10.1111/tpj.12307

Resistance gene enrichment sequencing (<scp>R</scp>en<scp>S</scp>eq) enables reannotation of the <scp>NB</scp>‐<scp>LRR</scp> gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Cited by: 327
Author(s): Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan MacLean, Peter J. A. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D. G. Jones
Software Mentions: 3
Published: over 12 years ago

10.1128/JVI.01869-20

The Human Adenovirus 2 Transcriptome: an Amazing Complexity of Alternatively Spliced mRNAs
Cited by: 11
Author(s): Amanda Westergren Jakobsson, Bo Segerman, Ola Wallerman, Sara Bergström Lind, Hongxing Zhao, Carl-Johan Rubin, Ulf Pettersson, Göran Akusjärvi
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.7156

Spread of the non-native anemone <i>Anemonia alicemartinae</i> Häussermann &amp; Försterra, 2001 along the Humboldt-current large marine ecosystem: an ecological niche model approach
Cited by: 7
Author(s): Javier Pinochet, Reinaldo Rivera, Paula E. Neill, Antonio Brante, Cristián E. Hernández
Software Mentions: 3
Published: almost 7 years ago

10.1515/jib-2018-0080

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer
Cited by: 0
Author(s): Nimisha Asati, Abhinav Mishra, Ayush Shukla, Tiratha Raj Singh
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-6-173

Normal uniform mixture differential gene expression detection for cDNA microarrays
Cited by: 74
Author(s): Nema Dean, Adrian E. Raftery
Software Mentions: 3
Published: almost 21 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

10.1186/1476-9255-7-50

TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients
Cited by: 26
Author(s): Ju X Huang, Lin Wang, Meng Ji
Software Mentions: 3
Published: over 15 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: about 11 years ago

10.7150/ijms.51743

Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland
Cited by: 5
Author(s): Yi Zheng, Hao Jiang, Hao-Qi Wang, Haixiang Guo, Dong-Xu Han, Yongping Huang, Yan Gao, Bao Yuan
Software Mentions: 3
Published: over 5 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/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

10.1038/s42003-020-0775-x

Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology
Cited by: 24
Author(s): Qiushi Liu, Jing Lei, Alistair C. Darby, Tatsuhiko Kadowaki
Software Mentions: 3
Published: over 6 years ago

10.1186/s13071-016-1341-8

Reconstruction of the insulin-like signalling pathway of Haemonchus contortus
Cited by: 14
Author(s): Namitha Mohandas, Min Hu, Andreas J. Stroehlein, Neil D. Young, Paul W. Sternberg, James B. Lok, Robin B. Gasser
Software Mentions: 3
Published: over 10 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

10.1155/2013/610297

Power and Stability Properties of Resampling-Based Multiple Testing Procedures with Applications to Gene Oncology Studies
Cited by: 12
Author(s): Dongmei Li, Timothy D. Dye
Software Mentions: 3
Published: over 13 years ago

10.7717/peerj.4040

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples
Cited by: 19
Author(s): Zeeshan Ahmed, Duygu Ucar
Software Mentions: 3
Published: over 8 years ago

10.3892/ijo.2014.2648

Microarray phosphatome profiling of breast cancer patients unveils a complex phosphatase regulatory role of the MAPK and PI3K pathways in estrogen receptor-negative breast cancers
Cited by: 13
Author(s): Ramón González Manzano, E. Martinez-Navarro, Jerónimo Forteza, Antonio Brugarolas
Software Mentions: 3
Published: over 11 years ago

10.3390/s18020474

Design and Implementation of Cloud-Centric Configuration Repository for DIY IoT Applications
Cited by: 37
Author(s): Shabir Ahmad, Hang Lei, Do‐Hyeun Kim
Software Mentions: 3
Published: over 8 years ago

10.3390/s18051465

Smart Waste Collection System with Low Consumption LoRaWAN Nodes and Route Optimization
Cited by: 48
Author(s): Álvaro Lozano, Javier Caridad, Juan F. De Paz, Gabriel Villarrubia González, Javier Bajo
Software Mentions: 3
Published: about 8 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

