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

10.3390/v11010033
A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium
Cited by: 5
Author(s): Wei Zou, Min Xiong, Xuefeng Deng, John F. Engelhardt, Ziying Yan, Jianming Qiu
Software Mentions: 3
Published: almost 6 years ago
10.1186/1471-2105-11-73
BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Cited by: 11
Author(s): Mark Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini
Software Mentions: 3
Published: almost 15 years ago
10.1093/gbe/evt199
The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatus
Cited by: 40
Author(s): Lex E. Flagel, John H. Willis
Software Mentions: 3
Published: almost 11 years ago
10.1093/gbe/evu272
Evolutionary Dynamics of GLD-1–mRNA Complexes in Caenorhabditis Nematodes
Cited by: 7
Author(s): Alana V. Beadell, Eric S. Haag
Software Mentions: 3
Published: almost 10 years ago
10.3390/v12070782
High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
Cited by: 4
Author(s): Sílvia Inês Sardi, Renata Carvalho, Luis Gustavo Carvalho Pacheco, João Fernando Lourenço de Almeida, Emilia M M D A Belitardo, Carina S. Pinheiro, Gúbio Soares Campos, Eric Roberto Guimarães Rocha Aguiar
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-018-2319-7
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
Cited by: 21
Author(s): Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
Software Mentions: 3
Published: about 6 years ago
10.1186/s13059-021-02270-w
simATAC: a single-cell ATAC-seq simulation framework
Cited by: 12
Author(s): Zeinab Navidi, Lin Zhang, Bo Wang
Software Mentions: 3
Published: over 3 years ago
10.1186/1743-422X-8-285
Cellular transcriptional profiling in human lung epithelial cells infected by different subtypes of influenza A viruses reveals an overall down-regulation of the host p53 pathway
Cited by: 38
Author(s): Benjamin Terrier, Laurence Josset, Julien Textoris, Virginie Marcel, Gaëlle Cartet, Olivier Ferraris, Catherine Nguyen, Bruno Lina, Jean‐Jacques Diaz, Jean-Christophe Bourdon, Manuel Rosa‐Calatrava
Software Mentions: 3
Published: over 13 years ago
10.1371/journal.pone.0015617
A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology
Cited by: 61
Author(s): Martin Blythe, Damian Kao, Sunir Malla, Joanna Rowsell, Reginald H. Wilson, Deborah Evans, Jamie Jowett, Amy Hall, Virginie Lemay, Sabrina Lam, A. Aziz Aboobaker
Software Mentions: 3
Published: almost 14 years ago
10.3758/s13414-015-0860-2
The long and the short of priming in visual search
Cited by: 24
Author(s): Wouter Kruijne, Martijn Meeter
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0151522
Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Cited by: 25
Author(s): Paul Pavlidis, Vignesh Dhandapani, Jana Jeevan Rameneni, Xiaonan Li, Ganesan Sivanandhan, Su Ryun Choi, Wenxing Pang, Subin Im, Yong Pyo Lim
Software Mentions: 3
Published: over 8 years ago
10.1186/1471-2407-14-64
Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Cited by: 21
Author(s): Marion Fehlker, Matthew R. Huska, Thomas Jöns, Miguel A. Andrade‐Navarro, Wolfgang Kemmner
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0040194
Microarray-Based Sketches of the HERV Transcriptome Landscape
Cited by: 46
Author(s): Philippe Pérot, Nathalie Mugnier, Cécile Montgiraud, Juliette Gimenez, Magali Jaillard, Bertrand Bonnaud, François Mallet
Software Mentions: 3
Published: over 12 years ago
10.1186/s13059-020-02045-9
Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing
Cited by: 11
Author(s): Naveen Ramesh, Emi Sei, Pei Ching Tsai, Shanshan Bai, Yuehui Zhao, Patricia Troncoso, Paul G. Corn, Christopher J. Logothetis, Amado J. Zurita, Nicholas E. Navin
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-59541-y
Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice
Cited by: 78
Author(s): Hitoshi Inokawa, Yasuhiro Umemura, Akihiro Shimba, Eiryo Kawakami, Nobuya Koike, Yoshiki Tsuchiya, Masaru Ohashi, Yoichi Minami, Guangwei Cui, T. Asahi, Ryutaro Ono, Yuh Sasawaki, Eiichi Konishi, Seung-Hee Yoo, Chen Zheng, Satoshi Teramukai, Koichi Ikuta, Kazuhiro Yagita
Software Mentions: 3
Published: almost 5 years ago
10.1186/s13059-020-01968-7
NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing
Cited by: 53
Author(s): Cheng Yong Tham, Roberto Tirado-Magallanes, Yufen Goh, Melissa J. Fullwood, Bryan T. H. Koh, Wilson Wang, Chin Hin Ng, Wee Joo Chng, Alexandre H. Thiéry, Daniel G. Tenen, Touati Benoukraf
Software Mentions: 3
Published: over 4 years ago
10.1186/1471-2407-7-61
Identification of a robust gene signature that predicts breast cancer outcome in independent data sets
Cited by: 37
Author(s): James E. Korkola, Ekaterini Blaveri, Sandy DeVries, Dan H. Moore, E. Shelley Hwang, Yunn Yi Chen, Anne L. Estep, Karen Chew, Ronald H. Jensen, Frederic M. Waldman
Software Mentions: 3
Published: over 17 years ago
10.15252/msb.20188584
Path‐seq identifies an essential mycolate remodeling program for mycobacterial host adaptation
Cited by: 49
Author(s): Eliza J.R. Peterson, Rebeca Bailo, Alissa C. Rothchild, Mario L. Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, Abrar A. Abidi, Charlotte Cooper, Alan Aderem, Apoorva Bhatt, Nitin S. Baliga
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2105-16-S7-S5
Heterozygous genome assembly via binary classification of homologous sequence
Cited by: 13
Author(s): Paul Bodily, Mao Fujimoto, Cameron Ortega, Nozomu Okuda, Joseph Price, Mark J. Clement, Quinn Snell
Software Mentions: 3
Published: over 9 years ago
10.1186/gb-2005-6-2-r16
Cited by: 335
Author(s): Sung Choe, Michael Boutros, Alan D. Michelson, George M. Church, Marc S. Halfon
Software Mentions: 3
Published: almost 20 years ago
10.3892/mmr.2015.3318
PUFA diets alter the microRNA expression profiles in an inflammation rat model
Cited by: 34
Author(s): Zheng Zhang, Yubin Ge, Jinyu Zhang, Meilan Xue, Quan Li, Dongliang Lin, Wenhui Ma
Software Mentions: 3
Published: almost 10 years ago
10.1186/gb-2005-6-2-r20
Cited by: 18
Author(s): Stephen R. Master, Alexander J. Stoddard, Leonard C. Bailey, Tien-Chi Pan, Katherine D. Dugan, Lewis A. Chodosh
Software Mentions: 3
Published: almost 20 years ago
10.3390/ani11092557
Identification of Circular RNAs in the Anterior Pituitary in Rats Treated with GnRH
Cited by: 3
Author(s): Haixiang Guo, Bao Yuan, Meng-Ting Su, Yi Zheng, Jinyu Zhang, Dong-Xu Han, Hao-Qi Wang, Yongping Huang, Hao Jiang, Jiabao Zhang
Software Mentions: 3
Published: about 3 years ago
10.1002/mgg3.1503
Identification of common differentially expressed genes in Turner (45,X) and Klinefelter (47,XXY) syndromes using bioinformatics analysis
Cited by: 5
Author(s): María Carolina Manotas, Juan M. Calderón, Liliana López‐Kleine, Fernando Suárez‐Obando, Olga Moreno, Alejandra Rojas
Software Mentions: 3
Published: about 4 years ago
10.1186/s13059-014-0571-3
CIRI: an efficient and unbiased algorithm for de novo circular RNA identification
Cited by: 780
Author(s): Yuan Gao, Jinfeng Wang, Fangqing Zhao
Software Mentions: 3
Published: almost 10 years ago
10.1186/1471-2105-12-382
Mulcom: a multiple comparison statistical test for microarray data in Bioconductor
Cited by: 5
Author(s): Claudio Isella, Tommaso Renzulli, Davide Corà, Enzo Medico
Software Mentions: 3
Published: about 13 years ago
10.1186/s13059-014-0540-x
Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity
Cited by: 33
