Wei, Toyoaki Tenzen, Hongkai Ji
Software Mentions: 4
Published: over 10 years ago
10.1155/2015/760423
HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis
Cited by: 5
Author(s): Miao‐Kun Sun, Karthik Raja Velmurugan, David Keimig, Hehuang Xie
Software Mentions: 4
Published: almost 9 years ago
10.1038/bcj.2016.77
lncRNA profiling in early-stage chronic lymphocytic leukemia identifies transcriptional fingerprints with relevance in clinical outcome
Cited by: 40
Author(s): Domenica Ronchetti, Martina Manzoni, Luca Agnelli, Cristina Vinci, Sonia Fabris, Giovanna Cutrona, Serena Matis, Monica Colombo, S. Galletti, Elisa Taìana, Anna Grazia Recchia, Sabrina Bossio, Massimo Gentile, Caterina Musolino, Francesco Di Raimondo, Andrea Grilli, Silvio Bicciato, Agostino Cortelezzi, Pierfrancesco Tassone, Fortunato Morabito, Manlio Ferrarini, Antonino Neri
Software Mentions: 4
Published: about 8 years ago
10.3389/fimmu.2018.01626
Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence
Cited by: 23
Author(s): Alejandro M. Labella, Esther García-Rosado, Isabel Bandı́n, Carlos P. Dopazo, Dolores Castro, M. Carmen Alonso, Juan J. Borrego
Software Mentions: 4
Published: over 6 years ago