bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1186/s12864-020-07034-7

Single cell transcriptomes reveal expression patterns of chemoreceptor genes in olfactory sensory neurons of the Caribbean spiny lobster, Panulirus argus
Cited by: 19
Author(s): Mihika T. Kozma, Hanh Ngo-Vu, Matthew T. Rump, Yuriy V. Bobkov, Barry W. Ache, Charles D. Derby
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-019-5967-8

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies
Cited by: 11
Author(s): Isabel Garcia Sousa, Kelly Cristina Rodrigues Simi, Manuela Maragno do Almo, Maryani Andressa Gomes Bezerra, Gero Doose, Tainá Raiol, Peter F. Stadler, Steve Hoffmann, Andréa Queiroz Maranhão, Marcelo M. Brigido
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-07236-z

Initial response of ovarian tissue transcriptome to vitrification or microwave-assisted dehydration in the domestic cat model
Cited by: 5
Author(s): Olga Amelkina, Pierre Comizzoli
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-019-5917-5

Transcriptional characterisation of the Exaiptasia pallida pedal disc
Cited by: 10
Author(s): Peter A. Davey, Marcos Rodrigues, Jessica L. Clarke, Nick Aldred
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-07209-2

Changes in transcriptomic and metabolomic profiles of morphotypes of Ophiocordyceps sinensis within the hemocoel of its host larvae, Thitarodes xiaojinensis
Cited by: 9
Author(s): Miaomiao Li, Qian Meng, Huan Zhang, Ruihao Shu, Yanni Zhao, Peipei Wu, Xuan Li, Guiling Zhou, Qilian Qin, Jihong Zhang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-019-6221-0

Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens
Cited by: 52
Author(s): Lu Liu, Xiaojing Liu, Huanxian Cui, Ranran Liu, Guiping Zhao, Jie Wen
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-021-08014-1

Female developmental environment delays development of male honeybee (Apis mellifera)
Cited by: 1
Author(s): Yi Bo Liu, Yi Yao, Amal Abdelmawla, Yun Lin Zheng, Zhi Zeng
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-020-6747-1

Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus
Cited by: 29
Author(s): Mengdi Li, Ruihua Wang, Xiaoming Wu, Jianbo Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-016-2384-0

Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells
Cited by: 30
Author(s): Alexandra Popa, Kévin Lebrigand, Pascal Barbry, Rainer Waldmann
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-018-4471-x

Transcriptome analysis reveals mechanisms of geroprotective effects of fucoxanthin in Drosophila
Cited by: 22
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Nadezhda Zemskaya, А. С. Белый, Eugenia Dobrovolskaya, Anna Patova, Zulfiya G. Guvatova, E. N. Lukyanova, Anastasiya V. Snezhkina, Anna V. Kudryavtseva
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-018-4918-0

Highly focused transcriptional response of Anopheles coluzzii to O’nyong nyong arbovirus during the primary midgut infection
Cited by: 17
Author(s): Guillaume Carissimo, Adrien Pain, Eugeni Belda, Kenneth D. Vernick
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-017-3897-x

Comparative muscle transcriptome associated with carcass traits of Nellore cattle
Cited by: 40
Author(s): Bárbara Silva-Vignato, Luiz Lehmann Coutinho, Mirele Daiana Poleti, Luciana Correia de Almeida Regitano, Júlio César de Carvalho Balieiro
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-4570-8

Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish
Cited by: 35
Author(s): Kai Kristoffer Lie, Ole K. Tørresen, Monica Hongrø Solbakken, Ivar Rønnestad, Ave Tooming‐Klunderud, Alexander Johan Nederbragt, Sissel Jentoft, Øystein Sæle
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-019-5524-5

The NAC family transcription factor GmNAC42–1 regulates biosynthesis of the anticancer and neuroprotective glyceollins in soybean
Cited by: 21
Author(s): Asraful Jahan, Brianna Harris, Matthew Lowery, Katie Coburn, Aniello M. Infante, Ryan Percifield, Amanda G. Ammer, Nik Kovinich
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-06884-5

Identification of candidate genes and regulatory factors related to growth rate through hypothalamus transcriptome analyses in broiler chickens
Cited by: 9
Author(s): Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Połtowicz, Joanna Nowak, Katarzyna Ropka‐Molik, Natalia Derebecka, Joanna Wesoły, Dorota Wojtysiak
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-1907-4

Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata
Cited by: 74
Author(s): Rodolphe Poupardin, Konrad Schöttner, Jaroslava Korbelová, Jan Provazník, David Doležel, Dinko Pavlinic, Vladimı́r Beneš, Vladimı́r Košťál
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-016-2638-x

Temporal Dysynchrony in brain connectivity gene expression following hypoxia
Cited by: 3
Author(s): Brett Milash, Junyuan Gao, Tamara J. Stevenson, Jong Hyun Son, Tiffanie Dahl, Joshua L. Bonkowsky
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4481-8

Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation
Cited by: 20
Author(s): Manuel Wittchen, Tobias Busche, Andrew H. Gaspar, Ju Huck Lee, Hung Ton‐That, Jörn Kalinowski, Andreas Tauch
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-020-06855-w

Transcriptomic and proteomic analyses of ovarian follicles reveal the role of VLDLR in chicken follicle selection
Cited by: 23
Author(s): Qiuyue Chen, Yiya Wang, Zemin Liu, Xiaoli Guo, Yuena Sun, Kang Li, Yunliang Jiang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-017-3741-3

Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection
Cited by: 43
Author(s): Rune Andreassen, Nardos Tesfaye Woldemariam, Ine Østråt Egeland, Oleg Agafonov, Hilde Sindre, Bjørn Høyheim
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-6408-4

Effect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon
Cited by: 11
Author(s): Jin-Hyoung Kim, Daniel J. Macqueen, James R. Winton, John D. Hansen, Hyun Park, Robert H. Devlin
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-017-4361-7

Training the salmon’s genes: influence of aerobic exercise, swimming performance and selection on gene expression in Atlantic salmon
Cited by: 12
Author(s): Nick Robinson, Gerrit Timmerhaus, Matthew Baranski, Øivind Andersen, Harald Takle, Aleksei Krasnov
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-015-1247-4

H2A.Z marks antisense promoters and has positive effects on antisense transcript levels in budding yeast
Cited by: 19
Author(s): Muxin Gu, Yanin Naiyachit, Thomas J. Wood, Catherine B. Millar
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-020-07177-7

Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens
Cited by: 12
Author(s): Jia Feng, Haijun Zhang, Shu‐geng Wu, Guang‐hai Qi, Jing Wang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-4400-4

Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries)
Cited by: 33
Author(s): Kisun Pokharel, Jaana Peippo, Mervi Honkatukia, Arja Seppälä, Johanna Rautiainen, Nasser Ghanem, Tuula-Marjatta Hamama, M.A. Crowe, Magnus Andersson, Menghua Li, Juha Kantanen
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-019-5493-8

Genome-wide transcriptome analysis reveals the molecular mechanism of high temperature-induced floral abortion in Litchi chinensis
Cited by: 13
Author(s): Hao Líu, Congcong Wang, Houbin Chen, Biyan Zhou
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-06961-9

Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks
Cited by: 16
Author(s): Jing Liu, Fei Shen, Yumei Xiao, Hongcheng Fang, Changwei Qiu, Wei Li, Ting Wu, Xuefeng Xu, Yi Wang, Xinzhong Zhang, Zhenhai Han
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-021-07876-9

Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma
Cited by: 8
Author(s): Christos Dimitrakopoulos, Sravanth K. Hindupur, Marco Colombi, Dritan Liko, Charlotte K.Y. Ng, Salvatore Piscuoglio, Jonas Behr, Ariane L. Moore, Jochen Singer, Hans‐Joachim Ruscheweyh, Matthias S. Matter, Dirk Mossmann, Luigi Terracciano, Michael N. Hall, Niko Beerenwinkel
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-6120-4

RNA-Seq based transcriptome analysis during bovine viral diarrhoea virus (BVDV) infection
Cited by: 28
Author(s): Cun Liu, Yanhan Liu, Lin Liang, Shangjin Cui, Yanming Zhang
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-018-5319-0

Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle
Cited by: 13
Author(s): Prerna Vohra, Roy R. Chaudhuri, Matthew Mayho, Christina Vrettou, Cosmin Chintoan-Uta, Nicholas R. Thomson, Jayne Hope, John Hopkins, Mark P. Stevens
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-018-4451-1

Differential gene expression in the evolution of sex pheromone communication in New Zealand’s endemic leafroller moths of the genera Ctenopseustis and Planotortrix
Cited by: 9
Author(s): Alessandro Grapputo, Amali H. Thrimawithana, Bernd Steinwender, Richard D. Newcomb
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-021-07951-1