Author(s): Stuart Dowall, David A. Matthews, Isabel García-Dorival, Irene Taylor, John Kenny, Christiane Hertz‐Fowler, Neil Hall, Kara Corbin-Lickfett, Cyril Empig, Kyle Schlunegger, John N. Barr, Miles W. Carroll, Roger Hewson, Julian A. Hiscox
Software Mentions: 3
Published: about 10 years ago
10.1186/1471-2105-10-418
TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Cited by: 57
Author(s): Haiquan Li, Vagner A. Benedito, Michael K. Udvardi, Patrick Xuechun Zhao
Software Mentions: 3
Published: almost 15 years ago
10.1186/1751-0473-8-6
RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Cited by: 1
Author(s): Izawa Akiko, Jun Sese
Software Mentions: 3
Published: over 11 years ago
10.1186/1471-2105-13-S14-S5
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: about 12 years ago
10.3390/molecules24030631
Stratification of Breast Cancer by Integrating Gene Expression Data and Clinical Variables
Cited by: 8
Author(s): Zongzhen He, Junying Zhang, Xiguo Yuan, Jianing Xi, Zhaowen Liu, Yuanyuan Zhang
Software Mentions: 3
Published: almost 6 years ago
10.3390/molecules22101734
Analysis of Genetic Diversity and Structure Pattern of Indigofera Pseudotinctoria in Karst Habitats of the Wushan Mountains Using AFLP Markers
Cited by: 6
Author(s): Yanting Fan, Chenglin Zhang, Wen Bing Wu, Wei He, Li Zhang, Xiao Ma
Software Mentions: 3
Published: about 7 years ago
10.1186/gb-2014-15-5-r71
A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions
Cited by: 28
Author(s): Alayne Brunner, Jun Li, Xiangqian Guo, Robert T. Sweeney, Sushama Varma, Shirley Zhu, Rui Li, Robert Tibshirani, Robert B. West
Software Mentions: 3
Published: almost 11 years ago
10.1186/gm340
Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets
Cited by: 141
Author(s): Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Antônio Reverter, Mark A. Ragan
Software Mentions: 3
Published: almost 13 years ago
10.1186/s12885-016-2453-4
Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes
Cited by: 26
Author(s): Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xiaoting Ke, Anne Margrete Øyan, Karl H. Kalland
Software Mentions: 3
Published: over 8 years ago
10.1186/gb-2013-14-3-r30
CRAC: an integrated approach to the analysis of RNA-seq reads
Cited by: 70
Author(s): Philippe Naveilhan, Mikaël Salson, Thérèse Commes, Éric Rivals
Software Mentions: 3
Published: almost 12 years ago
10.1186/gb-2012-13-5-r34
A new approach for detecting low-level mutations in next-generation sequence data
Cited by: 87
Author(s): Mingkun Li, Mark Stoneking
Software Mentions: 3
Published: almost 13 years ago
10.1186/1476-4598-12-140
Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Cited by: 53
Author(s): Ângela Aguirres Fachel, Ana Carolina Tahira, Santiago A. Vilella-Arias, Vinicius Maracaja‐Coutinho, Etel Rp Gimba, Giselle Maria Vignal, Franz Campos, Eduardo M. Reis, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: about 11 years ago
10.1186/gb-2012-13-8-r75
Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
Cited by: 220
Author(s): Alayne Brunner, Andrew H. Beck, Badreddin Edris, Robert T. Sweeney, Shirley Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W. Foley, Daniela Witten, Craig P. Giacomini, Ryan A. Flynn, Jonathan R. Pollack, Robert Tibshirani, Howard Y. Chang, Matt van de Rijn, Robert B. West
Software Mentions: 3
Published: almost 13 years ago
10.1186/gb-2013-14-8-r93
Web Apollo: a web-based genomic annotation editing platform
Cited by: 312
Author(s): Eduardo Lee, Gregg Helt, Justin Reese, Monica Muñoz-Torres, Christopher P. Childers, Robert Buels, Lincoln Stein, Ian Holmes, Christine G. Elsik, Suzanna Lewis
Software Mentions: 3
Published: almost 12 years ago
10.1186/gb-2007-8-5-r79
