bioconductor: EBSeq | Projects | Ecosyste.ms: Papers

10.3389/fpls.2017.01233

Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry
Cited by: 76
Author(s): Irina Ionescu, Gregorio López‐Ortega, Meike Burow, Almudena Bayo-Canha, Alexander Junge, Oliver Gericke, Birger Lindberg Møller, Raquel Sánchez‐Pérez
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2021.639368

Cycad-Weevil Pollination Symbiosis Is Characterized by Rapidly Evolving and Highly Specific Plant-Insect Chemical Communication
Cited by: 7
Author(s): Shayla Salzman, Damon J. Crook, Michael Calonje, Dennis Wm. Stevenson, Naomi E. Pierce, Robin Hopkins
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2017.00322

isomiR2Function: An Integrated Workflow for Identifying MicroRNA Variants in Plants
Cited by: 9
Author(s): Kun Yang, Gaurav Sablok, Guang Hang Qiao, Qiang Nie, Xiaopeng Wen
Software Mentions: 3
Published: over 7 years ago

10.1038/hortres.2017.5

Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments
Cited by: 22
Author(s): Yuling Wang, Xinfu Zhang, Ran Wang, Ying-Xin Bai, Chenglian Liu, Yuan Yang, Yingjie Yang, Shaolan Yang
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/erw386

Post-transcriptional regulation of photosynthetic genes is a key driver of C4leaf ontogeny
Cited by: 15
Author(s): Niklaus Fankhauser, Sylvain Aubry
Software Mentions: 3
Published: about 8 years ago

10.1038/srep18470

Genome-wide analysis of microRNAs identifies the lipid metabolism pathway to be a defining factor in adipose tissue from different sheep
Cited by: 37
Author(s): Xiangyang Miao, Qingmiao Luo, Xiaoqiong Qin, Yuntao Guo
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-020-61007-0

De novo transcriptome of the diatom Cylindrotheca closterium identifies genes involved in the metabolism of anti-inflammatory compounds
Cited by: 21
Author(s): Ali Murat Elagoz, Luca Ambrosino, Chiara Lauritano
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-70673-z

Unique molecular signatures of antiviral memory CD8+ T cells associated with asymptomatic recurrent ocular herpes
Cited by: 2
Author(s): Swayam Prakash, Subhransu Roy, Ruchi Srivastava, Pierre-Gregoire A Coulon, Nisha R Dhanushkodi, Hawa Vahed, Allen Jankeel, Roger Geertsema, Cassandra Amezquita, Lan Nguyễn, Ilhem Messaoudi, Amanda M. Burkhardt, Lbachir BenMohamed
Software Mentions: 3
Published: over 4 years ago

10.1128/mSphere.00065-20

Convergence between Regulation of Carbon Utilization and Catabolic Repression in Xanthophyllomyces dendrorhous
Cited by: 3
Author(s): Pilar Martínez-Moya, Sebastián Campusano, Pamela Córdova, Alberto Paradela, Dionisia Sepúlveda, Jennifer Alcaı́no, Marcelo Baeza, Víctor Cifuentes
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.19027

Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network
Cited by: 27
Author(s): Meihua Christina Kuang, Paul D. Hutchins, John N. Russell, Joshua J. Coon, Chris Todd Hittinger
Software Mentions: 3
Published: about 8 years ago

10.3390/ijms16035975

RNA-Seq Transcriptome Analysis of Maize Inbred Carrying Nicosulfuron-Tolerant and Nicosulfuron-Susceptible Alleles
Cited by: 26
Author(s): Xiaomin Liu, Xiaogang Xu, Binghua Li, Xueqing Wang, Guiqi Wang, Yaqian Li
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms22158249

Transcriptome-Based WGCNA Analysis Reveals Regulated Metabolite Fluxes between Floral Color and Scent in Narcissus tazetta Flower
Cited by: 20
Author(s): Jingwen Yang, Yujun Ren, Deyu Zhang, Xuewei Chen, Jiazhi Huang, Yun Xu, Cristina Belén Aucapiña Criollo, Yu Zhang, Ying Miao
Software Mentions: 3
Published: over 3 years ago

