bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1155/2021/8846951

Construction of Potential Gene Expression and Regulation Networks in Prostate Cancer Using Bioinformatics Tools
Cited by: 4
Author(s): Heyu Liu, Lirong Li, Fan Yu, Yaping Lü, Changhong Zhu, Wei Xia
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41398-020-01012-z

Characterization of the intergenerational impact of in utero and postnatal oxycodone exposure
Cited by: 16
Author(s): Katherine E. Odegaard, Victoria L. Schaal, Alexander R. Clark, Sneh Koul, Austin Gowen, Jagadesan Sankarasubramani, Xiao Peng, Chittibabu Guda, Steven J. Lisco, Sowmya V. Yelamanchili, Gurudutt Pendyala
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41398-020-01065-0

Full function of exon junction complex factor, Rbm8a, is critical for interneuron development
Cited by: 15
Author(s): Colleen McSweeney, Fengqin Dong, Miranda Chen, Jessica Vitale, Li Xu, Nicole A. Crowley, Bernhard Lüscher, Donghua Zou, Ying Mao
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms21030817

Role of Phagocytosis in the Pro-Inflammatory Response in LDL-Induced Foam Cell Formation; a Transcriptome Analysis
Cited by: 16
Author(s): Alexander N. Orekhov, Nikita G. Nikiforov, Vasily N. Sukhorukov, M. Kubekina, Igor A. Sobenin, Wei-Kai Wu, Kathy Foxx, Sergey S. Pintus, Philip Stegmaier, Daria Stelmashenko, Alexander Kel, Alexei Gratchev, Alexandra А. Melnichenko, Reinhard Wetzker, Volha I Summerhill, Ichiro Manabe, Yumiko Oishi
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21030745

Divergent Regulation of Myotube Formation and Gene Expression by E2 and EPA during In-Vitro Differentiation of C2C12 Myoblasts
Cited by: 8
Author(s): Orly Lacham‐Kaplan, Donny M. Camera, John A. Hawley
Software Mentions: 1
Published: over 6 years ago

10.1038/s41398-021-01270-5

Genome-wide gene expression changes in postpartum depression point towards an altered immune landscape
Cited by: 10
Author(s): Divya Mehta, Karen Grewen, Brenda Pearson, Shivangi Wani, Leanne Wallace, Anjali K. Henders, Elisabeth B. Binder, Vibe G. Frøkjær, Samantha Meltzer‐Brody, Naomi R. Wray, Alison M. Stuebe
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07879-6

Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development
Cited by: 5
Author(s): Yun Tang, Jing-Yi Chen, Guohua Ding, Lin Zhen-shan
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-020-6494-3

Transcriptomic analysis of the testicular fusion in Spodoptera litura
Cited by: 5
Author(s): Yaqing Chang, Jun Ou, Yucheng Liu, Qiong Wu, Liang Wen, Sichun Zheng, Li Sheng, Qili Feng, Lin Liu
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.11755

Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale)
Cited by: 2
Author(s): Mengjun Huang, Haitao Xing, Zhexin Li, Honglei Li, Lin Wu, Yi Jiang
Software Mentions: 1
Published: about 5 years ago

10.3390/nu10111721

The Effect of Dietary Mushroom Agaricus bisporus on Intestinal Microbiota Composition and Host Immunological Function
Cited by: 25
Author(s): Gloria Solano‐Aguilar, Saebyeol Jang, Sukla Lakshman, Richi Gupta, Ethiopia Beshah, Masoumeh Sikaroodi, Bryan T. Vinyard, Aleksey Molokin, Patrick M. Gillevet, Joseph F. Urban
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms21041360

Molecular Evidences for the Interactions of Auxin, Gibberellin, and Cytokinin in Bent Peduncle Phenomenon in Rose (Rosa sp.)
Cited by: 3
Author(s): Weikun Jing, Shuai Zhang, Youwei Fan, Yinglong Deng, Chengpeng Wang, Jiao Lü, Xiaoming Sun, Nan Ma, Muhammad Furqan Shahid, Yonghong Li, Xiaofeng Zhou
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.5307

A novel long non-coding RNA, AC012456.4, as a valuable and independent prognostic biomarker of survival in oral squamous cell carcinoma
Cited by: 11
Author(s): Xuegang Hu, Zailing Qiu, Jianchai Zeng, Tingting Xiao, Zhihong Ke, Hongbing Lyu
Software Mentions: 1
Published: about 8 years ago