An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
Cited by: 42
Author(s): Michał Okoniewski, Timothy Yates, Siân Dibben, Crispin Miller
Software Mentions: 3
Published: almost 18 years ago
10.1186/gb-2011-12-3-r22
Improving RNA-Seq expression estimates by correcting for fragment bias
Cited by: 1,136
Author(s): Anjeanette Roberts, Cole Trapnell, Julie Donaghey, John L. Rinn, Lior Pachter
Software Mentions: 3
Published: almost 14 years ago
10.1186/gb-2013-14-5-r51
Characterizing and measuring bias in sequence data
Cited by: 708
Author(s): Michael G. Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J. Lennon, Ryan Hegarty, Chad Nusbaum, David B. Jaffe
Software Mentions: 3
Published: almost 12 years ago
10.1186/bcr3150
Relevance of PTEN loss in brain metastasis formation in breast cancer patients
Cited by: 87
Author(s): Harriet Wikman, Katrin Lamszus, Niclas Detels, Liubov Uslar, Michaela Wrage, Christian Benner, Ina Hohensee, Bauke Ylstra, Kathrin Eylmann, Marc Zapatka, Guido Sauter, Dirk Kemming, Markus Glatzel, Volkmar Müller, Manfred Westphal, Klaus Pantel
Software Mentions: 3
Published: over 12 years ago
10.3390/microorganisms9030584
Implications of Tributyrin on Gut Microbiota Shifts Related to Performances of Weaning Piglets
Cited by: 15
Author(s): Francesco Miragoli, Vania Patrone, Aldo Prandini, Samantha Sigolo, Matteo Dell’Anno, Luciana Rossi, Alice Senizza, L. Morelli, Maria Luisa Callegari
Software Mentions: 3
Published: over 3 years ago
10.3390/genes12071064
Genetic and Transcriptomic Analysis Reveal the Molecular Basis of Photoperiod-Regulated Flowering in Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan)
Cited by: 7
Author(s): Zhen Tian, Molly Jahn, Xiaodong Qin, Hesbon Ochieng Obel, Fan Yang, Ji Li, Jinfeng Chen
Software Mentions: 3
Published: over 3 years ago
10.3390/genes11091000
Comparative Transcriptome Analysis of Pine Trees Treated with Resistance-Inducing Substances against the Nematode Bursaphelenchus xylophilus
Cited by: 6
Author(s): Jung–Wook Park, Hee Won Jeon, Hyejung Jung, Hyun‐Hee Lee, Junheon Kim, Ae Ran Park, Namgyu Kim, Gil Soo Han, Jin-Cheol Kim, Young-Su Seo
Software Mentions: 3
Published: about 4 years ago
10.3390/genes11111290
Platinum-Quality Mitogenome Haplotypes from United States Populations
Cited by: 14
Author(s): Cassandra R. Taylor, Kevin M. Kiesler, Kimberly Sturk-Andreaggi, J. Ring, Walther Parson, Moses S. Schanfield, Peter M. Vallone, Charla Marshall
Software Mentions: 3
Published: about 4 years ago
10.1590/1678-4685-GMB-2017-0075
Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarction
Cited by: 16
Author(s): Fan Lin, Heyu Meng, Xudong Guo, Xiangdong Li, F. Meng
Software Mentions: 3
Published: over 6 years ago
10.3390/genes10010009
Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management
Cited by: 44
Author(s): Stephanie J. Galla, Natalie Forsdick, Liz Brown, Marc P. Hoeppner, Michael Knapp, Richard F. Maloney, Roger Moraga, Anna W. Santure, Tammy E. Steeves
Software Mentions: 3
Published: almost 6 years ago
10.1186/s12915-021-01108-y
Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
Cited by: 14
Author(s): Nicole Gruenheit, Amy Baldwin, Balint Stewart, Sarah Jaques, Thomas Keller, Katie Parkinson, William Salvidge, Robert Baines, Chris Brimson, Jason B. Wolf, Rex L. Chisholm, Adrian J. Harwood, Christopher Thompson
Software Mentions: 3
Published: about 3 years ago
10.1186/s12915-021-01114-0
Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species
Cited by: 7
Author(s): Lianggang Huang, Xuejie Li, Lü Dong, Bin Wang, Li Pan
Software Mentions: 3
Published: about 3 years ago
10.1186/s12859-015-0775-x
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
Cited by: 21