10.18632/oncotarget.8209

C-terminal truncated hepatitis B virus X protein promotes hepatocellular carcinogenesis through induction of cancer and stem cell-like properties
Cited by: 41
Author(s): Kai-Yu Ng, Stella Chai, Man Tong, Xin‐Yuan Guan, Chi-Ho Lin, Yick–Pang Ching, Dan Xie, Alfred S.L. Cheng, Stephanie Ma
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0162838

The Involvement of Mig1 from Xanthophyllomyces dendrorhous in Catabolic Repression: An Active Mechanism Contributing to the Regulation of Carotenoid Production
Cited by: 24
Author(s): Jennifer Alcaı́no, Natalia Bravo, Pamela Córdova, Andrés E. Marcoleta, Gabriela Contreras, Salvador Barahona, Dionisia Sepúlveda, María Fernández‐Lobato, Marcelo Baeza, Víctor Cifuentes
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0223134

Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto
Cited by: 10
Author(s): Sofia Paraskevopoulou, Alice B. Dennis, Guntram Weithoff, Stefanie Hartmann, Ralph Tiedemann
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0141446

Gene Expression Analysis of Pak Choi in Response to Vernalization
Cited by: 18
Author(s): Mengxia Sun, Xianhui Qi, Leiping Hou, Xiaoyong Xu, Zhujun Zhu, Meilan Li
Software Mentions: 2
Published: about 9 years ago

10.1155/2020/2109325

Disease-Specific Autoantibodies Induce Trained Immunity in RA Synovial Tissues and Its Gene Signature Correlates with the Response to Clinical Therapy
Cited by: 3
Author(s): Xiaoli Dai, Xiaoqiu Dai, Zheng Gong, Chen Yang, Keqin Zeng, Fang‐Yuan Gong, Qiao Zhong, Xiao‐Ming Gao
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0225073

Next generation sequencing and RNA-seq characterization of adipose tissue in the Nile crocodile (Crocodylus niloticus) in South Africa: Possible mechanism(s) of pathogenesis and pathophysiology of pansteatitis
Cited by: 3
Author(s): O. I. Azeez, Jan G. Myburgh, Anna-Marì Bosman, Jonathan Featherston, Kgomotso P. Sibeko-Matjilla, Marinda C. Oosthuizen, Joseph Panashe Chamunorwa
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms19124069

Notched Belly Grain 4, a Novel Allele of Dwarf 11, Regulates Grain Shape and Seed Germination in Rice (Oryza sativa L.)
Cited by: 15
Author(s): Xiaohong Tong, Yifeng Wang, Aixin Sun, Babatunde Kazeem Bello, Shen Ni, Jian Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0193193

Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L.
Cited by: 12
Author(s): Yufeng Yang, Yannan Wang, Licong Jia, Gangyi Yang, Xianzhu Xu, Hong Zhai, Shaozhen He, Junxia Li, Xiaodong Dai, Na Qin, Cancan Zhu, Qingchang Liu
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20081955

miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA
Cited by: 11
Author(s): Lianna Fung, Herlinda Guzman, Evgueni A. Sevrioukov, Adam Idica, Eddie Park, Aurore Bochnakian, Iben Daugaard, Douglas Jury, A Mortazavi, Dimitrios G. Zisoulis, Irene M. Pedersen
Software Mentions: 2
Published: over 5 years ago

10.3390/md18080386

De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates
Cited by: 19
Author(s): Giorgio Maria Vingiani, Dārta Štālberga, Pasquale De Luca, Adrianna Ianora, Danièle De Luca, Chiara Lauritano
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0139401

The Effects of Synthetic Estrogen Exposure on the Sexually Dimorphic Liver Transcriptome of the Sex-Role-Reversed Gulf Pipefish
Cited by: 15
Author(s): Emily Rose, Sarah P. Flanagan, Adam G. Jones
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0135046

Candidate Resistant Genes of Sand Pear (Pyrus pyrifolia Nakai) to Alternaria alternata Revealed by Transcriptome Sequencing
Cited by: 20
Author(s): Xiaoping Yang, Hongju Hu, Dawei Yu, Zilin Sun, Xinhua He, Jingguo Zhang, Qiliang Chen, Rui Tian, Jing Fan
Software Mentions: 2
Published: over 9 years ago