Transcriptomic analysis of the seminal vesicle response to the reproductive toxicant acrylamide
Cited by: 6
Author(s): David A. Skerrett‐Byrne, Brett Nixon, Elizabeth G. Bromfield, James Breen, Natalie A. Trigg, Simone J. Stanger, Ilana R. Bernstein, Andy Anderson, Tessa Lord, Raymond Aitken, Shaun D. Roman, Sarah A. Robertson, John E. Schjenken
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-016-3334-6

Transcriptome profiling in the damselfly Ischnura elegans identifies genes with sex-biased expression
Cited by: 24
Author(s): Pallavi Chauhan, Maren Wellenreuther, Bengt Hansson
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-021-07888-5

Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage
Cited by: 14
Author(s): Ailing Zhang, Jicheng Yang, Min Sun, Chuang Lin, Puding Zhou, Juncai Ren, Dan Luo, Xiaoshan Wang, Congyu Ma, Xinquan Zhang, Guangyan Feng, Gang Nie, Linkai Huang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07528-y

Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium
Cited by: 14
Author(s): B. Dnate’ Baxter, Eric D. Larson, Laëtitia Merle, Paul Feinstein, Arianna Gentile Polese, Andrew N. Bubak, Christy S. Niemeyer, James E. Hassell, Doug P. Shepherd, Vijay R. Ramakrishnan, Maria A. Nagel, Diego Restrepo
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5987-4

Deep RNA-Seq reveals miRNome differences in mammary tissue of lactating Holstein and Montbéliarde cows
Cited by: 24
Author(s): Pierre-Alexis Billa, Yannick Faulconnier, T. Ye, Mathilde Chervet, Fabienne Le Provost, José Pires, Christine Leroux
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-6648-3

Sexual-biased gene expression of olfactory-related genes in the antennae of Conogethes pinicolalis (Lepidoptera: Crambidae)
Cited by: 7
Author(s): Dapeng Jing, Tiantao Zhang, Shuxiong Bai, Kanglai He, Sivaprasath Prabu, Jing Luan, Zhenying Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-6391-9

Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance
Cited by: 20
Author(s): Roni Tadmor‐Levi, Adi Doron‐Faigenboim, Evgeniya Marcos‐Hadad, Jules Petit, Gideon Hulata, Maria Forlenza, G.F. Wiegertjes, Lior David
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-018-4500-9

Transcriptomic changes in Cucurbita pepo fruit after cold storage: differential response between two cultivars contrasting in chilling sensitivity
Cited by: 20
Author(s): Fátima Carvajal, Raquel Rosales, Francisco Palma, Susana Manzano, Joaquı́n Cañizares, Manuel Jamilena, Dolores Garrido
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-021-07506-4

Immune-related genes of the larval Holotrichia parallela in response to entomopathogenic nematodes Heterorhabditis beicherriana LF
Cited by: 7
Author(s): Li ErTao, Jianhui Qin, Honglin Feng, Jinqiao Li, Xiaofeng Li, Innocent Nyamwasa, Yujin Cao, Weibin Ruan, Kebin Li, Jing Yin
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07785-x

Simultaneous changes in anthocyanin, chlorophyll, and carotenoid contents produce green variegation in pink–leaved ornamental kale
Cited by: 7
Author(s): Yang Liu, Xin Feng, Yuting Zhang, Fuhui Zhou, Pengfang Zhu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5512-9

Sex differences in gene regulation in the dorsal root ganglion after nerve injury
Cited by: 52
Author(s): K Stephens, Weiqiang Zhou, Zhicheng Ji, Zhiyong Chen, Shaoqiu He, Hongkai Ji, Yun Guan, Sean D. Taverna
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-018-4590-4

Paramutation-like features of multiple natural epialleles in tomato
Cited by: 16
Author(s): Quentin Gouil, David C. Baulcombe
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-019-5988-3

Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis
Cited by: 70
Author(s): Yeyun Li, Xuewen Wang, Qiuyan Ban, Xiangxiang Zhu, Changjun Jiang, Chaoling Wei, Jeffrey L. Bennetzen
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-3875-3

Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice
Cited by: 14
Author(s): Justin M. Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John R. Hoidal, Namakkal S. Rajasekaran
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-021-07513-5

Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data
Cited by: 3
Author(s): B. E. A. Fantinatti, Érika Stefani Perez, Bruna Tereza Thomazini Zanella, Jéssica Silvino Valente, Tassiana Gutierrez de Paula, Edson Assunção Mareco, Robson Francisco Carvalho, Silvano Piazza, Michela Alessandra Denti, Maeli Dal-Pai-Silva
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07715-x

De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn
Cited by: 16
Author(s): Yufu Gao, Dong-Hui Zhao, Jiaqi Zhang, Jia-Shuo Chen, Jialin Li, Zhuo Weng, Liping Rong
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-6250-8

Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum
Cited by: 8
Author(s): Qi Yang, Shibiao Liu, Xiaoning Han, Jingyi Ma, Wenhong Deng, Xinli Wang, Hongwei Guo, Xinli Xia
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-019-5991-8

Contrasting gene expression patterns in grain of high and low asparagine wheat genotypes in response to sulphur supply
Cited by: 18
Author(s): Tanya Y. Curtis, Sarah Raffan, Yongfang Wan, Robert C. King, Asier Gonzalez-Uriarte, Nigel G. Halford
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-06914-2

New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C)
Cited by: 17
Author(s): Kunyin Jiang, Hongtao Nie, Dongdong Li, Xiwu Yan
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-021-07737-5

Transcriptome analysis of five ovarian stages reveals gonad maturation in female Macrobrachium nipponense
Cited by: 15
Author(s): Yuning Zhang, Sufei Jiang, Hui Qiao, Yiwei Xiong, Hongtuo Fu, Wenyi Zhang, Yongsheng Gong, Shubo Jin, Yan Wu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07871-0

Transcriptomic analyses of cacao flavonoids produced in photobioreactors
Cited by: 2
Author(s): Adriana M. Gallego, Luisa F. Rojas, Wilmar Giovanni Valencia, Lucía Atehortúa, Aura I. Urrea, Andrew S. Fister, Mark J. Guiltinan, Siela N. Maximova, Natalia Pabón‐Mora
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07518-0

A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast
Cited by: 17
Author(s): Nicholas J. McGlincy, Zuriah A. Meacham, Kendra Reynaud, Ryan Muller, Rachel Baum, Nicholas T. Ingolia
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07840-7

Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea
Cited by: 6
Author(s): Xin Guo, Zhaohui Wang, Lei Liu, Yang Li
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-6048-8

RNA-seq of eight different poplar clones reveals conserved up-regulation of gene expression in response to insect herbivory
Cited by: 2
Author(s): Niels A. Müller, Birgit Kersten, Matthias Fladung, Hilke Schroeder
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-15-557

Transcriptome-wide analysis of microRNA expression in the malaria mosquito Anopheles gambiae
Cited by: 49
Author(s): Inna Biryukova, Tao Ye, Elena A. Levashina
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12916-020-01899-x

EPHA7 mutation as a predictive biomarker for immune checkpoint inhibitors in multiple cancers
Cited by: 25
Author(s): Zhen Zhang, Haoxiang Wu, Wu-Hao Lin, Zi‐Xian Wang, Lu-Ping Yang, Zhao-Lei Zeng, Hongyu Luo
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12920-018-0389-z

Integrative pathway-based survival prediction utilizing the interaction between gene expression and DNA methylation in breast cancer
Cited by: 18
Author(s): So Yeon Kim, Tae Rim Kim, Hyun-Hwan Jeong, Kyung-Ah Sohn
Software Mentions: 1
Published: about 8 years ago

10.1186/s12920-021-00875-5

Coding and non-coding RNA interactions reveal immune-related pathways in peripheral blood mononuclear cells derived from patients with proliferative vitreoretinopathy
Cited by: 5
Author(s): Yicheng Ni, Fangyuan Liu, Xiao Hu, Yingyan Qin, Zhaotian Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12920-018-0469-0

Regulatory network analysis reveals the oncogenesis roles of feed-forward loops and therapeutic target in T-cell acute lymphoblastic leukemia
Cited by: 6
Author(s): Mengxuan Xia, Qiong Zhang, Mei Luo, Pan Li, Yingxue Wang, Qian Lei, An‐Yuan Guo
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12920-021-00957-4

Robust biomarker discovery for hepatocellular carcinoma from high-throughput data by multiple feature selection methods
Cited by: 13
Author(s): Zishuang Zhang, Zhi-Ping Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12866-018-1352-z