Author(s): Jilong Li, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: about 9 years ago
10.3390/genes3030545
Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Cited by: 47
Author(s): Federica Torri, Ivo D. Dinov, Alen Zamanyan, Sam Hobel, Alex Genco, Petros Petrosyan, Andrew P. Clark, Zhizhong Liu, Paul Eggert, Jonathan Pierce, James A. Knowles, Joseph Ames, Carl Kesselman, Arthur W. Toga, Steven G. Potkin, Marquis P. Vawter, Fabìo Macciardi
Software Mentions: 3
Published: about 12 years ago
10.1042/BSR20203204
<i>FRZB</i> as a key molecule in abdominal aortic aneurysm progression affecting vascular integrity
Cited by: 6
Author(s): Chang‐Kyu Oh, Yeji Ko, Jeong-Jun Park, Hye Jin Heo, Junmo Kang, Eun Jung Kwon, Ji Wan Kang, Yoonsung Lee, Kyungjae Myung, Jin Mo Kang, Dai Sik Ko, Yun Hak Kim
Software Mentions: 3
Published: almost 4 years ago
10.1534/g3.116.032839
Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs
Cited by: 31
Author(s): Yi‐Fang Zhao, Ye Hou, Fei Liu, An Liu, Jing Lü, Changzhi Zhao, Yu Luan, Yuanxin Miao, Shuhong Zhao, Xinyun Li
Software Mentions: 3
Published: about 8 years ago
10.1534/g3.116.028290
Transcriptomic Analysis Identifies Candidate Genes and Gene Sets Controlling the Response of Porcine Peripheral Blood Mononuclear Cells to Poly I:C Stimulation
Cited by: 10
Author(s): Jiying Wang, Yanping Wang, Huaizhong Wang, Haifei Wang, Jianfeng Liu, Ying Wu, Jianfeng Guo
Software Mentions: 3
Published: over 8 years ago
10.3390/biom11050738
Metabolomics-Guided Hypothesis Generation for Mechanisms of Intestinal Protection by Live Biotherapeutic Products
Cited by: 11
Author(s): Jiayu Ye, Lauren A. E. Erland, Sandeep Singh Gill, Stephanie L. Bishop, Andrea Verdugo‐Meza, Susan J. Murch, Deanna L. Gibson
Software Mentions: 3
Published: over 3 years ago
10.1186/s12859-018-2318-8
Identification of differentially expressed genes by means of outlier detection
Cited by: 5
Author(s): Itziar Irigoien, C. Arenas
Software Mentions: 3
Published: about 6 years ago
10.1186/s12859-019-2683-y
RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets
Cited by: 17
Author(s): Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo, Claudia Coronnello
Software Mentions: 3
Published: over 5 years ago
10.1534/g3.114.012351
A New Dataset of Spermatogenic <i>vs.</i> Oogenic Transcriptomes in the Nematode <i>Caenorhabditis elegans</i>
Cited by: 138
Author(s): Marco Antonio Ortiz, Daniel Noble, Elena P. Sorokin, Judith Kimble
Software Mentions: 3
Published: about 10 years ago
10.3390/biom8040182
Identification of the Genetic Variation and Gene Exchange between Citrus Trifoliata and Citrus Clementina
Cited by: 4
Author(s): Tianjia Liu, Jingjing Zhou, Fa-Yi Chen, Zhi-Meng Gan, Yongping Li, Jin‐Zhi Zhang, Chun-Gen Hu
Software Mentions: 3
Published: almost 6 years ago
10.3390/biomedicines9070845
Serum miRNA Profiling for Early PDAC Diagnosis and Prognosis: A Retrospective Study
Cited by: 7
Author(s): Ada Aita, Caterina Millino, Cosimo Sperti, Beniamina Pacchioni, Mario Plebani, Cristiano De Pittà, Daniela Basso
Software Mentions: 3
Published: over 3 years ago
10.1534/g3.119.400431
Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize
Cited by: 25
Author(s): Sarah N. Anderson, Michelle C. Stitzer, Peng Zhou, Jeffrey Ross‐Ibarra, Cory D. Hirsch, Nathan M. Springer
Software Mentions: 3
Published: about 5 years ago
10.3390/genes11010053
SparkRA: Enabling Big Data Scalability for the GATK RNA-seq Pipeline with Apache Spark
Cited by: 7
Author(s): Zaid Al-Ars, Saiyi Wang, Hamid Mushtaq
Software Mentions: 3
Published: almost 5 years ago
10.3389/fnins.2020.00486
Periodicity Pitch Perception
Cited by: 2
Author(s): F. Klefenz, Tamás Harczos
Software Mentions: 3