10.15252/emmm.201910895

Follistatin is a novel therapeutic target and biomarker in <scp>FLT</scp> 3/ <scp>ITD</scp> acute myeloid leukemia
Cited by: 11
Author(s): Ben He, Ning Yang, Cheuk Him Man, Nelson Ka Lam Ng, Chae Yin Cher, Ho Ching Leung, Leo Lai Hok Kan, Bowie Y. Cheng, Simon S. K. Lam, Michelle Lu Lu Wang, Chun Xiao Zhang, Harry Kwok, Grace Cheng, Rakesh Sharma, Alvin Chun Hang, Chi Wai Eric So, Yok Lam Kwong, Anskar Yu Hung Leung
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.2142

Transcriptome response to temperature stress in the wolf spider Pardosa pseudoannulata (Araneae: Lycosidae)
Cited by: 30
Author(s): Rong Xiao, Liang Wang, Yingshuai Cao, Guren Zhang
Software Mentions: 2
Published: over 8 years ago

10.1155/2019/6159490

Integrated Analysis of LncRNA-mRNA Coexpression in the Extracellular Matrix of Developing Deciduous Teeth in Miniature Pigs
Cited by: 1
Author(s): Yang Li, Guoqing Li, Fu Wang, Xiaoshan Wu, Zhifang Wu, Jinsong Wang, Chunmei Zhang, Junqi He, Hao Wang, Songlin Wang
Software Mentions: 2
Published: almost 6 years ago

10.1080/08927014.2016.1233325

Profiling of adhesive-related genes in the freshwater cnidarianHydra magnipapillataby transcriptomics and proteomics
Cited by: 36
Author(s): Marcos Rodrigues, Thomas Ostermann, Leopold Kremeser, Herbert Lindner, Christian Beisel, Eugène Berezikov, Bert Hobmayer, Peter Ladurner
Software Mentions: 2
Published: about 8 years ago

10.12688/f1000research.25750.1

RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development
Cited by: 2
Author(s): Maria G. Ivanchenko, Olivia R. Ozguc, Stephanie R. Bollmann, Valerie N. Fraser, Molly Megraw
Software Mentions: 2
Published: about 4 years ago

10.1186/1756-0500-6-503

Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
Cited by: 18
Author(s): Emmanuel González, Simon Joly
Software Mentions: 2
Published: almost 11 years ago

10.3389/fgene.2020.00135

Pituitary-Derived Circular RNAs Expression and Regulatory Network Prediction During the Onset of Puberty in Landrace × Yorkshire Crossbred Pigs
Cited by: 6
Author(s): Zitao Chen, Xiangchun Pan, Yaru Kong, Yao Jiang, Yuyi Zhong, Hao Zhang, Zhe Zhang, Xiaolong Yuan, Jiaqi Li
Software Mentions: 2
Published: over 4 years ago

10.1186/s12870-015-0636-9

Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil
Cited by: 21
Author(s): Emmanuel González, Nicholas J. B. Brereton, Julie Marleau, Werther Guidi Nissim, Michel Labrecque, Frédéric E. Pitre, Simon Joly
Software Mentions: 2
Published: about 9 years ago

10.3389/fgene.2020.00474

Bulked Segregant RNA-Seq Reveals Distinct Expression Profiling in Chinese Wheat Cultivar Jimai 23 Responding to Powdery Mildew
Cited by: 10
Author(s): Tong Zhu, Liru Wu, Huagang He, Jiancheng Song, Mengshu Jia, Liancheng Liu, Xiaolu Wang, Ran Han, Liping Niu, Wei Du, Xu Zhang, Wenrui Wang, Liang Xiao, Haosheng Li, Jing Liu, Hongxing Xu, Cheng Liu, Pengtao Ma
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2021.579800

Whole-Transcriptome Analysis of Yak and Cattle Heart Tissues Reveals Regulatory Pathways Associated With High-Altitude Adaptation
Cited by: 4
Author(s): Hui Wang, Jincheng Zhong, Jikun Wang, Zhixin Chai, Chengfu Zhang, Jinwei Xin, Jiabo Wang, Xin Cai, Zhijuan Wu, Qiumei Ji
Software Mentions: 2
Published: over 3 years ago

10.1186/s12870-016-0969-z

MicroRNA 157-targeted SPL genes regulate floral organ size and ovule production in cotton
Cited by: 49
Author(s): Nian Liu, Lili Tu, Lichen Wang, Haiyan Hu, Jiao Xu, Xianlong Zhang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12870-020-02539-5