The spent culture supernatant of Pseudomonas syringae contains azelaic acid
Cited by: 11
Author(s): Sree Gowrinadh Javvadi, Paola Cescutti, Roberto Rizzo, Valentina Lonzarich, Luciano Navarini, Danilo Licastro, Corrado Guarnaccia, Vittorio Venturi
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12866-020-01894-5

Evaluation of fecal DNA extraction protocols for human gut microbiome studies
Cited by: 18
Author(s): Mi Young Lim, Yong Soo Park, Jung-Ha Kim, Young-Do Nam
Software Mentions: 1
Published: over 6 years ago

10.1186/s12866-020-01873-w

Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber
Cited by: 10
Author(s): Shigang Gao, Rong Zeng, Lihui Xu, Zhiwei Song, Ping Gao, Fangyin Dai
Software Mentions: 1
Published: over 6 years ago

10.1186/s12866-019-1578-4

Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds
Cited by: 6
Author(s): Thorsten Bufe, André Hennig, Jochen Klumpp, Agnes Weiß, Kay Nieselt, Herbert Schmidt
Software Mentions: 1
Published: about 7 years ago

10.1186/s12866-021-02214-1

Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study
Cited by: 19
Author(s): Lucas Moitinho‐Silva, Michelle Wegener, Sandra May, Florian Schrinner, Awais Akhtar, Teide Jens Boysen, Eva Schaeffer, Clint Hansen, Timo Schmidt, Malte Rühlemann, Matthias Hübenthal, Philipp Rausch, Mustafa T. Kondakci, Walter Maetzler, Stephan Weidinger, Matthias Laudes, Philip Süß, Dominik M. Schulte, Ralf Junker, Felix Sommer, Burkhard Weisser, Corinna Bang, André Franke
Software Mentions: 1
Published: over 5 years ago

10.1186/s12866-019-1462-2

Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model
Cited by: 10
Author(s): Barbara U. Metzler‐Zebeli, Monica A. Newman, Dietmar Grüll, Qendrim Zebeli
Software Mentions: 1
Published: over 7 years ago

10.1186/s12866-019-1497-4

Exploring the tissue tropism of pseudorabies virus based on miRNA level analysis
Cited by: 1
Author(s): Fan Yu, Ling Zhu, Xiangang Sun, Wenting Lyu, Lei Xu, Yin Yuan, Jun Zhao, Jianbo Huang, Yichao Den, Zhiyi Jiang, Shiyao Xu, Mao Xiyu, Zhinan Xu
Software Mentions: 1
Published: over 7 years ago

10.1186/s12866-017-0966-x

Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
Cited by: 12
Author(s): Vijay Kumar Sharma, Darrell O. Bayles, David P. Alt, Torey Looft, Brian W. Brunelle, Judith A. Stasko
Software Mentions: 1
Published: over 9 years ago

10.1186/s12866-021-02295-y

Skin microbiota dynamics following B. subtilis formulation challenge: an in vivo study in mice
Cited by: 5
Author(s): Veronica Moskovicz, Rina T. Greenblatt Ben-El, Guy Horev, Boaz Mizrahi
Software Mentions: 1
Published: about 5 years ago

10.1186/s12866-021-02304-0

The Mesorhizobium huakuii transcriptional regulator AbiEi plays a critical role in nodulation and is important for bacterial stress response
Cited by: 3
Author(s): Xiaohong Chen, Aiqi Hu, Qian Zou, Sha Luo, Hetao Wu, Chunxiao Yan, Tao Liu, Donglan He, Xiaohua Li, Guyue Cheng
Software Mentions: 1
Published: about 5 years ago

10.1186/s12866-021-02257-4

Regulation of virulence and β-lactamase gene expression in Staphylococcus aureus isolates: cooperation of two-component systems in bloodstream superbugs
Cited by: 7
Author(s): Sanaz Dehbashi, Hamed Tahmasebi, Behrouz Zeyni, Mohammad Reza Arabestani
Software Mentions: 1
Published: over 5 years ago

10.1186/s12866-018-1225-5

Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015
Cited by: 9
Author(s): Liu Cong, Dongying Fan, Yanfang Li, Yue Chen, Lili Huang, Yan Xia
Software Mentions: 1
Published: about 8 years ago

10.1186/s12867-019-0124-0

Transcriptomic responses to grazing reveal the metabolic pathway leading to the biosynthesis of domoic acid and highlight different defense strategies in diatoms
Cited by: 20
Author(s): Sara Harðardóttir, Sylke Wohlrab, Ditte Marie Hjort, Bernd Krock, Torkel Gissel Nielsen, Uwe John, Nina Lundholm
Software Mentions: 1
Published: over 7 years ago