Published: over 4 years ago
10.1155/2021/7326853
Identification of Genes Universally Differentially Expressed in Gastric Cancer
Cited by: 6
Author(s): Yidan Shi, Lishuang Qi, Haifeng Chen, Jiahui Zhang, Qingzhou Guan, Jun He, Meifeng Li, Zheng Guo, Haidan Yan, Ping Li
Software Mentions: 3
Published: almost 4 years ago
10.3389/fnins.2018.00587
BrainWave: A Matlab Toolbox for Beamformer Source Analysis of MEG Data
Cited by: 19
Author(s): Cecilia Jobst, Paul Ferrari, Silvia Isabella, Douglas Cheyne
Software Mentions: 3
Published: over 6 years ago
10.3389/fpsyg.2021.622433
Understanding the Multidimensional and Dynamic Nature of Facial Expressions Based on Indicators for Appraisal Components as Basis for Measuring Drivers' Fear
Cited by: 2
Author(s): Meng Zhang, Klas Ihme, Uwe Drewitz, Meike Jipp
Software Mentions: 3
Published: almost 4 years ago
10.1186/1471-2105-6-129
Considerations when using the significance analysis of microarrays (SAM) algorithm
Cited by: 110
Author(s): Ola Larsson, Claes Wahlestedt, James A. Timmons
Software Mentions: 3
Published: over 19 years ago
10.3389/fmicb.2017.01784
Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: about 7 years ago
10.1186/1471-2105-16-S7-S10
MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)
Cited by: 14
Author(s): Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, S. C. Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, Yingrui Li, Ruiqiang Li, Jun Wang, Xinhua Zhu, Shaoliang Peng, Tak Wah Lam
Software Mentions: 3
Published: over 9 years ago
10.1186/s12864-017-3679-5
Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies
Cited by: 21
Author(s): William W. Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J. Craig Venter, Chad Garner, Karen E. Nelson, Weizhong Li
Software Mentions: 3
Published: over 7 years ago
10.1186/s13062-016-0152-3
Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
Cited by: 14
Author(s): Suyan Tian, Howard H. Chang, Chi Wang
Software Mentions: 3
Published: about 8 years ago
10.1186/s12859-019-2903-5
A comparison of three programming languages for a full-fledged next-generation sequencing tool
Cited by: 10
Author(s): Pascal Costanza, Charlotte Herzeel, Wilfried Verachtert
Software Mentions: 3
Published: over 5 years ago
10.1093/bioinformatics/btu205
ReadXplorer—visualization and analysis of mapped sequences
Cited by: 94
Author(s): Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
Software Mentions: 3
Published: over 10 years ago
10.1186/1471-2164-10-361
Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae)
Cited by: 18
Author(s): Richard H. Baker, Jenna Morgan, Xianhui Wang, Jeffrey L. Boore, Gerald S. Wilkinson
Software Mentions: 3
Published: almost 16 years ago
10.1186/1471-2105-14-143
Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis
Cited by: 23
Author(s): Lifang Zhang, Juan Zhang, Gang Yang, Di Wu, Lina Jiang, Zhining Wen, Menglong Li
Software Mentions: 3
Published: over 11 years ago
10.1093/bioinformatics/btaa707
The optimal discovery procedure for significance analysis of general gene expression studies
Cited by: 1
Author(s): Andrew J. Bass, J. Douglas Storey
Software Mentions: 3
Published: over 4 years ago
10.1093/bioinformatics/bty338
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs
Cited by: 49
Author(s): Matthew B. Stocks, Irina Mohorianu, Matthew Beckers, Claudia Paicu, Simon Moxon, Joshua Thody, Tamás Dalmay, Vincent Moulton
Software Mentions: 3
Published: over 6 years ago
10.3389/fmed.2020.615306
Integrative Informatics Analysis of Transcriptome and Identification of Interacted Genes in the Glomeruli and Tubules in CKD
Cited by: 5
Author(s): Lingyun Liu, Fuzhe Ma, Yuanyuan Hao, Zhengzi Yi, Xiaoxia Yu, Bo Xu, Chengguo Wei, Jinghai Hu