Identification of the vernalization gene VRN-B1 responsible for heading date variation by QTL mapping using a RIL population in wheat
Cited by: 13
Author(s): Yuting Li, Hui Xiong, Huijun Guo, Chunyun Zhou, Yi Xie, Liyan Zhao, Jun Gu, Shirong Zhao, Yuping Ding, Luxiang Liu
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2018.03209

Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1
Cited by: 19
Author(s): Kriti Sengupta, Martin Swain, Paul Livingstone, David E. Whitworth, Pradipta Saha
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-019-5682-5

Tissue specific human fibroblast differential expression based on RNAsequencing analysis
Cited by: 36
Author(s): Alexander G. Foote, Ziyue Wang, Christina Kendziorski, Susan L. Thibeault
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2018.01376

Extremophiles as a Model of a Natural Ecosystem: Transcriptional Coordination of Genes Reveals Distinct Selective Responses of Plants Under Climate Change Scenarios
Cited by: 9
Author(s): Stephanie Karenina Bajay, Mariana Vargas Cruz, Carla Cristina da Silva, Natália Faraj Murad, Marcelo Mendes Brandão, Anete Pereira de Souza
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-14-916

Comparative inner ear transcriptome analysis between the Rickett’s big-footed bats (Myotis ricketti) and the greater short-nosed fruit bats (Cynopterus sphinx)
Cited by: 23
Author(s): Dong Dong, Ming Lei, Yang Liu, Shuyi Zhang
Software Mentions: 2
Published: almost 12 years ago

10.3389/fpls.2021.714907

Knockdown of miR393 Promotes the Growth and Biomass Production in Poplar
Cited by: 11
Author(s): Liwei Chu, Xuejiao He, Wenbo Shu, Limin Wang, Fang Tang
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2021.667678

Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development
Cited by: 9
Author(s): Parul Gupta, Matthew Geniza, Sushma Naithani, Jeremy Phillips, Ebaad Haq, Pankaj Jaiswal
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms21093288

Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit
Cited by: 22
Author(s): Yanyan Wu, Juan Xu, Xuelei Han, Guo Qiao, Kun Yang, Wen Zhuang, Xiaopeng Wen
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2017.00553

Comprehensive Transcriptome Analyses Reveal Differential Gene Expression Profiles of Camellia sinensis Axillary Buds at Para-, Endo-, Ecodormancy, and Bud Flush Stages
Cited by: 62
Author(s): Xinyuan Hao, Yajun Yang, Chuan Yue, Lu Wang, David P. Horvath, Xinchao Wang
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.118.200292

Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte
Cited by: 19
Author(s): Nadia M. Atallah, Olga Vitek, Federico Gaiti, Miloš Tanurdžić, Jo Ann Banks
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.118.201008

Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development
Cited by: 72
Author(s): Andrea Minio, Mélanie Massonnet, Rosa Figueroa‐Balderas, Amanda M. Vondras, Bárbara Blanco-Ulate, Dario Cantu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-07332-0

Hepatic transcriptome perturbations in dairy cows fed different forage resources
Cited by: 5
Author(s): Shengtao Gao, Lu Ma, Yangdong Zhang, Jiaqi Wang, JuanJuan Loor, Dengpan Bu
Software Mentions: 2
Published: almost 4 years ago

10.3390/genes10100800

Pollination Drop Proteome and Reproductive Organ Transcriptome Comparison in Gnetum Reveals Entomophilous Adaptation
Cited by: 7
Author(s): Chen Hou, Richard M. Saunders, Nan Deng, Tao Wan, Yingjuan Su
Software Mentions: 2
Published: about 5 years ago

10.3390/genes12050764

Characteristics of the AT-Hook Motif Containing Nuclear Localized (AHL) Genes in Carrot Provides Insight into Their Role in Plant Growth and Storage Root Development
Cited by: 4
Author(s): Gabriela Machaj, Dariusz Grzebelus
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-015-1939-9

A transcriptome approach towards understanding the development of ripening capacity in ‘Bartlett’ pears (Pyrus communis L.)
Cited by: 24
Author(s): Ngoc T. Nham, Sérgio Tonetto de Freitas, Andrew J. Macnish, Kevin M. Carr, Trisha Kietikul, Angelo Jose Guilatco, Cai‐Zhong Jiang, Florence Negre-Zakharov, Elizabeth Mitcham
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-015-0620-6

