cran: SAM | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giy168

Newde novoassembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing
Cited by: 5
Author(s): Karine A. Martinez-Viaud, Cindy Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St. Leger, Jennie Le, Aparna Natarajan, Marlem Rivera, Marbie Guillergan, Erich B. Jaeger, Brian Steffy, Aleksey V. Zimin
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giz040

Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls
Cited by: 41
Author(s): Brent S. Pedersen, Aaron R. Quinlan
Software Mentions: 3
Published: about 7 years ago

10.1093/gigascience/giab008

Twelve years of SAMtools and BCFtools
Cited by: 3,237
Author(s): Petr Danecek, James K. Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M. Keane, Shane McCarthy, Robert M. Davies, Heng Li
Software Mentions: 3
Published: over 5 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: almost 6 years ago

10.1186/1471-2164-13-74

GemSIM: general, error-model based simulator of next-generation sequencing data
Cited by: 141
Author(s): Kerensa McElroy, Fabio Luciani, Torsten Thomas
Software Mentions: 3
Published: over 14 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: over 7 years ago

10.1186/s13073-020-00809-3

Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier
Cited by: 49
Author(s): Eiru Kim, Traver Hart
Software Mentions: 3
Published: over 5 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: almost 15 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: over 15 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: about 11 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: about 10 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: over 12 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: almost 14 years ago

10.1186/gm130

Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes
Cited by: 228
Author(s): Iain J. Gallagher, Camilla Schéele, Pernille Keller, Annemette Nielsen, Judit Reményi, Christian P. Fischer, Karim Roder, John Babraj, Claes Wahlestedt, György Hutvágner, Bente Klarlund Pedersen, James A. Timmons
Software Mentions: 3
Published: over 16 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: about 19 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 7 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: about 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: over 11 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: over 11 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: over 12 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: almost 5 years ago

10.1186/s12859-020-3388-y

ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles
Cited by: 64
Author(s): Xudong Zhao, Qing Jiao, Hangyu Li, Yiming Wu, Hanxu Wang, Shan Huang, Guohua Wang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-021-02270-w

simATAC: a single-cell ATAC-seq simulation framework
Cited by: 12
Author(s): Zeinab Navidi, Lin Zhang, Bo Wang
Software Mentions: 3
Published: over 5 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: over 5 years ago

10.1186/s12864-015-1293-y

Genome-wide survey and expression analysis of F-box genes in chickpea
Cited by: 59
Author(s): Shefali Gupta, Vanika Garg, Chandra Kant, Sabhyata Bhatia
Software Mentions: 3
Published: over 11 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: over 14 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 6 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: over 16 years ago

10.1128/mBio.01568-20

Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
Cited by: 26
Author(s): Shirley E. Braspenning, Tomohiko Sadaoka, Judith Breuer, Georges M. G. M. Verjans, Werner J. D. Ouwendijk, Daniel P. Depledge
Software Mentions: 3
Published: over 5 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: almost 6 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: almost 14 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: over 7 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: over 8 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: over 14 years ago

10.1007/s00251-014-0820-3

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics
Cited by: 15
Author(s): Wouter J. Veneman, Jan de Sonneville, Kees-Jan van der Kolk, Anita Ordas, Zaid Al-Ars, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: almost 9 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: almost 10 years ago

10.1186/1476-4598-12-140

Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Cited by: 53
Author(s): Ângela Aguirres Fachel, Ana Carolina Tahira, Santiago A. Vilella-Arias, Vinicius Maracaja‐Coutinho, Etel Rp Gimba, Giselle Maria Vignal, Franz Campos, Eduardo M. Reis, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: over 12 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: over 11 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: over 11 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: over 12 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: over 21 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: about 14 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: about 5 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: over 13 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: over 13 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: over 13 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: over 21 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: almost 5 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: over 4 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: over 15 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: over 10 years ago