10.3390/s17030578

Assessing the Spectral Properties of Sunlit and Shaded Components in Rice Canopies with Near-Ground Imaging Spectroscopy Data
Cited by: 21
Author(s): Kai Zhou, Xinqiang Deng, Xia Yao, Yongchao Tian, Weixing Cao, Yan Zhu, Susan L. Ustin, Tao Cheng
Software Mentions: 3
Published: about 9 years ago

10.3390/s18124330

Variational Pansharpening for Hyperspectral Imagery Constrained by Spectral Shape and Gram–Schmidt Transformation
Cited by: 10
Author(s): Z. J. Huang, Qihao Chen, Xiuguo Liu
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-95698-w

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients
Cited by: 9
Author(s): Kota Fujisawa, Mamoru Shimo, Y-h. Taguchi, Shinya Ikematsu, Ryota Miyata
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-93555-4

The conserved ASTN2/BRINP1 locus at 9q33.1–33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain
Cited by: 1
Author(s): Josep Pol-Fuster, Francesca Cañellas, Laura Ruiz-Guerra, Aina Medina-Dols, Bàrbara Bisbal-Carrió, Bernat Ortega-Vila, Jaume Llinàs, Jessica Hernández-Rodríguez, Jerònia Lladó, Gabriel Olmos, Konstantin Strauch, Damián Heine-Suñer, Cristòfol Vives-Bauzà, Antònia Flaquer
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-94396-x

Niche partitioning among dead wood-dependent beetles
Cited by: 1
Author(s): Jakub Horák
Software Mentions: 3
Published: almost 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

10.3390/s100301967

A Comparison of Spectral Angle Mapper and Artificial Neural Network Classifiers Combined with Landsat TM Imagery Analysis for Obtaining Burnt Area Mapping
Cited by: 102
Author(s): George P. Petropoulos, Krishna Prasad Vadrevu, Gavriil Xanthopoulos, G. Karantounias, Marko Scholze
Software Mentions: 3
Published: about 16 years ago

10.1038/s41598-021-90243-1

Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infection
Cited by: 17
Author(s): Miroslava Čuperlović-Culf, Emma Cunningham, Hossen Teimoorinia, Anuradha Surendra, Xiaobei Pan, Steffany A. L. Bennett, Mijin Jung, Bernadette McGuiness, Anthony Peter Passmore, David Beverland, Brian D. Green
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-83459-8

Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
Cited by: 5
Author(s): M. Joseph Tomlinson, Shawn W. Polson, Jing Qiu, Juniper A. Lake, William Lee, Behnam Abasht
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: almost 5 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: about 18 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

10.1038/s41598-020-76533-0

High definition transcranial direct current stimulation modulates abnormal neurophysiological activity in post-stroke aphasia
Cited by: 16
Author(s): Priyanka P. Shah-Basak, Gayatri Sivaratnam, Selina Teti, Alexander Francois-Nienaber, Maryam Yossofzai, Sabrina E M Armstrong, Sumiti Nayar, Regina Jokel, Jed A. Meltzer
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-77600-2

Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici
Cited by: 4
Author(s): Pingyong Wang, Xiuhong Xu, Guangwei Zhao, Yue He, C. T. Hou, Weihu Kong, Jian Zhang, Shuimiao Liu, Yong Xu, Zhigao Xu
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: over 16 years ago

10.1038/s41598-020-74877-1

Low E2F2 activity is associated with high genomic instability and PARPi resistance
Cited by: 4
Author(s): Jonathan Rennhack, Eran R. Andrechek
Software Mentions: 3
Published: over 5 years ago

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: over 7 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

10.1186/1471-2105-14-220

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

10.1038/s41598-021-92395-6

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction
Cited by: 1
Author(s): Tai Tsun Wu, Jian Liu, Zhiye Guo, Jie Hou, Jianlin Cheng
Software Mentions: 3
Published: almost 5 years ago

10.1038/srep39487

Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach
Cited by: 24
Author(s): Li Li, Ilana Greene, Benjamin Readhead, Madhav C. Menon, Brian Kidd, Andrew Uzilov, Chengguo Wei, Nimrod Philippe, Bernd Schröppel, John Cijiang He, Rong Chen, Joel T. Dudley, Barbara Murphy
Software Mentions: 3
Published: over 9 years ago