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy
Cited by: 401
Author(s): Mihaela Angelova, Pornpimol Charoentong, Hubert Hackl, M. Fischer, René Snajder, Anne Krogsdam, Maximilian J. Waldner, Gabriela Bindea, Bernhard Mlecnik, Jérôme Galon, Zlatko Trajanoski
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-021-07786-w

Ovary-derived circular RNAs profile analysis during the onset of puberty in gilts
Cited by: 8
Author(s): Xiangchun Pan, Wentao Gong, Yingting He, Nian Li, Hao Zhang, Zhe Zhang, Jiaqi Li, Xiaolong Yuan
Software Mentions: 2
Published: over 3 years ago

10.1016/j.gpb.2018.07.008

Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity
Cited by: 10
Author(s): Sixue Liu, Zuyu Yang, Guanghao Li, Chunyan Li, Ye Luo, Qiang Gong, Xin Wu, Tao Li, Zhiqian Zhang, Baocai Xing, Xiaolan Xu, Xuemei Lu
Software Mentions: 2
Published: almost 5 years ago

10.1093/gigascience/gix023

Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics
Cited by: 91
Author(s): Yuling Lin, Min Jiang, Renchun Lai, Zhangyan Wu, Yukun Chen, Lili Yu, Chunzhen Cheng, Yuan-Chun Jin, Qifeng Tian, Qingfeng Li, Weihua Liu, Chengguang Zhang, Lixia Lin, Yan Hu, Dongmin Zhang, Minkyaw Thu, Zi-Hao Zhang, Shengcai Liu, Chunshui Zhong, Xiaodong Fang, Jian Wang, Huanming Yang, Rajeev K. Varshney, Ye Yin, Lai Zhang
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms22073532

Withholding of M-CSF Supplement Reprograms Macrophages to M2-Like via Endogenous CSF-1 Activation
Cited by: 9
Author(s): Yu‐Chih Chen, Yin‐Siew Lai, Yan‐Der Hsuuw, Ko‐Tung Chang
Software Mentions: 2
Published: over 3 years ago

10.1038/s41438-018-0067-5

The origin and biosynthesis of the naphthalenoid moiety of juglone in black walnut
Cited by: 38
Author(s): Rachel M. McCoy, Sagar M. Utturkar, Joseph W. Crook, Jyothi Thimmapuram, Joshua R. Widhalm
Software Mentions: 2
Published: about 6 years ago

10.3390/jdb8040034

Mud Loss Restricts Yki-Dependent Hyperplasia in Drosophila Epithelia
Cited by: 2
Author(s): Amalia S. Parra, Christopher A. Johnston
Software Mentions: 2
Published: almost 4 years ago

10.18632/oncotarget.22995

RNA-seq expression profiling of rat MCAO model following reperfusion Orexin-A
Cited by: 16
Author(s): Chunmei Wang, Yanyou Pan, Minghui Liu, Baohua Cheng, Bo Bai, Jing Chen
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-015-1253-6

Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights
Cited by: 27
Author(s): Jane Khudyakov, Likit Preeyanon, Cory D. Champagne, Rudy M. Ortiz, Daniel E. Crocker
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijms221910604

MERTK+/hi M2c Macrophages Induced by Baicalin Alleviate Non-Alcoholic Fatty Liver Disease
Cited by: 11
Author(s): Júnior, Yin‐Siew Lai, Hoa Thi Minh Nguyen, Farrah P. Salmanida, Ko‐Tung Chang
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-017-18757-1

Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys
Cited by: 55
Author(s): Paige Herman, Angelos Papatheodorou, Stephanie A. Bryant, Courtney K. M. Waterbury, Joseph R. Herdy, Anthony A. Arcese, Joseph D. Buxbaum, Jeramiah J. Smith, James L. Morgan, Ona Bloom
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-021-07563-9

Strategies for detecting and identifying biological signals amidst the variation commonly found in RNA sequencing data
Cited by: 3
Author(s): William W. Wilfinger, Robert G. Miller, Hamid R. Eghbalnia, Karol Mackey, Piotr Chomczyński
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-018-24727-y

Comparative transcriptome analysis to investigate the potential role of miRNAs in milk protein/fat quality
Cited by: 17
Author(s): Xuehui Wang, Li Zhang, Jing Jin, Anting Xia, Chunmei Wang, Yingjun Cui, Bo Qu, LI Qing-zhang, Sheng Chen
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-26953-w

Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas
Cited by: 13
Author(s): Zhicai She, Li Li, Jie Meng, Zhen Jia, Huayong Que, Guofan Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/s40478-019-0727-1

Tenascin-C expression contributes to pediatric brainstem glioma tumor phenotype and represents a novel biomarker of disease
Cited by: 23
Author(s): Jin Qi, Darian R. Esfahani, Tai‐Chung Huang, Patrick A. Ozark, Elizabeth T. Bartom, Rintaro Hashizume, Erin R. Bonner, Shi An, Craig Horbinski, C. David James, Amanda Saratsis
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-74085-x

Genetic analysis of the molecular regulation of electric fields-guided glia migration
Cited by: 2
Author(s): Li Yao, Teresa D. Shippy, Yongchao Li
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-75855-3

Understanding complex dynamics of behavioral, neurochemical and transcriptomic changes induced by prolonged chronic unpredictable stress in zebrafish
Cited by: 17
Author(s): Konstantin A. Demin, Anton M. Lakstygal, Nataliya A. Krotova, Alexey Masharsky, Natsuki Tagawa, Maria V. Chernysh, Nikita P. Ilyin, Alexander S. Taranov, David S. Galstyan, Ksenia A. Derzhavina, Nataliia A. Levchenko, Т. А. Колесникова, Mikael S. Mor, Marina L. Vasyutina, Evgeniya V. Efimova, Nataliia V. Katolikova, Andrey D. Prjibelski, Raul R. Gainetdinov, Murilo S. de Abreu, Tamara G. Amstislavskaya, Tatyana Strekalova, Allan V. Kalueff
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-017-4257-6

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI
Cited by: 38
Author(s): Weijing Wang, Wenjie Jiang, Lin Hou, Haiping Duan, Yili Wu, Chunsheng Xu, Qihua Tan, Shuxia Li, Dongfeng Zhang
Software Mentions: 2
Published: about 7 years ago

10.7150/thno.42259

Stem cell-derived exosomes prevent pyroptosis and repair ischemic muscle injury through a novel exosome/circHIPK3/ FOXO3a pathway
Cited by: 96
Author(s): Bing Yan, Yu Zhang, Chun Liang, Bin Liu, Fengzhi Ding, Yanli Wang, Bao Ting Zhu, Ranzun Zhao, Xiyong Yu, Yangxin Li
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41388-020-1210-y

Phosphorylation independent eIF4E translational reprogramming of selective mRNAs determines tamoxifen resistance in breast cancer
Cited by: 17
Author(s): Chun Gong, Ho Tsoi, Ka Chun Mok, J.T. K. Cheung, Ellen P.S. Man, Keiji Fujino, Ashely Wong, Eric W.‐F. Lam, Ui‐Soon Khoo
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-019-3302-7

Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments
Cited by: 20
Author(s): Benjamin Hur, Dong‐Won Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee, Sun Kim
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms17122033

Transcriptome Profiling Analysis of Wolf Spider Pardosa pseudoannulata (Araneae: Lycosidae) after Cadmium Exposure
Cited by: 28
Author(s): Changchun Li, Yong Wang, Guoyuan Li, Yun Yao, Yunfeng Dai, Jian Chen, Yu Peng
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.7528

Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
Cited by: 8
Author(s): Jianzhou Qu, Shutu Xu, Xiaokang Tian, Ting Li, Licheng Wang, Yuyue Zhong, Jiquan Xue, Dongwei Guo
Software Mentions: 2
Published: about 5 years ago

10.3390/v12030311

Suppression of a Subset of Interferon-Induced Genes by Human Papillomavirus Type 16 E7 via a Cyclin Dependent Kinase 8-Dependent Mechanism
Cited by: 5
Author(s): Sadie Rice, Seong‐Man Kim, Cynthia Rodríguez, William K. Songock, G. Raikhy, Rebecca Lopez, Lauren A. Henderson, Arjun Yusufji, Jason M. Bodily
Software Mentions: 2
Published: over 4 years ago