10.1186/s12868-021-00661-0

NRXN1α+/- is associated with increased excitability in ASD iPSC-derived neurons
Cited by: 12
Author(s): Sahar Avazzadeh, Leo R. Quinlan, Jamie Reilly, Katya McDonagh, Amirhossein Jalali, Yanqin Wang, Veronica McInerney, Janusz Krawczyk, Yicheng Ding, Jacqueline Fitzgerald, Matthew L. O’Sullivan, Eva Forman, Sally Ann Lynch, Sean Ennis, Niamh Feerick, Richard B. Reilly, Weidong Li, Xu Shen, Guangming Yang, Yin Lu, Hilde Peeters, Peter Dockery, Timothy O’Brien, Sanbing Shen, Louise Gallagher
Software Mentions: 1
Published: about 5 years ago

10.1186/s40795-021-00454-y

Effect of a dietary and exercise intervention in women with overweight and obesity undergoing fertility treatments: protocol for a randomized controlled trial
Cited by: 0
Author(s): Kindann Fawcett, Audrey Martinez, Meghan Crimmins, Clark Sims, Elisabet Børsheim, Aline Andres
Software Mentions: 1
Published: about 5 years ago

10.1186/s12870-021-02954-2

Cold acclimation can specifically inhibit chlorophyll biosynthesis in young leaves of Pakchoi
Cited by: 7
Author(s): Wang Hui-yu, Zhubo Li, Lingyun Yuan, Haihong Zhou, Xilin Hou, Xilin Hou
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-020-02526-w

Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses
Cited by: 30
Author(s): Qinbin Zhang, Hui Liu, Xiaolin Wu, Wei Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-021-03063-w

Integrated metabolome and transcriptome analysis of the anthocyanin biosynthetic pathway in relation to color mutation in miniature roses
Cited by: 20
Author(s): Jiaojiao Lu, Qing Zhang, Lixin Lang, Chuang Jiang, Xiaofeng Wang, Hao Sun
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-03128-w

Transcriptome analysis of resistant and susceptible mulberry responses to Meloidogyne enterolobii infection
Cited by: 4
Author(s): Hanjuan Shao, Yu Fu, Pan Zhang, Chunping You, Chuanren Li, Huan Peng
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-02872-3

Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar
Cited by: 14
Author(s): Zihao Cheng, Xuemei Zhang, Wenjing Yao, Kai Zhao, Lin Liu, Guisheng Fan, Boru Zhou, Tongmin Jiang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-019-1654-9

Comparative transcriptome analysis reveals gene network regulating cadmium uptake and translocation in peanut roots under iron deficiency
Cited by: 33
Author(s): Chen Chu, Qiqi Cao, Qing Jiang, Li Jin, Rugang Yu, Gangrong Shi
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-021-02944-4

Auxin regulated metabolic changes underlying sepal retention and development after pollination in spinach
Cited by: 11
Author(s): Mahpara Fatima, Xiaokai Ma, Ping Zhou, Madiha Zaynab, Ray Ming
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-03131-1

Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis
Cited by: 13
Author(s): Jianhua Zhao, Chengzhen Sun, Fu-Ming Shi, Shanshan Ma, Jinshuang Zheng, Xin Du, Liping Zhang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-02846-5

Molecular cloning and characterization of GhERF105, a gene contributing to the regulation of gland formation in upland cotton (Gossypium hirsutum L.)
Cited by: 10
Author(s): Chaofeng Wu, Hongyan Cheng, Shuyan Li, Dongyun Zuo, Zhongxu Lin, Youping Zhang, Limin Lv, Qiaolian Wang, Guoli Song
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-03032-3

Transcriptome and metabolite profiling analyses provide insight into volatile compounds of the apple cultivar ‘Ruixue’ and its parents during fruit development
Cited by: 30
Author(s): Xiaojie Liu, Nini Hao, Feng Ran, Zhipeng Meng, Yanan Li, Zhengyang Zhao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-020-02448-7

A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]
Cited by: 33
Author(s): Shunkai Hu, Mi Zhang, Yiqing Yang, Wei Xuan, Zhongwei Zou, Emmanuel Arkorful, Yi Chen, Qingping Ma, Anburaj Jeyaraj, Xuan Chen, Xinghui Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-02342-2