10.1038/srep41238

Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity
Cited by: 43
Author(s): Yukti Choudhury, Yi‐Chin Toh, Jiangwa Xing, Yinghua Qu, Jonathan Poh, Huan Li, Hui Shan Tan, Ravindran Kanesvaran, Hanry Yu, Min‐Han Tan
Software Mentions: 3
Published: over 9 years ago

10.1038/srep37563

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
Cited by: 21
Author(s): Marcus Davidsson, Paula Díaz-Fernández, Oliver D. Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Software Mentions: 3
Published: over 9 years ago

10.1038/srep32965

Predicting the synergy of multiple stress effects
Cited by: 157
Author(s): Matthias Liess, Kaarina Foit, Saskia Knillmann, Ralf B. Schäfer, Hans-Dieter Ließ
Software Mentions: 3
Published: over 9 years ago

10.1038/srep38096

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)
Cited by: 81
Author(s): Fang-Nong Lai, Hong-Li Zhai, Ming Cheng, Jun‐Yu Ma, Shun‐Feng Cheng, Wei Ge, Guoliang Zhang, Junjie Wang, Ruiqian Zhang, Xue Wang, Min Liu, Jiuzhou Song, Wei Shen
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-020-65724-4

Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database
Cited by: 6
Author(s): Yinan Zhang, Qinfeng Qu, RAO Mingzhen, Zhang Nana, Yu Zhao, Fei Tao
Software Mentions: 3
Published: about 6 years ago

10.1038/srep27623

Multiplex giant magnetoresistive biosensor microarrays identify interferon-associated autoantibodies in systemic lupus erythematosus
Cited by: 31
Author(s): J. Lee, D. James Haddon, Hannah Wand, J. M. Price, Vivian K. Diep, Drew A. Hall, Michelle Petri, Emily C. Baechler, Imelda Balboni, Paul J. Utz, Shan X. Wang
Software Mentions: 3
Published: almost 10 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

10.1186/s12864-015-1975-5

Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
Cited by: 32
Author(s): Elizabeth Hénaff, Luís Zapata, Josep M. Casacuberta, Stephan Ossowski
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-9-85

Statistical issues in the analysis of Illumina data
Cited by: 91
Author(s): Mark J. Dunning, Nuno L. Barbosa‐Morais, Andy G. Lynch, Simon Tavaré, Matthew E. Ritchie
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pone.0219551

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes
Cited by: 16
Author(s): Han-Ming Liu, Dan Yang, Zhao-Fa Liu, Shengzhou Hu, Yan Shen-hai, Xian-Wen He
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-93893-3

Microarray-based selection of a serum biomarker panel that can discriminate between latent and active pulmonary TB
Cited by: 6
Author(s): Zhihui Li, Jianjun Hu, Pengchong Liu, Dan Cui, Hongqin Di, Shucai Wu
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.17903

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Cited by: 32
Author(s): Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates, Péter L. Nagy, Liang Tong, Songtao Jia
Software Mentions: 3
Published: over 9 years ago

10.1186/1755-8794-3-32

A sequence-based approach to identify reference genes for gene expression analysis
Cited by: 39
Author(s): Raj Chari, Kim M. Lonergan, Larissa A. Pikor, Bradley P. Coe, Chang-Qi Zhu, Tommy H.T. Chan, Calum MacAulay, Ming‐Sound Tsao, Stephen Lam, Raymond T. Ng, Wan L. Lam
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12864-015-1670-6

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites
Cited by: 31
Author(s): Jason S. Cumbie, Maria G. Ivanchenko, Molly Megraw
Software Mentions: 3
Published: almost 11 years ago

10.1002/prot.25697

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
Cited by: 142
Author(s): Jie Hou, Tai Tsun Wu, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-019-5502-y

Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes
Cited by: 2
Author(s): Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang, Zheng Guo
Software Mentions: 3
Published: over 7 years ago