10.1111/pbi.12578

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy
Cited by: 37
Author(s): Bradley C. Campbell, Edward K. Gilding, Emma Mace, Shuaishuai Tai, Yongfu Tao, Peter J. Prentis, Pauline Thomelin, David R. Jordan, Ian D. Godwin
Software Mentions: 2
Published: over 8 years ago

10.3390/plants8070216

The AabHLH35 Transcription Factor Identified from Anthurium andraeanum is Involved in Cold and Drought Tolerance
Cited by: 15
Author(s): Li Jiang, Xiaowen Tian, Shuting Li, Yanhong Fu, Jingya Xu, Guangdong Wang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.3000498

Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids
Cited by: 116
Author(s): Sapna Chhabra, Lizhong Liu, Ryan Goh, Xiangyu Kong, Aryeh Warmflash
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1005690

Compound Heterozygosity for Y Box Proteins Causes Sterility Due to Loss of Translational Repression
Cited by: 35
Author(s): Elizabeth M. Snyder, Ramani Soundararajan, Manju Sharma, Andrea Dearth, Benjamin Smith, Robert E. Braun
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1008252

The demethylase NMAD-1 regulates DNA replication and repair in the Caenorhabditis elegans germline
Cited by: 16
Author(s): Simon Yuan Wang, Ming Hui, Hiroki Shibuya, Satoru Uzawa, Zach Klapholz O’Brown, Sage Wesenberg, Nara Shin, Takamune T. Saito, Jinmin Gao, Barbara J Meyer, Mónica P. Colaiácovo, Eric Lieberman Greer
Software Mentions: 2
Published: over 5 years ago

10.1099/mgen.0.000031

Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073
Cited by: 14
Author(s): Heer H. Mehta, Yuxuan Liu, Michael Q. Zhang, Stephen Spiro
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.3303

Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes
Cited by: 9
Author(s): Hanting Chen, Cao Deng, Hongtao Nie, Gang Fan, Yang He
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-26157-2

Genome-wide analysis of circular RNAs in bovine cumulus cells treated with BMP15 and GDF9
Cited by: 22
Author(s): Yao Fu, Hao Jiang, Jianbo Li, Xiaolong Sun, Zhe Zhang, Sheng Li, Yan Gao, Bao Yuan
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-019-3429-4

Transcriptional alterations in Caenorhabditis elegans following exposure to an anthelmintic fraction of the plant Picria fel-terrae Lour.
Cited by: 2
Author(s): Rasika Kumarasingha, Neil D. Young, Tiong Chia Yeo, Diana S L Lim, Chu Lee Tu, Enzo A. Palombo, Jillian M Shaw, Robin B. Gasser, Peter R. Boag
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2017.01115

Transcriptomic Response of Purple Willow (Salix purpurea) to Arsenic Stress
Cited by: 31
Author(s): Aymeric Yanitch, Nicholas J. B. Brereton, Emmanuel González, Michel Labrecque, Simon Joly, Frédéric E. Pitre
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-43054-4

UM171 expands distinct types of myeloid and NK progenitors from human pluripotent stem cells
Cited by: 20
Author(s): Walatta-Tseyon Mesquitta, Matthew Wandsnider, Ho Jung Kang, James A. Thomson, Oleg V. Moskvin, Kran Suknuntha, Igor I. Slukvin
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-44062-0

Co-overexpression of AVP1 and OsSIZ1 in Arabidopsis substantially enhances plant tolerance to drought, salt, and heat stresses
Cited by: 25
Author(s): Nardana Esmaeili, Xiaohong Yang, Yifan Cai, Li Sun, Xunlu Zhu, Guoxin Shen, Paxton Payton, Weiping Fang, Hong Zhang
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2017.00879

miR397/Laccase Gene Mediated Network Improves Tolerance to Fenoxaprop-P-ethyl in Beckmannia syzigachne and Oryza sativa
Cited by: 22
Author(s): Lang Pan, Hongwei Zhao, Qin Yu, Lianyang Bai, Liyao Dong
Software Mentions: 1
Published: over 7 years ago

10.1186/s12974-021-02212-0

Microglial responses to CSF1 overexpression do not promote the expansion of other glial lineages
Cited by: 3
Author(s): Ishani De, Vilena I. Maklakova, Suzanne J. Litscher, Michelle M. Boyd, Lucas C. Klemm, Ziyue Wang, Christina Kendziorski, Lara S. Collier
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22041517