10.3906/biy-2101-61

Identification of differentially expressed microRNAs in primary esophageal achalasia by next-generation sequencing
Cited by: 2
Author(s): Mahin Gholipour, Javad Mikaeli, Seyed Javad Mowla, Mohammad Reza Bakhtiarizadeh, Marie Saghaeian Jazi, Naeme Javid, Narges Fazlollahi, Masoud Khoshnia, Nasser Behnampour, Abdolvahab Moradi
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-018-5318-1

Differential responses of Lasiopodomys mandarinus and Lasiopodomys brandtii to chronic hypoxia: a cross-species brain transcriptome analysis
Cited by: 13
Author(s): Qianqian Dong, Luye Shi, Yangwei Li, Mengwan Jiang, Hong Sun, Baishi Wang, Han Cheng, Yifeng Zhang, Tian Shao, Yuhua Shi, Zhenlong Wang
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.10328

Deregulation of lysophosphatidic acid metabolism in oral cancer promotes cell migration via the up-regulation of COX-2
Cited by: 3
Author(s): Mariati Abdul Rahman, Malcolm Tan, Steven P. Johnson, Robert Hollows, Wen Lin Chai, Jason Peter Mansell, Lee Fah Yap, Ian C. Paterson
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.11135

Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem
Cited by: 0
Author(s): Gina A. Garzón-Martínez, Francy Liliana García Arias, Felix E. Enciso-Rodríguez, Mauricio Soto‐Suárez, Carolina González, Aureliano Bombarely, Luz Stella Barrero, Jaime A. Osorio Guarín
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7442

Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression
Cited by: 4
Author(s): Feng Pang, Mengmeng Zhang, Guohua Li, Zhenxing Zhang, Haifeng Huang, Baobao Li, Chengqiang Wang, Xiaohong Yang, Yiying Zheng, Q. An, Luyin Zhang, Lijun Du, Fengyang Wang
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.3959

Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
Cited by: 37
Author(s): Jiuqiang Guan, Keren Long, Jideng Ma, Jinwei Zhang, Dafang He, Long Jin, Qianzi Tang, Anan Jiang, Xun Wang, Yaodong Hu, Shilin Tian, Zhi Jiang, Mingzhou Li, Xiaolin Luo
Software Mentions: 1
Published: almost 9 years ago

10.1128/mBio.02383-14

High-Throughput Analysis of Gene Essentiality and Sporulation in Clostridium difficile
Cited by: 133
Author(s): Marcin Dembek, Lars Barquist, Christine J. Boinett, Amy K. Cain, Matthew Mayho, Trevor D. Lawley, Neil F. Fairweather, Robert P. Fagan
Software Mentions: 1
Published: over 11 years ago

10.7717/peerj.8368

Genome-wide analysis of lncRNAs, miRNAs, and mRNAs forming a prognostic scoring system in esophageal squamous cell carcinoma
Cited by: 12
Author(s): Xun Shi, You Li, Yehuan Sun, Xu Zhao, Xin Sun, Tuotuo Gong, Zhinan Liang, Yuan Ma, Xiaozhi Zhang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-1667-1

De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways
Cited by: 46
Author(s): Bas Verbruggen, Lisa K. Bickley, Eduarda M. Santos, Charles R. Tyler, Grant D. Stentiford, Kelly S. Bateman, Ronny van Aerle
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-020-6539-7

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings
Cited by: 11
Author(s): Feng‐Yao Wu, Fengying Lu, Xin Fan, Chao Jin, Chuanmin Liu, Qunxing Pan, Huawei Sun, Xiaofei Zhang
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21062128

Cardiac miRNA Expression and their mRNA Targets in a Rat Model of Prediabetes
Cited by: 8
Author(s): Éva Sághy, Imre Vörös, Bence Ágg, Bernadett Kiss, Gábor Koncsos, Zoltán V. Varga, Anikó Görbe, Zoltán Giricz, Rainer Schulz, Péter Ferdinándy
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-14-763

Comparative transcriptome analysis of geographically distinct virulent and attenuated Babesia bovis strains reveals similar gene expression changes through attenuation
Cited by: 50
Author(s): Monica J. Pedroni, Kerry S. Sondgeroth, Gina M Gallego-López, Ignacio Echaide, Audrey O.T. Lau
Software Mentions: 1
Published: almost 13 years ago