Software Mentions: 3
Published: almost 4 years ago
10.3389/fimmu.2018.00497
Overall Downregulation of mRNAs and Enrichment of H3K4me3 Change Near Genome-Wide Association Study Signals in Systemic Lupus Erythematosus: Cell-Specific Effects
Cited by: 11
Author(s): Zhe Zhang, Lei Shi, Li Song, Kelly Maurer, Michele A. Petri, Kathleen E. Sullivan
Software Mentions: 3
Published: over 6 years ago
10.3389/fmicb.2015.00850
Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality
Cited by: 20
Author(s): Shahzad Ali, Jonathan Shao, Mary D. Strem, Wilbert Phillips‐Mora, David Zhang, Lyndel W. Meinhardt, Bryan A. Bailey
Software Mentions: 3
Published: about 9 years ago
10.3389/fvets.2019.00308
A Pine Enhanced Biochar Does Not Decrease Enteric CH4 Emissions, but Alters the Rumen Microbiota
Cited by: 24
Author(s): Stephanie A. Terry, Gabriel de Oliveira Ribeiro, Robert J. Gruninger, A. V. Chaves, K. A. Beauchemin, E. K. Okine, Tim A. McAllister
Software Mentions: 3
Published: about 5 years ago
10.1093/bioinformatics/btab102
Genozip: a universal extensible genomic data compressor
Cited by: 15
Author(s): Divon Mordechai Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas
Software Mentions: 3
Published: almost 4 years ago
10.3389/fnhum.2013.00076
BOLD Responses in Human Primary Visual Cortex are Insensitive to Substantial Changes in Neural Activity
Cited by: 32
Author(s): Jennifer B. Swettenham, Suresh Muthukumaraswamy, Krish Devi Singh
Software Mentions: 3
Published: almost 12 years ago
10.1186/1471-2105-9-144
Empirical Bayes analysis of single nucleotide polymorphisms
Cited by: 21
Author(s): Holger Schwender, Katja Ickstadt
Software Mentions: 3
Published: over 16 years ago
10.1186/s12864-018-4510-7
Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster
Cited by: 30
Author(s): Michael P. Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay, A. Gregory Matera
Software Mentions: 3
Published: over 6 years ago
10.3389/fimmu.2019.01384
The Rheumatoid Arthritis Risk Gene AIRE Is Induced by Cytokines in Fibroblast-Like Synoviocytes and Augments the Pro-inflammatory Response
Cited by: 12
Author(s): Beatrice Bergström, Christina Lundqvist, Georgios K. Vasileiadis, Hans Carlsten, Olov Ekwall, Anna-Karin Hultgård Ekwall
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2164-10-467
An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)
Cited by: 59
Author(s): Albert Mascarell-Creus, Joaquı́n Cañizares, Josep Vilarrasa-Blasi, Santiago Mora-Garcı́a, José Blanca, Daniel González-Ibeas, Montserrat Saladié, Cristina Roig, Wim Deleu, Belén Picó-Silvent, Núria López‐Bigas, Miguel A. Aranda, Jordi García-Más, F. Nuez, Pere Puigdomènech, Ana I. Caño‐Delgado
Software Mentions: 3
Published: about 15 years ago
10.1002/ece3.646
Environmental effects on molecular and phenotypic variation in populations of<i>Eruca sativa</i>across a steep climatic gradient
Cited by: 31
Author(s): Erik Westberg, Shachar Ohali, Anatoly Shevelevich, Pinchas Fine, Oz Barazani
Software Mentions: 3
Published: over 11 years ago
10.1186/1471-2105-14-220
NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data
Cited by: 15
Author(s): Xinyun Ma, Xuegong Zhang
Software Mentions: 3
Published: over 11 years ago
10.1002/ece3.4504
Methylation divergence of invasive<i>Ciona</i>ascidians: Significant population structure and local environmental influence
Cited by: 17
Author(s): Ping Ni, Shiguo Li, Ya‐Ping Lin, Wei Xiong, Xuena Huang, Aibin Zhan
Software Mentions: 3
Published: about 6 years ago
10.1002/ece3.2213
Is individual consistency in body mass and reproductive decisions linked to individual specialization in foraging behavior in a long‐lived seabird?
