10.1186/s12864-017-4374-2

A survey on cellular RNA editing activity in response to Candida albicans infections
Cited by: 3
Author(s): Yao‐Wei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Zhong Wu, Xuan Li, Chen Chen, Pei Hao
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: over 8 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

10.1186/1471-2164-15-337

Transcriptome differences between two sister desert poplar species under salt stress
Cited by: 36
Author(s): Jian Zhang, Jiexiong Feng, Jing Lü, Yongzhi Yang, Xu Zhang, Dongshi Wan, Jianquan Liu
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-020-6570-8

MicroRNA expression profile analysis in sperm reveals hsa-mir-191 as an auspicious omen of in vitro fertilization
Cited by: 37
Author(s): Hua Xu, Xin Wang, Zhikai Wang, Jianhui Li, Zhiming Xu, Maohua Miao, Guowu Chen, Xiang-Dong Lei, Jun Wu, Huijuan Shi, Ke Wang, Tiancheng Zhang, Xiaoxi Sun
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4521-4

Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species
Cited by: 20
Author(s): Yan Zhong, Xiaohui Zhang, Zong‐Ming Cheng
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-019-5556-x

Linear models enable powerful differential activity analysis in massively parallel reporter assays
Cited by: 272
Author(s): Leslie Myint, Dimitrios Avramopoulos, Loyal A. Goff, Kasper D. Hansen
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-07151-3

Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production
Cited by: 3
Author(s): Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Yangji Cidan, Xiaoying Chen, Hui Jiang, Jincheng Zhong, Qiumei Ji
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-019-5574-8

YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei
Cited by: 28
Author(s): Eva Hitzenhammer, Christoph Büschl, Michael Sulyok, Rainer Schuhmacher, Bernhard Kluger, Elisabeth Wischnitzki, Monika Schmoll
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-016-2720-4

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Cited by: 27
Author(s): Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong, Paul Stothard, Joan K. Lunney, Graham Plastow, John C. S. Harding
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-019-6223-y

Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process
Cited by: 23
Author(s): Rannyele Passos Ribeiro, Guillermo Ponz‐Segrelles, Christoph Bleidorn, M. Teresa Aguado
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5525-4

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon
Cited by: 22
Author(s): Amin R. Mohamed, Klara L. Verbyla, Hawlader Abdullah Al-Mamun, Sean McWilliam, Bradley S. Evans, Hilary King, Peter D. Kube, James W. Kijas
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-1461-0

GRACOMICS: software for graphical comparison of multiple results with omics data
Cited by: 7
Author(s): Minseok Seo, Joon Yoon, Taesung Park
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-016-2574-9

De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood
Cited by: 12
Author(s): Abbot O. Oghenekaro, Tommaso Raffaello, Andriy Kovalchuk, Fred O. Asiegbu
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-015-2088-x

De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum
Cited by: 22
Author(s): Valeria Petrella, Serena Aceto, Francesco Musacchia, Vincenza Colonna, Mark D. Robinson, Vladimı́r Beneš, G. Cicotti, Gioia Bongiorno, Luigi Gradoni, Petr Volf, Marco Salvemini
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-14-171

Transcriptomics of morphological color change in polychromatic Midas cichlids
Cited by: 76
Author(s): Frederico Henning, Julia C. Jones, Paolo Franchini, Axel Meyer
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-016-2906-9

An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC)
Cited by: 18
Author(s): Yuanyuan Wang, Xingyi Guo, Michael J. Bray, Zhiyong Ding, Zhongming Zhao
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-020-6721-y

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Cited by: 50
Author(s): Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-016-3433-4

Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model
Cited by: 24
Author(s): Kathy Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching‐Ling Lien, Brendan H. Grubbs, Tracy C. Grikscheit
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-017-3973-2

Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars
Cited by: 37
Author(s): Rugang Yu, Dan Li, Xiaodong Du, Shenglan Xia, Caifeng Liu, Gangrong Shi
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-15-954

Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples
Cited by: 33
Author(s): Igseo Choi, Hua Bao, Arun Kommadath, Afshin Hosseini, Xinwei Sun, Yan Meng, Paul Stothard, Graham Plastow, Christopher K. Tuggle, James M. Reecy, Eric R. Fritz-Waters, Samuel M. Abrams, Joan K. Lunney, Leluo Guan
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-020-07099-4

Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed
Cited by: 3
Author(s): Xi Liu, Frédéric Herault, Christian Diot, Erwan Corre
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-020-6482-7

Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression
Cited by: 15
Author(s): Wenlei Fan, Wenjing Liu, Hehe Liu, Qingshi Meng, Yaxi Xu, Yuming Guo, Baowei Wang, Zhengkui Zhou, Shuisheng Hou
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5984-7

An insight into the sialome, mialome and virome of the horn fly, Haematobia irritans
Cited by: 14
Author(s): José M. C. Ribeiro, Humberto Julio Debat, Mariana Boiani, X. Ures, Sérgio Paulo Dejato da Rocha, Martı́n Breijo
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-13-484

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing
Cited by: 180
Author(s): José A Robles, Sumaira Qureshi, Stuart Stephen, Susan R. Wilson, Conrad J. Burden, Jennifer Taylor
Software Mentions: 3
Published: about 14 years ago

10.1186/s12864-016-2784-1

Psychoactive pharmaceuticals at environmental concentrations induce in vitro gene expression associated with neurological disorders
Cited by: 15
Author(s): Gaurav Kaushik, Yu Xia, Luobin Yang, Michael A. Thomas
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-14-236

Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
Cited by: 73
Author(s): S. Ueno, Christophe Klopp, Jean‐Charles Leplé, Jérémy Derory, Céline Noirot, Valérie Leger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-015-2043-x

Whole transcriptome analysis of Penicillium digitatum strains treatmented with prochloraz reveals their drug-resistant mechanisms
Cited by: 41
Author(s): Jing Liu, Shengqiang Wang, Tingting Qin, Na Li, Yuhui Niu, Dandan Li, Yongze Yuan, Hui Geng, Xiong Li, De Li Liu
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-018-5303-8

Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
Cited by: 13
Author(s): Mario Vailati-Riboni, Ryan Bucktrout, Siyuan Zhan, Ashley Geiger, Joshua C McCann, R.M. Akers, Juan J. Loor
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-019-5953-1

Systematic evaluation of RNA-Seq preparation protocol performance
Cited by: 26
Author(s): Hsueh-Ping Chao, Yueping Chen, Yoko Takata, Mary W. Tomida, Kevin Lin, Jason Kirk, Melissa S. Simper, Carol Mikulec, Joyce E. Rundhaug, Susan M. Fischer, Taiping Chen, Dean G. Tang, Yue Lu, Jianjun Shen
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-5236-2

Power in pairs: assessing the statistical value of paired samples in tests for differential expression
Cited by: 24
Author(s): John R. Stevens, Jennifer S. Herrick, Roger K. Wolff, Martha L. Slattery
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-015-1741-8

Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection
Cited by: 13
Author(s): Martine Schroyen, Juan P. Steibel, James E. Koltes, Igseo Choi, Nancy E. Raney, Christopher J. Eisley, Eric R. Fritz-Waters, James M. Reecy, Jack C. M. Dekkers, R. Rowland, Joan K. Lunney, Catherine W. Ernst, Christopher K. Tuggle
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-15-18

Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics
Cited by: 62
Author(s): Feng Lin, Meixia Zhao, Douglas Baumann, Jieqing Ping, Lianjun Sun, Yunfeng Liu, Biao Zhang, Ziyang Tang, Elisa Hughes, R. W. Doerge, Teresa J. Hughes, Jianxin Ma
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12864-019-5429-3

Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection
Cited by: 11
Author(s): Chen Huang, Dongliang Leng, Shixue Sun, Xiaohua Douglas Zhang
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-15-808

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes
Cited by: 47
Author(s): Pallavi Chauhan, Bengt Hansson, Ken Kraaijeveld, Peter de Knijff, Erik I. Svensson, Maren Wellenreuther
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12864-020-07272-9

Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]
Cited by: 5
Author(s): Zilong Zhao, Dan Liu, Yanjiao Cui, Suying Li, Dan Liang, Daizhen Sun, Jianhe Wang, Zhengli Liu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-4596-y

Divergent transcriptomic responses underlying the ranaviruses-amphibian interaction processes on interspecies infection of Chinese giant salamander
Cited by: 14
Author(s): Ke Fei, Jian‐Fang Gui, Zhongyuan Chen, Tao Li, Cun-Ke Lei, Zi-Hao Wang, Qi-Ya Zhang
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-14-688

Guide: a desktop application for analysing gene expression data
Cited by: 5
Author(s): Jarny Choi
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-019-5452-4

Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds
Cited by: 16
Author(s): Per K.I. Wilhelmsson, Jake O. Chandler, Noé Fernandez-Pozo, Kai Graeber, Kristian K. Ullrich, Waheed Arshad, Safina Khan, Johannes A. Hofberger, Karl Buchta, Patrick P. Edger, J. Chris Pires, M. Eric Schranz, Gerhard Leubner‐Metzger, Stefan A. Rensing
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-019-5894-8

Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp
Cited by: 35
Author(s): Ming Luo, Lanmei Wang, Hao Yin, Wenbin Zhu, Jianjun Fu, Zaijie Dong
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-017-4107-6

Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma
Cited by: 30
Author(s): Laurence Tessier, Olivier Côté, Mary E. Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders, Dorothee Bienzle
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-018-4781-z

Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius
Cited by: 3
Author(s): Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu, Yi-Ywan M. Chen
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-015-1626-x

Characterizing the neurotranscriptomic states in alternative stress coping styles
Cited by: 37
Author(s): Ryan Y. Wong, Melissa S. Lamm, John Godwin
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-15-754

Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci
Cited by: 21
Author(s): Enoch Ng’oma, Marco Groth, Roberto Ripa, Matthias Platzer, Alessandro Cellerino
Software Mentions: 3
Published: about 12 years ago

10.1186/s12864-017-3592-y

A reference gene set for sex pheromone biosynthesis and degradation genes from the diamondback moth, Plutella xylostella, based on genome and transcriptome digital gene expression analyses
Cited by: 46
Author(s): Peng He, Yun‐Fei Zhang, Duan‐Yang Hong, Jun Wang, Xingliang Wang, Ling-Hua Zuo, Xianfu Tang, Weiming Xu, Ming He
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-16-S6-S2

FunPat: function-based pattern analysis on RNA-seq time series data
Cited by: 56
Author(s): Tiziana Sanavia, Francesca Finotello, Barbara Di Camillo
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-021-07655-6

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Cited by: 9
Author(s): Virginia Mwape, Fredrick M. Mobegi, Roshan Regmi, Toby E. Newman, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2995-5

RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.)
Cited by: 57
Author(s): Kazuma Suzuki, Tomohiro Suzuki, Takashi Nakatsuka, Hideo Dohra, Masumi Yamagishi, Kohei Matsuyama, Hideyuki Matsuura
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-016-3356-0

The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions
Cited by: 17
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Ekaterina Proshkina, А. С. Белый, Alexander Fedintsev, Svetlana Zhikrivetskaya, Zulfiya G. Guvatova, А. Ф. Садритдинова, А. В. Снежкина, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-018-5210-z

Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce
Cited by: 14
Author(s): Edita Jurak, Hitoshi Suzuki, Gijs van Erven, Julie-Anne Gandier, Pauline Wong, Kin Chan, Chi-Yip Ho, Yunchen Gong, Elisabeth R. M. Tillier, Marie‐Noëlle Rosso, Mirjam A. Kabel, Shingo Miyauchi, Emma R. Master
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-019-6340-7

The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers
Cited by: 11
Author(s): Xiaohong Ou, Shipeng Li, Peiran Liao, Xiuming Cui, Binglian Zheng, Ye Yang, Dahui Liu, Yun Zheng
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5618-0

Effect of paleopolyploidy and allopolyploidy on gene expression in banana
Cited by: 20
Author(s): Alberto Cenci, Yann Hueber, Yasmín Zorrilla-Fontanesi, Jelle van Wesemael, Ewaut Kissel, Marie Gislard, Julie Sardos, Rony Swennen, Nicolás Roux, Sébastien Carpentier, Mathieu Rouard
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-13-596

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells
Cited by: 1
Author(s): Maria Bro Kloster, Anders Ellern Bilgrau, María Rodrigo-Domingo, Kim Steve Bergkvist, Alexander Schmitz, Mads Sønderkær, Julie Støve Bødker, Steffen Falgreen, Mette Nyegaard, Hans Erik Johnsen, Kåre Lehmann Nielsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12864-021-07536-y

Expression characteristics of pineal miRNAs at ovine different reproductive stages and the identification of miRNAs targeting the AANAT gene
Cited by: 1
Author(s): Ran Di, Qiu Yue Liu, Shu Hui Song, Dong Tian, Jian He, Ying Ge, Xiang Yu Wang, Wen Hu, Joram M. Mwacharo, Zhang Yuan Pan, Jian Dong Wang, Qing Ma, G. L. Cao, Hui Jin, Liang Xiao, M. X. Chu
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-13-459