Overexpression of PpSnRK1α in tomato enhanced salt tolerance by regulating ABA signaling pathway and reactive oxygen metabolism
Cited by: 36
Author(s): Wenru Wang, Jiahui Liang, Guifang Wang, Maoxiang Sun, Futian Peng, Yuansong Xiao
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-019-1731-0

RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
Cited by: 55
Author(s): Tingting Dong, Mingku Zhu, Jiawen Yu, Rongpeng Han, Cheng Tang, Tao Xu, Jingran Liu, Zongyun Li
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-020-2284-y

Transcriptome profiling of differentially expressed genes in cytoplasmic male-sterile line and its fertility restorer line in pigeon pea (Cajanus cajan L.)
Cited by: 11
Author(s): Swati Saxena, Sarika Sahu, Tanvi Kaila, Deepti Nigam, Pavan K. Chaduvla, A. Ramachandra Rao, Sankaran Sandhya, Nagendra Singh, Kishor Gaikwad
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-019-1709-y

Mal de Río Cuarto virus infection causes hormone imbalance and sugar accumulation in wheat leaves
Cited by: 17
Author(s): Luis Alejandro de Haro, Sofía Maité Arellano, Ondřej Novák, Regina Feil, Analía Delina Dumón, María Fernanda Mattio, Danuše Tarkowská, Gabriela Llauger, Miroslav Strnad, John E. Lunn, Stephen Pearce, Carlos María Figueroa, Mariana del Vas
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-020-2267-z

Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools
Cited by: 16
Author(s): Lucía de la Rosa Fernández, E. Zambrana, Elena Ramírez-Parra
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-020-02555-5

Heat-response patterns of the heat shock transcription factor family in advanced development stages of wheat (Triticum aestivum L.) and thermotolerance-regulation by TaHsfA2–10
Cited by: 18
Author(s): Xiulin Guo, Shuo Yuan, Huaning Zhang, Yuanyuan Zhang, Yujie Zhang, Guiyan Wang, Yaqing Li, Guoliang Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-021-02899-6

Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana
Cited by: 11
Author(s): Guiming Deng, Fangcheng Bi, Jing Liu, Wei He, Chunyu Li, Tingting Dong, Qiaosong Yang, Hongyuan Gao, Tongxin Dou, Xiaohong Zhong, Peng Miao, Ganjun Yi, Chunhua Hu, Ou Sheng
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-019-1998-1

Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis
Cited by: 28
Author(s): Agustín Sabbione, Lucas D. Daurelio, Abelardo Carlos Vegetti, Manuel Talón, Francisco R. Tadeo, Marcela C. Dotto
Software Mentions: 1
Published: about 7 years ago

10.1186/s12870-021-03121-3

Metabolome and transcriptome profiling provide insights into green apple peel reveals light- and UV-B-responsive pathway in anthocyanins accumulation
Cited by: 15
Author(s): Ruirui Ding, Xingkai Che, Zhen Shen, Yuanhu Zhang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-018-1242-4

Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing
Cited by: 68
Author(s): Xiucun Zeng, XU Yao-zhao, Jinjin Jiang, Fenqin Zhang, Lan Ma, Dewei Wu, Youping Wang, Weizheng Sun
Software Mentions: 1
Published: over 8 years ago

10.1186/s12870-019-1652-y

Swift metabolite changes and leaf shedding are milestones in the acclimation process of grapevine under prolonged water stress
Cited by: 28
Author(s): Asfaw Degu, Uri Hochberg, D. Wong, Giorgio Alberti, Naftali Lazarovitch, Enrico Peterlunger, Simone D. Castellarin, José Carlos Herrera, Aaron Fait
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-020-02554-6

Integrated metabolomics and transcriptome analysis on flavonoid biosynthesis in safflower (Carthamus tinctorius L.) under MeJA treatment
Cited by: 42
Author(s): Chen Jiang, Jie Wang, Rui Wang, Bin Xian, Chaoxiang Ren, Qianqian Liu, Qinghua Wu, Jin Pei
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-019-2124-0

Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima?
Cited by: 12
Author(s): Cátia Monteiro, Huiru Li, Kai Bischof, Inka Bartsch, Klaus Valentin, Matthieu Le Corre, Jonas Collén, Lars Harms, Gernot Glöckner, S. Heinrich
Software Mentions: 1
Published: almost 7 years ago

Projects: bioconductor: DESeq2

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583