10.1042/BSR20203204

FRZB 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: over 5 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: over 19 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: over 14 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: almost 5 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: almost 6 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: about 5 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: over 5 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 8 years ago

10.1186/s12859-018-2318-8

Identification of differentially expressed genes by means of outlier detection
Cited by: 5
Author(s): Itziar Irigoien, C. Arenas
Software Mentions: 3
Published: over 7 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: about 7 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: over 6 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: over 7 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: almost 5 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: over 14 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: almost 14 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: over 6 years ago

10.1186/s12859-015-0812-9

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles
Cited by: 5
Author(s): Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-9-446

Molecular architecture of the fruit fly's airway epithelial immune system
Cited by: 58
Author(s): Christina Wagner, Kerstin Isermann, Heinz Fehrenbach, Thomas Roeder
Software Mentions: 3
Published: over 17 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: over 5 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: about 21 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: 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: about 9 years ago

10.1186/s13062-016-0152-3

Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
Cited by: 14
Author(s): Suyan Tian, Howard H. Chang, Chi Wang
Software Mentions: 3
Published: over 9 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: about 7 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: over 7 years ago

10.1534/g3.111.000240

Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
Cited by: 1,474
Author(s): Julian M. Catchen, Angel Amores, Paul A. Hohenlohe, William A. Cresko, John H. Postlethwait
Software Mentions: 3
Published: almost 15 years ago

10.1534/g3.114.012351

A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegans
Cited by: 138
Author(s): Marco Antonio Ortiz, Daniel Noble, Elena P. Sorokin, Judith Kimble
Software Mentions: 3
Published: almost 12 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: over 17 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: about 13 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: over 6 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: almost 6 years ago

10.3389/fnins.2020.00486

Periodicity Pitch Perception
Cited by: 2
Author(s): F. Klefenz, Tamás Harczos
Software Mentions: 3
Published: about 6 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: about 8 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: almost 8 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: over 5 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: about 10 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: over 5 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: almost 11 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: over 5 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 8 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: over 8 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: about 8 years ago

10.3389/fimmu.2020.595877

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors
Cited by: 5
Author(s): Vladimir A. Veselovsky, Marina S. Dyachkova, Egor Menyailo, Polina S. Polyaeva, Evgenii I. Olekhnovich, Egor Shitikov, Dmitry Bespiatykh, Tatiana A. Semashko, Artem S. Kasianov, Elena N. Ilina, В Н Даниленко, Ksenia M. Klimina
Software Mentions: 3
Published: over 5 years ago

10.1186/ar2855

Insights in to the pathogenesis of axial spondyloarthropathy based on gene expression profiles
Cited by: 45
Author(s): Srilakshmi M Sharma, Dongseok Choi, Stephen R. Planck, Christina A. Harrington, Carrie R. Austin, J. A. Lewis, Tessa N. Diebel, Tammy M. Martin, Justine R. Smith, James T. Rosenbaum
Software Mentions: 3
Published: over 17 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: almost 6 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: almost 13 years ago

10.3389/fimmu.2020.01475

Small RNA Deep Sequencing Identifies a Unique miRNA Signature Released in Serum Exosomes in a Mouse Model of Sjögren's Syndrome
Cited by: 8
Author(s): Shruti Singh Kakan, Srikanth Reddy Janga, Benjamin Cooperman, David W. Craig, Maria C. Edman, Curtis T. Okamoto, Sarah F. Hamm‐Alvarez
Software Mentions: 3
Published: almost 6 years ago

10.1186/1752-0509-7-S2-S9

Identifying novel glioma associated pathways based on systems biology level meta-analysis
Cited by: 10
Author(s): Yangfan Hu, Jinquan Li, Wenying Yan, Jiajia Chen, Yin Li, Guang Hu, Bairong Shen
Software Mentions: 3
Published: over 13 years ago

Projects: cran: SAM

Science Score: 85/100

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Penalties:

Papers Mentioning SAM 4,566