10.1016/j.mcpro.2021.100125

Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network
Cited by: 6
Author(s): Cristian V. A. Munteanu, Gabriela Chirițoiu, Marioara Chirițoiu, Simona Ghenea, Andrei-José Petrescu, Ștefana M. Petrescu
Software Mentions: 3
Published: over 5 years ago

10.1029/2019RG000686

Spaceborne Cloud and Precipitation Radars: Status, Challenges, and Ways Forward
Cited by: 65
Author(s): Alessandro Battaglia, Pavlos Kollias, Ranvir Dhillon, Richard Roy, Simone Tanelli, Katia Lamer, Mircea Grecu, Matthew Lebsock, Daniel Watters, Kamil Mróz, Gerald M. Heymsfield, Lihua Li, Katsuko Furukawa
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.ppat.1005943

Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
Cited by: 21
Author(s): Janet C. Lindow, Elsio A. Wunder, Stephen J. Popper, Jinsoo Min, Praveen Mannam, Anup Srivastava, Yi Yao, Kathryn P. Hacker, Khadir Raddassi, Patty J Lee, Ruth R. Montgomery, Albert C. Shaw, José E. Hagan, Guilherme C. Araújo, Nívison Nery, David A. Relman, Charles C. Kim, Mitermayer Galvão dos Reis, Albert I. Ko
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.ppat.1009175

Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response
Cited by: 5
Author(s): Qi Wang, Nadia Shakoor, Adam Boyher, Kira M. Veley, Jeffrey C. Berry, Todd C. Mockler, Rebecca Bart
Software Mentions: 3
Published: over 5 years ago

10.1093/jxb/erx010

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Cited by: 48
Author(s): Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jérôme Verdier, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 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

10.1093/jxb/erx349

Transfer of a starch phenotype from wild wheat to bread wheat by deletion of a locus controlling B-type starch granule content
Cited by: 21
Author(s): Tansy Chia, Nikolai M Adamski, Benedetta Saccomanno, Andrew J. Greenland, Alastair Nash, Cristóbal Uauy, Kay Trafford
Software Mentions: 3
Published: almost 9 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in <i>Arabidopsis</i>
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: about 6 years ago

10.1038/s41597-020-0427-5

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
Cited by: 35
Author(s): Joan Mas-Lloret, Mireia Obón-Santacana, Gemma Ibáñez‐Sanz, Elisabet Guinó, Miguel L Pato, Francisco Rodríguez-Moranta, Alfredo Mata, Ana García-Rodríguez, Vı́ctor Moreno, Ville N. Pimenoff
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2105-15-79

The characteristic direction: a geometrical approach to identify differentially expressed genes
Cited by: 142
Author(s): Neil R. Clark, Kevin Hu, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma’ayan
Software Mentions: 3
Published: about 12 years ago

10.1029/2020MS002138

Clouds and Convective Self‐Aggregation in a Multimodel Ensemble of Radiative‐Convective Equilibrium Simulations
Cited by: 69
Author(s): Allison A. Wing, Catherine L. Stauffer, Tobias Becker, Kevin A. Reed, Min‐Seop Ahn, Nathan Arnold, Sandrine Bony, Mark Branson, G. H. Bryan, Jean‐Pierre Chaboureau, Stephan R. de Roode, Gayatri Kulkarni, Cathy Hohenegger, I‐Kuan Hu, Fredrik Jansson, Todd R. Jones, Marat Khairoutdinov, Dae Hyun Kim, Zane Martin, Shuhei Matsugishi, Brian Medeiros, Hiroaki Miura, Yumin Moon, Sebastian K. Müller, Tomoki Ohno, Max Popp, Thara Prabhakaran, David A. Randall, Rosimar Ríos-Berríos, Nicolas Rochetin, Romain Roehrig, David M. Romps, James H. Ruppert, Masaki Satoh, Levi G. Silvers, Martin S. Singh, Björn Stevens, Lorenzo Tomassini, Chiel C. van Heerwaarden, Shuguang Wang, Ming Zhao
Software Mentions: 3
Published: almost 6 years ago