10.1128/mBio.01384-18

Inhibition of EGFR Signaling Protects from Mucormycosis
Cited by: 42
Author(s): Tonya Watkins, Teclegiorgis Gebremariam, Marc Swidergall, Amol C. Shetty, Karen T. Graf, Abdullah Alqarihi, Sondus Alkhazraji, Abrar I. Alsaadi, Vonetta L. Edwards, Scott G. Filler, Ashraf S. Ibrahim, Vincent M. Bruno
Software Mentions: 1
Published: almost 8 years ago

10.7717/peerj.4500

Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq
Cited by: 30
Author(s): Liuxin Xiang, Chaowei Cai, Jieru Cheng, Lu Wang, Chaofeng Wu, Yùzhēn Shí, Jingzhi Luo, Lin He, Yushan Deng, Xiao Zhang, Yǒulù Yuán, Yingfan Cai
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.2977

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genusMacrobrachium: identification and expression validation in a model species (M. koombooloomba)
Cited by: 26
Author(s): Rahi Lifat, Shorash Amin, Peter B. Mather, David A. Hurwood
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.6402

In silico analysis reveals a shared immune signature in CASP8-mutated carcinomas with varying correlations to prognosis
Cited by: 7
Author(s): Yashoda Ghanekar, Subhashini Sadasivam
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00789-19

A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer
Cited by: 65
Author(s): Dawn E. Holmes, Toshiyuki Ueki, Haiyan Tang, Junhu Zhou, Jessica A. Smith, Gina Chaput, Derek R. Lovley
Software Mentions: 1
Published: almost 7 years ago

10.1128/mBio.02176-19

Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers
Cited by: 40
Author(s): Jiwei Zhang, Kevin A.T. Silverstein, Jesús D. Castaño, Melania Figueroa, Jonathan S. Schilling
Software Mentions: 1
Published: over 6 years ago

10.1128/mBio.02243-19

Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis
Cited by: 37
Author(s): Tjorven Hinzke, Manuel Kleiner, Corinna Breusing, Horst Felbeck, Robert Häsler, Stefan M. Sievert, Rabea Schlüter, Philip Rosenstiel, Thorsten B. H. Reusch, Thomas Schweder, Stephanie Markert
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.7261

Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus
Cited by: 10
Author(s): Ying Xue, Jun Ma, Yehua He, Shuang Yu, Zhen Yuan Lin, Yingyuan Xiong, Fatima Rafique, Fuxing Jiang, Lina Sun, Min Ma, Yujue Zhou, Xi Li, Zhuo Huang
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.1549

In plantacomparative transcriptomics of host-adapted strains ofRalstonia solanacearum
Cited by: 25
Author(s): Florent Ailloud, Tiffany M. Lowe, Isabelle Robène, Stéphane Cruveiller, Caitilyn Allen, Philippe Prior
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.8035

Transcriptome sequencing of Verticillium dahliae from a cotton farm reveals positive correlation between virulence and tolerance of sugar-induced hyperosmosis
Cited by: 0
Author(s): Jin Li, Juan Perucho, Yuanyuan Liu, Wenwen Xia, Fengfeng Cheng, Wenhui Tian, Lin Zhang, Jianbo Zhu, Aiying Wang
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.8403

Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses
Cited by: 12
Author(s): Yue Li, Xiaoyan Zhou, Jiali Liu, Yin Yang, Xin Yuan, Rui Yang, Qi Wang, Jing Ji, Qian He
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-020-07214-5

Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus
Cited by: 10
Author(s): Yufei Xiao, Junji Li, Ye Zhang, Xiaoning Zhang, Hailong Liu, Zihai Qin, Bowen Chen
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7743

Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats
Cited by: 3
Author(s): Shuang Fu, Yuhuan Meng, Shudai Lin, Wenlu Zhang, Yuting He, Lizhen Huang, Hongli Du
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-2472-1

Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis
Cited by: 31
Author(s): Jordane Despres, Evelyne Forano, Pascale Lepercq, Sophie Comtet-Marre, Grégory Jubelin, Carl J. Yeoman, Margret E. Berg Miller, Christopher J. Fields, Nicolas Terrapon, Carine Le Bourvellec, Cathérine M.G.C. Renard, Bernard Henrissat, Bryan A. White, Pascale Mosoni
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms21072385

Genome and Transcriptome Sequencing of casper and roy Zebrafish Mutants Provides Novel Genetic Clues for Iridophore Loss
Cited by: 2
Author(s): Chao Bian, Weiting Chen, Zhiqiang Ruan, Zhe Hu, Yu Huang, Yunyun Lv, Tengfei Xu, Jia Li, Qiong Shi, Wei Ge
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.11239

Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves
Cited by: 9
Author(s): Lanya Shui, Kaisen Huo, Yan Chen, Zilin Zhang, Yanfang Li, Jun Niu
Software Mentions: 1
Published: over 5 years ago

10.3390/nu13020468

Vitamin E Deficiency Disrupts Gene Expression Networks during Zebrafish Development
Cited by: 11
Author(s): Brian Head, Stephen A. Ramsey, Chrissa Kioussi, Robert L. Tanguay, Maret G. Traber
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21082738

Chemical Defoliant Promotes Leaf Abscission by Altering ROS Metabolism and Photosynthetic Efficiency in Gossypium hirsutum
Cited by: 20
Author(s): Dingsha Jin, Xiangru Wang, Yanchao Xu, Heng Gui, Hengheng Zhang, Qiang Dong, Ripon Kumar Sikder, Guozheng Yang, Meizhen Song
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.3529

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
Cited by: 11
Author(s): Michael Gerth, Gregory D. D. Hurst
Software Mentions: 1
Published: about 9 years ago

10.1016/j.patter.2021.100246

Quantum processor-inspired machine learning in the biomedical sciences
Cited by: 14
Author(s): Richard Y. Li, Sharvari Gujja, Sweta R. Bajaj, Omar Gamel, Nicholas A. Cilfone, Jeffrey R. Gulcher, Daniel A. Lidar, Thomas Chittenden
Software Mentions: 1
Published: about 5 years ago

10.3390/pathogens6040068

Prebiotic Oligosaccharides Potentiate Host Protective Responses against L. Monocytogenes Infection
Cited by: 20
Author(s): Poyin Chen, Taylor Reiter, Bihua C. Huang, Nguyet Kong, Bart C. Weimer
Software Mentions: 1
Published: over 8 years ago

10.1186/s13071-020-3914-9

Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis
Cited by: 6
Author(s): Lucas Gentil Azevedo, Artur T. L. Queiroz, Aldina Barral, Luciane Amorim Santos, Pablo Ivan Pereira Ramos
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-13-278

Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers
Cited by: 86
Author(s): Ying Wang, Vinayak Brahmakshatriya, Blanca Lupiani, Sanjay M. Reddy, Benjamin Soibam, Ashley Benham, Preethi H. Gunaratne, Hsiao‐Ching Liu, Nares Trakooljul, Nancy H. Ing, Ron Okimoto, Huaijun Zhou
Software Mentions: 1
Published: about 14 years ago

10.1128/mSphere.00283-16

Global Role of Cyclic AMP Signaling in pH-Dependent Responses in Candida albicans
Cited by: 14
Author(s): Jeffrey M. Hollomon, Nora Grahl, Sven D. Willger, Katja Koeppen, Deborah A. Hogan
Software Mentions: 1
Published: over 9 years ago

10.1128/mSphere.00245-17

Transcriptomic Signatures of Tacaribe Virus-Infected Jamaican Fruit Bats
Cited by: 17
Author(s): Diana L. Gerrard, Ann Hawkinson, Tyler Sherman, Cassandra M. Modahl, Gretchen Hume, Corey L. Campbell, Tony Schountz, Seth Frietze
Software Mentions: 1
Published: almost 9 years ago

10.1128/mSphereDirect.00375-17

The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
Cited by: 12
Author(s): Jannik Donner, Michael Reck, Boyke Bunk, Michael Jarek, Constantin Benjamin App, Jan P. Meier‐Kolthoff, Jörg Overmann, Rolf Müller, Andreas Kirschning, Irene Wagner‐Döbler
Software Mentions: 1
Published: almost 9 years ago

10.1128/mSphere.00094-17

Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea
Cited by: 14
Author(s): Louisi Souza de Oliveira, Diogo A. Tschoeke, Ana Carolina Rubem Magalhães Lopes, Daniela Bueno Sudatti, Pedro Milet Meirelles, Cristiane C. Thompson, Renato Crespo Pereira, Fabiano L. Thompson
Software Mentions: 1
Published: over 8 years ago

10.1186/s13071-020-3910-0

Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport
Cited by: 3
Author(s): Marziyeh Anari, Andreas J. Stroehlein, Ross S. Hall, Bill C.H. Chang, Robin B. Gasser, Neil D. Young
Software Mentions: 1
Published: over 6 years ago