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
Cited by: 52
Author(s): Agnieszka Podolska, Christian Anthon, Mads Bak, Niels Tommerup, Kerstin Skovgaard, Peter M. H. Heegaard, Jan Gorodkin, Susanna Cirera, Merete Fredholm
Software Mentions: 3
Published: about 14 years ago

10.1186/s12864-018-4488-1

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes
Cited by: 38
Author(s): Mahsa Khorramdelazad, Ido Bar, Paul Whatmore, Gabrielle Smetham, Vijay Bhaaskaria, Yuedong Yang, Shahla Hosseini Bai, Nitin Mantri, Yaoqi Zhou, Rebecca Ford
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-021-07367-x

The semi-dwarfing gene Rht-dp from dwarf polish wheat (Triticum polonicum L.) is the "Green Revolution” gene Rht-B1b
Cited by: 12
Author(s): Songyue Chai, Yao Qin, Xu Zhang, Xue Xiao, Xing Fan, Jian Zeng, Sha Li, Houyang Kang, Haiqin Zhang, Jun Li, Yong‐Hong Zhou, Yi Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-015-2068-1

A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication
Cited by: 15
Author(s): Pedro Rodenas-Cuadrado, Xiaowei Sylvia Chen, Lutz Wiegrebe, Uwe Firzlaff, Sonja C. Vernes
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-018-5325-2

Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.
Cited by: 12
Author(s): Junqiang Guo, Qingyi Wang, Li Liu, Shuchao Ren, Shipeng Li, Peiran Liao, Zhigang Zhao, Chenyu Lu, Bingbing Jiang, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-07277-4

Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
Cited by: 13
Author(s): Ning Li, Ziwei Meng, Tao Mei, Yueyuan Wang, Yulan Zhang, Shufen Li, Wu‐Jun Gao, Chuan‐Liang Deng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-07050-7

RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake
Cited by: 2
Author(s): Xiaofeng Guo, Xiaoling Gao, Brendan T. Keenan, Jane M. Zhu, Dimitra Sarantopoulou, Jie Liu, Raymond J. Galante, Gregory R. Grant, Allan I. Pack
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-020-6514-3

Transcriptomics supports local sensory regulation in the antenna of the kissing-bug Rhodnius prolixus
Cited by: 21
Author(s): José Manuel Latorre-Estivalis, Marcos Sterkel, Sheila Ons, Marcelo G. Lorenzo
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12920-020-00756-3

Analysis of exosomal circRNAs upon irradiation in pancreatic cancer cell repopulation
Cited by: 16
Author(s): Yiyun Chen, Mier Jiang, Ling Tian
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-020-0700-7

Transcriptome analysis of HPV-induced warts and healthy skin in humans
Cited by: 13
Author(s): Laith N. AL-Eitan, Amneh H. Tarkhan, Mansour A. Alghamdi, Firas Al‐Qarqaz, Hadeel Alkofahi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-021-00878-2

Expression and gene regulatory network of SNHG1 in hepatocellular carcinoma
Cited by: 4
Author(s): Chaoran Zheng, Shicheng Yu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12920-019-0551-2

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines
Cited by: 28
Author(s): Xing Yi Woo, Anuj Srivastava, Joel H. Graber, Vinod Kumar Yadav, Vishal Kumar Sarsani, Al Simons, Glen L. Beane, Stephen C. Grubb, Guruprasad Ananda, Rangjiao Liu, Grace A. Stafford, Jeffrey H. Chuang, Susan D. Airhart, R. Krishna Murthy Karuturi, Joshy George, Carol J. Bult
Software Mentions: 3
Published: over 7 years ago

10.1186/s12920-021-00975-2

Identification and validation of signal recognition particle 14 as a prognostic biomarker predicting overall survival in patients with acute myeloid leukemia
Cited by: 3
Author(s): Lingling Shi, Rui Huang, Yongrong Lai
Software Mentions: 3
Published: over 5 years ago

10.1186/1755-8794-6-S2-S1

Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening
Cited by: 7
Author(s): Mark A. van de Wiel, Renée X. de Menezes, Ellen Siebring-van Olst, Victor W. van Beusechem
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12920-021-00985-0