10.3390/microorganisms9091845

High Throughput Analysis Reveals Changes in Gut Microbiota and Specific Fecal Metabolomic Signature in Hematopoietic Stem Cell Transplant Patients
Cited by: 3
Author(s): Soumaya Kouidhi, Nessrine Souai, Oumaima Zidi, Ahmed Mosbah, Amel Lakhal, Tarek Ben Othmane, Dorra Belloumi, Farhat Ben Ayed, Elias Asimakis, Panagiota Stathopoulou, Ameur Chérif, George Tsiamis
Software Mentions: 3
Published: almost 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

10.1007/s13361-016-1544-4

Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging
Cited by: 37
Author(s): Sha Lou, Benjamin Balluff, Arjen H.G. Cleven, Judith V.M.G. Bovée, Liam A. McDonnell
Software Mentions: 3
Published: over 9 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

10.1186/1471-2105-15-S1-S2

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Cited by: 11
Author(s): Marco Masseroli, Barend Mons, Erik Bongcam‐Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
Software Mentions: 3
Published: over 12 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

10.3390/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

10.1120/jacmp.v17i3.6370

2016 AAPM Spring Clinical Meeting - Abstracts
Cited by: 0
Author(s):
Software Mentions: 3
Published: about 10 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

10.3390/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/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

10.3390/metabo11090627

Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer
Cited by: 0
Author(s): Nathalie Nguyen, Meifang Yu, Vinit Y. Reddy, Ariana Carolina Acevedo-Diaz, Enzo C. Mesarick, Joseph Abi Jaoude, Min Yuan, John M. Asara, Cullen M. Taniguchi
Software Mentions: 3
Published: over 4 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

10.1534/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

10.1534/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

10.3758/s13421-020-01082-w

The simultaneous recognition of multiple words: A process analysis
Cited by: 4
Author(s): Anne Voormann, Mikhail S. Spektor, Karl Christoph Klauer
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-8-346

A framework for significance analysis of gene expression data using dimension reduction methods
Cited by: 41
Author(s): Lars Gidskehaug, Endre Anderssen, Arnar Flatberg, Bjørn K. Alsberg
Software Mentions: 3
Published: over 18 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: almost 12 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

10.3389/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

10.1186/1471-2164-9-333

Structure and properties of transcriptional networks driving selenite stress response in yeasts
Cited by: 74
Author(s): Hélène Salin, Vivienne Fardeau, Eugenia Piccini, Gaëlle Lelandais, Véronique Tanty, Sophie Lemoine, Claude Jacq, Frédéric Devaux
Software Mentions: 3
Published: almost 18 years ago

10.1186/1471-2105-15-S1-S7

Reducing bias in RNA sequencing data: a novel approach to compute counts
Cited by: 39
Author(s): Francesca Finotello, Enrico Lavezzo, Luca Bianco, Luisa Barzon, Paolo Emilio Mazzon, Paolo Fontana, Stefano Toppo, Barbara Di Camillo
Software Mentions: 3
Published: over 12 years ago

10.3389/fpsyt.2021.685656

Metabolic Profiling Indicates Diversity in the Metabolic Physiologies Associated With Maternal Postpartum Depressive Symptoms
Cited by: 4
Author(s): Emma Bränn, Christina J. Malavaki, Emma Fransson, Maria-Konstantina Ioannidi, Hanna Henriksson, Fotios C. Papadopoulos, George P. Chrousos, Maria I. Klapa, Alkistis Skalkidou
Software Mentions: 3
Published: almost 5 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

10.1186/1471-2105-12-13

A Platform for Processing Expression of Short Time Series (PESTS)
Cited by: 16
Author(s): Ayan Sinha, Marianthi Markatou
Software Mentions: 3
Published: over 15 years ago

10.1186/s12864-017-4430-y

The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes
Cited by: 38
Author(s): Deepak Kumar Gupta, Martin Rühl, Bagdevi Mishra, Vanessa Kleofas, Martin Hofrichter, Robert Herzog, Marek J. Pecyna, Rahul Sharma, Harald Kellner, Florian Hennicke, Marco Thines
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-8-157

Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures
Cited by: 21
Author(s): Xin Lü, David L. Perkins
Software Mentions: 3
Published: about 19 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: almost 12 years ago