10.1128/mSphereDirect.00262-18

Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis
Cited by: 58
Author(s): Zhi-Luo Deng, Cornelia Gottschick, Sabin Bhuju, Clarissa Masur, Christoph Abels, Irene Wagner‐Döbler
Software Mentions: 1
Published: about 8 years ago

10.1186/s13071-020-04457-9

RNA sequencing analysis of altered expression of long noncoding RNAs associated with Schistosoma japonicum infection in the murine liver and spleen
Cited by: 9
Author(s): Tianqi Xia, Bikash Ranjan Giri, Jingyi Liu, Pengfei Du, Xue Li, Xuxin Li, Shun Li, Guofeng Cheng
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-1555-8

An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data
Cited by: 10
Author(s): Yejun Wang, Keith D. MacKenzie, Aaron P. White
Software Mentions: 1
Published: over 11 years ago

10.1128/mSphere.00366-18

Glucose Signaling Is Important for Nutrient Adaptation during Differentiation of Pleomorphic African Trypanosomes
Cited by: 33
Author(s): Yijian Qiu, Jillian E. Milanes, Jessica A. Jones, Rooksana E. Noorai, Vijay Shankar, James C. Morris
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13071-020-04173-4

Catalogue of stage-specific transcripts in Ixodes ricinus and their potential functions during the tick life-cycle
Cited by: 10
Author(s): Pavlína Věchtová, Zoltán Füssy, Radim Čegan, Ján Štěrba, Jan Erhart, Vladimı́r Beneš, Libor Grubhoffer
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21113824

ID1-Mediated BMP Signaling Pathway Potentiates Glucagon-Like Peptide-1 Secretion in Response to Nutrient Replenishment
Cited by: 0
Author(s): Jae Woong Jeong, Minki Kim, Jiwoo Lee, Hae Kyung Lee, Yun Woong Ko, Hyun-Kyung Kim, Sungsoon Fang
Software Mentions: 1
Published: about 6 years ago

10.1128/mSphere.00620-19

Global Transcriptomic Analysis of the Candida albicans Response to Treatment with a Novel Inhibitor of Filamentation
Cited by: 16
Author(s): Jesús A. Romo, Hao Zhang, Hong Cai, David Kadosh, Julia Koehler, Stephen P. Saville, Yufeng Wang, José L. Lopez-Ribot
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms21113982

AMPK Profiling in Rodent and Human Pancreatic Beta-Cells under Nutrient-Rich Metabolic Stress
Cited by: 15
Author(s): Thierry Brun, Cecilia Jiménez‐Sánchez, Jesper Grud Skat Madsen, Noushin Hadadi, Dominique Duhamel, Clarissa Bartley, Lucie Oberhauser, Mirko Trajkovski, Susanne Mandrup, Pierre Maechler
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-016-2552-2

De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.)
Cited by: 43
Author(s): Ming Li, Zhaoxu Liang, Yuan Zeng, Yan Ji, Kai–Chao Wu, Jun Liang, Shikun He, Guanyu Wang, Zhanghong Mo, Feiquan Tan, Li Song, Wang LunWang
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-4095-6

Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses
Cited by: 19
Author(s): Totta Ehret, Simone Spork, Christoph Dieterich, Richard Lucius, Emanuel Heitlinger
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13071-017-2312-4

Sialotranscriptomics of Rhipicephalus zambeziensis reveals intricate expression profiles of secretory proteins and suggests tight temporal transcriptional regulation during blood-feeding
Cited by: 20
Author(s): Minique H. de Castro, Daniël de Klerk, Ronel Pienaar, D. J. G. Rees, Ben J. Mans
Software Mentions: 1
Published: about 9 years ago

10.1128/mSphere.00983-19

20-Hydroxyecdysone Primes Innate Immune Responses That Limit Bacterial and Malarial Parasite Survival in Anopheles gambiae
Cited by: 28
Author(s): Richard A. K. Reynolds, Hyeogsun Kwon, Ryan C. Smith
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-021-04624-6

Time-resolved transcriptional profiling of Trichinella-infected murine myocytes helps to elucidate host–pathogen interactions in the muscle stage
Cited by: 1
Author(s): Xiaoxiang Hu, Xiaolei Liu, Chen Li, Zhang Yu-lu, Chengyao Li, Yanfeng Li, Yingxi Chen, Hao Guo, Xue Bai, Mingyuan Liu
Software Mentions: 1
Published: over 5 years ago