Label propagation-based semi-supervised feature selection on decoding clinical phenotypes with RNA-seq data
Cited by: 2
Author(s): Xue Jiang, Miao Chen, Weichen Song, Guan Ning Lin
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-019-0565-9

Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs
Cited by: 2
Author(s): Hua Zhong, Mingzhou Song
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12920-019-0548-x

Placental microRNAs in pregnancies with early onset intrauterine growth restriction and preeclampsia: potential impact on gene expression and pathophysiology
Cited by: 72
Author(s): Zain Awamleh, Gregory B. Gloor, V. K. M. Han
Software Mentions: 3
Published: over 7 years ago

10.1186/s12920-019-0580-x

A comprehensive genome-wide profiling comparison between HBV and HCV infected hepatocellular carcinoma
Cited by: 21
Author(s): Suofeng Sun, Yuan Li, Sun‐Young Han, Huiying Jia, Xiuling Li, Xiaofang Li
Software Mentions: 3
Published: about 7 years ago

10.1186/s12866-020-1722-1

Integrative analysis of outer membrane vesicles proteomics and whole-cell transcriptome analysis of eravacycline induced Acinetobacter baumannii strains
Cited by: 19
Author(s): Dinesh Kumar Kesavan, Aparna Vasudevan, Liang Wu, Jianguo Chen, Zhaoliang Su, Shengjun Wang, Huaxi Xu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12866-020-02020-1

Berberine alters gut microbial function through modulation of bile acids
Cited by: 10
Author(s): Patricia G. Wolf, Saravanan Devendran, Heidi L. Doden, Lindsey K. Ly, Tyler Moore, Hiroyuki Takei, Hiroshi Nittono, Tsuyoshi Murai, Takao Kurosawa, George E. Chlipala, Stefan J. Green, Genta Kakiyama, Purna C. Kashyap, Vance J. McCracken, H. Rex Gaskins, Patrick M. Gillevet, Jason M. Ridlon
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12866-021-02110-8

HilE is required for synergistic activation of SPI-1 gene expression in Salmonella enterica serovar Typhimurium
Cited by: 1
Author(s): Selwan Hamed, Riham M. Shawky, Mohamed Emara, James M. Slauch, Christopher V. Rao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12866-020-01762-2

Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer
Cited by: 32
Author(s): Qing Wang, Jianzhong Ye, Daiqiong Fang, Longxian Lv, Wenshuai Wu, Ding Shi, Yating Li, Liya Yang, Xiaoyuan Bian, Jingjing Wu, Xianwan Jiang, Kaicen Wang, Mark P. Hodson, L Thibaut, Joshua W. K. Ho, Eleni Giannoulatou
Software Mentions: 3
Published: over 6 years ago

10.1186/s12867-017-0099-7

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing
Cited by: 42
Author(s): Parisa Amini, Julia Ettlin, Lennart Opitz, Elena Clementi, Alexandra Malbon, Enni Markkanen
Software Mentions: 3
Published: about 9 years ago

10.1186/s12860-020-00331-9

Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages
Cited by: 18
Author(s): Sabin Bhandari, Ruomei Li, Jaione Simón-Santamaría, Peter McCourt, Steinar Johansen, Bård Smedsrød, Iñigo Martínez-Zubiaurre, Karen Kristine Sørensen
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-015-0511-8

Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)
Cited by: 276
Author(s): Zhenshan Liu, Mingming Xin, Jinxia Qin, Huiru Peng, Zhongfu Ni, Yingyin Yao, Qixin Sun
Software Mentions: 3
Published: over 11 years ago

10.1186/s12870-016-0932-z

Characterization of the cytokinin-responsive transcriptome in rice
Cited by: 34
Author(s): Tracy Raines, Ivory C. Blakley, Yu‐Chang Tsai, Jennifer M. Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G. Schäller, Ann E. Loraine, Joseph J. Kieber
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12870-019-1795-x

Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)
Cited by: 19
Author(s): Daniel R. Kohlhase, Jamie A. O’Rourke, Micheal D. K. Owen, Michelle A. Graham
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-020-02506-0

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods
Cited by: 25
Author(s): Néstor Kippes, Carl VanGessel, James Hamilton, Ani Akpinar, Hikmet Budak, Jorge Dubcovsky, Stephen Pearce
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2229-13-220

Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua
Cited by: 83
Author(s): Sandra Soetaert, Christophe Van Neste, Mado Vandewoestyne, Steven R. Head, Alain Goossens, Filip Van Nieuwerburgh, Dieter Deforce
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12870-019-2169-0

Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya
Cited by: 11
Author(s): Dessireé Zerpa‐Catanho, Jennifer Wai, Ming Li Wang, Liang Yu, Julie Nguyen, Ray Ming
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12870-017-1187-z

De novo transcriptome assembly from flower buds of dioecious, gynomonoecious and chemically masculinized female Coccinia grandis reveals genes associated with sex expression and modification
Cited by: 16
Author(s): Ravi Suresh Devani, Sangram Sinha, Jayeeta Banerjee, Rabindra Kumar Sinha, Abdelhafid Bendahmane, Anjan K. Banerjee
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12870-020-02634-7

The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development
Cited by: 12
Author(s): Dandan Wang, Zhaodong Hao, Xiaofei Long, Zhanjun Wang, Xianrui Zheng, Daiquan Ye, Peng Ye, Weihuang Wu, Xiangyang Hu, Guibin Wang, Renhua Zheng, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-021-03124-0

The role of strigolactones in P deficiency induced transcriptional changes in tomato roots
Cited by: 17
Author(s): Yanting Wang, Hernando G. Suárez Duran, Jan C. van Haarst, Elio Schijlen, Carolien Ruyter-Spira, Marnix H. Medema, Lemeng Dong, Harro J. Bouwmeester
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-015-0627-x

Transcriptomic comparison of the self-pollinated and cross-pollinated flowers of Erigeron breviscapus to analyze candidate self-incompatibility-associated genes
Cited by: 19
Author(s): Wei Zhang, Wei Xiang, Meng Heng-lin, Chunhua Ma, Ni-Hao Jiang, Guanghui Zhang, Shengchao Yang
Software Mentions: 3
Published: about 11 years ago

10.1186/s12870-017-1188-y

Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress
Cited by: 25
Author(s): Courtney P. Leisner, Craig R. Yendrek, Elizabeth A. Ainsworth
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12870-016-0775-7

B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)
Cited by: 53
Author(s): Wei Huang, Yan Du, Xin Zhao, Weiwei Jin
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-021-03009-2

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)
Cited by: 8
Author(s): Guozhong Zhu, Shuang Hou, Xiaohui Song, Xing Wang, Wei Wang, Quanjia Chen, Wangzhen Guo
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-021-03129-9

Tomato transcriptomic response to Tuta absoluta infestation
Cited by: 11
Author(s): Daniela D’Esposito, Daniele Manzo, Alessandro Ricciardi, Antonio P. Garonna, Antonino De Natale, Luigi Frusciante, Francesco Pennacchio, Maria Raffaella Ercolano
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-020-02459-4

Reducing the nicotine content of tobacco by grafting with eggplant
Cited by: 5
Author(s): Mengjuan Ren, Mengyue Zhang, Huijuan Yang, Hongzhi Shi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-019-1952-2

Genome-wide transcriptional adaptation to salt stress in Populus
Cited by: 28
Author(s): Jin-Gui Liu, Xiao Han, Tianbo Yang, Wenhui Cui, Aimin Wu, Chunxiang Fu, Baichen Wang, Lijun Liu
Software Mentions: 3
Published: about 7 years ago

10.1186/s12870-019-1802-2

Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube
Cited by: 8
Author(s): Zhang Zhong, C.K. Kang, Shuyi Zhang, Xingang Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-015-0643-x

Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions
Cited by: 29
Author(s): Shamila Abeynayake, Stephen Byrne, Istvàn Nagy, Kristina Jonavičienė, Thomas Etzerodt, Birte Boelt, Torben Asp
Software Mentions: 3
Published: about 11 years ago

10.1186/s12870-015-0468-7

Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
Cited by: 37
Author(s): Igor Fesenko, Georgij Arapidi, Alexander Skripnikov, Dmitry Alexeev, Elena S. Kostryukova, Alexander I. Manolov, Ilya Altukhov, Regina Khazigaleeva, A. V. Seredina, Sergey I. Kovalchuk, Rustam H. Ziganshin, В. Г. Згода, Svetlana E. Novikova, Tatiana A. Semashko, D. K. Slizhikova, Vasilij V Ptushenko, A. Yu. Gorbachev, Vadim M. Govorun, В. Т. Иванов
Software Mentions: 3
Published: almost 12 years ago