Cited by: 13
Author(s): Nina Dehnhard, Marcel Eens, Nicolas Sturaro, Gilles Lepoint, Laurent Demongin, Petra Quillfeldt, Maud Poisbleau
Software Mentions: 3
Published: over 8 years ago
10.3389/fimmu.2020.01481
Pediatric Burn Survivors Have Long-Term Immune Dysfunction With Diminished Vaccine Response
Cited by: 8
Author(s): Blair Z. Johnson, Sonia McAlister, Helen M. McGuire, Vetrichevvel Thirthar Palanivelu, Andrew Stevenson, Peter Richmond, Debra J. Palmer, Jessica Metcalfe, Susan L. Prescott, Fiona Wood, Barbara Fazekas de St Groth, Matthew D. Linden, Mark W. Fear, Vanessa S. Fear
Software Mentions: 3
Published: over 4 years ago
10.15252/emmm.202013901
Glycolysis downregulation is a hallmark of HIV‐1 latency and sensitizes infected cells to oxidative stress
Cited by: 23
Author(s): Iart Luca Shytaj, Francesco A. Procopio, Mohammad Tarek, Irene Carlón-Andrés, Hsin‐Yao Tang, Aaron R. Goldman, MohamedHusen Munshi, Virender Kumar Pal, Mattia Forcato, Sheetal Sreeram, Konstantin Leskov, Fengchun Ye, Bojana Lucic, Nicolly Cruz, Lishomwa C. Ndhlovu, Silvio Bicciato, Sergi Padilla‐Parra, Ricardo Sobhie Diaz, Amit Singh, Marina Lušić, Jonathan Karn, David Alvarez-Carbonell, Andrea Savarino
Software Mentions: 3
Published: over 3 years ago
10.1186/s13637-015-0034-5
Gene expression analysis supports tumor threshold over 2.0 cm for T-category breast cancer
Cited by: 2
Author(s): Hiroko Kato Solvang, Arnoldo Frigessi, Fatemeh Kaveh, Margit Riis, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen, Bettina Kulle Andreassen
Software Mentions: 3
Published: almost 9 years ago
10.1186/s13040-016-0095-3
Visual programming for next-generation sequencing data analytics
Cited by: 13
Author(s): Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
Software Mentions: 3
Published: over 8 years ago
10.1186/1746-1596-9-142
NF-κB signaling and vesicle transport are correlated with the reactivation of the memory trace of morphine dependence
Cited by: 9
Author(s): Junyi Ye, Zhaoyang Yang, Candong Li, Meimei Cai, Daizhan Zhou, Qin Zhang, Wei Y, Ting Wang, Yun Liu
Software Mentions: 3
Published: over 10 years ago
10.1186/1752-0509-8-S1-S5
Detection of type 2 diabetes related modules and genes based on epigenetic networks
Cited by: 6
Author(s): Liu Hui, Tongtong Wang, Hongbo Liu, Yanjun Wei, Guofeng Zhao, Jianzhong Su, Qiong Wu, Hong Qiao, Yan Zhang
Software Mentions: 3
Published: almost 11 years ago