Transcriptome Sequencing in the Preoptic Region of Rat Dams Reveals a Role of Androgen Receptor in the Control of Maternal Behavior
Cited by: 4
Author(s): András H. Lékó, Rashmi Kumari, Fanni Dóra, David W. Keller, Edina Brigitta Udvari, Vivien Csikós, Éva Renner, Árpád Dobolyi
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpls.2015.00964

Transcriptome sequencing of purple petal spot region in tree peony reveals differentially expressed anthocyanin structural genes
Cited by: 51
Author(s): Yanzhao Zhang, Yanwei Cheng, Huiyuan Ya, Shuzhen Xu, Jianming Han
Software Mentions: 1
Published: about 9 years ago

10.3389/fvets.2021.641022

Safety and Transcriptome Analysis of Live Attenuated Brucella Vaccine Strain S2 on Non-pregnant Cynomolgus Monkeys Without Abortive Effect on Pregnant Cynomolgus Monkeys
Cited by: 4
Author(s): Shan Sun, Hui Jiang, Qiaoling Li, Yufu Liu, Qiang Gao, Wei Liu, Yuming Qin, Yu Feng, Xiaowei Peng, Guanlong Xu, Qijun Shen, Xuezheng Fan, Jiabo Ding, Li Zhu
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.9096

Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling
Cited by: 2
Author(s): Xiaohui Yang, Xuewu Guo, Guangxia Chen, Dan Dong, Fang Liu, Yaolong Yang, Yang Yu, Guangcun Li
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms18091923

Structure of Pigment Metabolic Pathways and Their Contributions to White Tepal Color Formation of Chinese Narcissus tazetta var. chinensis cv Jinzhanyintai
Cited by: 16
Author(s): Yujun Ren, Jingwen Yang, Bingguo Lu, Yunliang Jiang, Haiyang Chen, Hong Yan, Binghua Wu, Ying Miao
Software Mentions: 1
Published: about 7 years ago

10.1155/2019/4946824

High Expression and Clinical Significance of Elafin in Colorectal Cancer
Cited by: 3
Author(s): Yun Liu, Yu Tian, Ting Wu, Yun Dai, Weihong Wang, Guigen Teng
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-020-6518-z

Coexpression and Transcriptome analyses identify active Apomixis-related genes in Paspalum notatum leaves
Cited by: 12
Author(s): Fabrício Augusto de Oliveira, B. B. Z. Vigna, Carla Cristina da Silva, A. P. Fávero, Frederico de Pina Matta, Ana Luisa Sousa Azevedo, Anete Pereira de Souza
Software Mentions: 1
Published: almost 5 years ago

10.1186/s40168-018-0432-5

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination
Cited by: 78
Author(s): Emmanuel González, Frédéric E. Pitre, Antoine Pagé, Julie Marleau, Werther Guidi Nissim, Marc St‐Arnaud, Michel Labrecque, Simon Joly, Étienne Yergeau, Nicholas J. B. Brereton
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0204404

Transcriptomic analysis reveals critical genes for the hair follicle of Inner Mongolia cashmere goat from catagen to telogen
Cited by: 25
Author(s): Rui Su, Yixing Fan, Xuguang Qiao, Xiaokai Li, Lei Zhang, Chun Li, Jinquan Li
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0123878

Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development
Cited by: 13
Author(s): Lili Song, Wei Zeng, Aimin Wu, Kelsey L. Picard, Edwin R. Lampugnani, Roshan Cheetamun, Cherie T. Beahan, Andrew Cassin, Andrew Lonsdale, Monika S. Doblin, Antony Bacic
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0187105

Differential transcriptome analysis reveals genes related to cold tolerance in seabuckthorn carpenter moth, Eogystia hippophaecolus
Cited by: 24
Author(s): Mingming Cui, Ping Hu, Tao Wang, Jing Tao, Shixiang Zong
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms19020396

Comparative Transcriptome Analyses Uncover Key Candidate Genes Mediating Flight Capacity in Bactrocera dorsalis (Hendel) and Bactrocera correcta (Bezzi) (Diptera: Tephritidae)
Cited by: 13
Author(s): Shaokun Guo, Zhijun Zhao, Lijun Liu, Zhihong Li, Jie Shen
Software Mentions: 1
Published: almost 7 years ago

Projects: bioconductor: EBSeq

Papers Mentioning EBSeq 261