10.1128/mSphere.00179-21

The pH-Responsive Transcription Factors YlRim101 and Mhy1 Regulate Alkaline pH-Induced Filamentation in the Dimorphic Yeast Yarrowia lipolytica
Cited by: 8
Author(s): Tao Shu, Xinyu He, Jia-Wen Chen, Yi-Sheng Mao, Xiang-Dong Gao
Software Mentions: 1
Published: about 5 years ago

10.3390/nu12113235

Animal and Cellular Studies Demonstrate Some of the Beneficial Impacts of Herring Milt Hydrolysates on Obesity-Induced Glucose Intolerance and Inflammation
Cited by: 10
Author(s): Rachel Durand, Adia Ouellette, Vanessa P. Houde, Frédéric Guénard, Thibaut Varin, Bruno Marcotte, Geneviève Pilon, Erwann Fraboulet, Marie‐Claude Vohl, André Marette, Laurent Bazinet
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-021-07402-x

Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum
Cited by: 6
Author(s): Akeem Owolabi Taiwo, Lincoln A. Harper, Mark Derbyshire
Software Mentions: 1
Published: over 5 years ago

10.1186/s13071-016-1856-z

Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages
Cited by: 15
Author(s): Manli He, Jing Xu, Ran He, Nengxing Shen, Xiaobin Gu, Xuerong Peng, Guangyou Yang
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13071-020-04155-6

Glucose transporter GLUT1 influences Plasmodium berghei infection in Anopheles stephensi
Cited by: 4
Author(s): Mengfei Wang, Jingwen Wang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12957-021-02362-8

Effects of EFNA1 on cell phenotype and prognosis of esophageal carcinoma
Cited by: 2
Author(s): Yongqiang Zhang, Jinning Zhang, Guanlong Pan, Tianhao Guan, Changhao Zhang, A. Hao, Yan Li, Hai Ren
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-4053-3

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)
Cited by: 26
Author(s): Ming Li, Zhaoxu Liang, Shikun He, Yuan Zeng, Yan Ji, Fang Wei, Kai–Chao Wu, Guanyu Wang, Ning Xia, Wang LunWang, Song Li, Huachun Tan, Feiquan Tan
Software Mentions: 1
Published: almost 9 years ago

10.1128/mSystems.00275-18

Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum
Cited by: 3
Author(s): Jake J. Flood, Shelley D. Copley
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-018-4437-z

Transcriptomic analysis reveals unique molecular factors for lipid hydrolysis, secondary cell-walls and oxidative protection associated with thermotolerance in perennial grass
Cited by: 13
Author(s): Yi Xu, Bingru Huang
Software Mentions: 1
Published: over 8 years ago

10.3390/v13071293

Transcriptome and Proteomic Analysis Reveals Up-Regulation of Innate Immunity-Related Genes Expression in Caprine Herpesvirus 1 Infected Madin Darby Bovine Kidney Cells
Cited by: 0
Author(s): Hao Fei, Xing Xie, Maojun Liu, Mao Li, Wenliang Li, Woonsung Na
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-13-322

Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species
Cited by: 6
Author(s): Claudia Voelckel, Nicole Gruenheit, Patrick J. Biggs, Oliver Deusch, Peter J. Lockhart
Software Mentions: 1
Published: over 14 years ago

10.3390/v13071325

Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-Infected Frog Tissues
Cited by: 1
Author(s): Yun Tian, Francisco De Jesús Andino, Collins N. Khwatenge, Jiuyi Li, Jacques Robert, Yongming Sang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41416-018-0321-5

Exploring the transcriptome of hormone-naive multifocal prostate cancer and matched lymph node metastases
Cited by: 7
Author(s): Linnéa Schmidt, Mia Møller, Christa Haldrup, Siri H. Strand, Søren Vang, Jakob Hedegaard, Søren Høyer, Michael Borre, Torben F. Ørntoft, Karina D. Sørensen
Software Mentions: 1
Published: over 7 years ago

10.1038/s41416-018-0263-y

Targeting peroxiredoxin 1 impairs growth of breast cancer cells and potently sensitises these cells to prooxidant agents
Cited by: 45
Author(s): Małgorzata Bajor, Agata O Zych, Agnieszka Graczyk-Jarzynka, Angelika Muchowicz, Małgorzata Firczuk, Lech Trzeciak, Paweł Gaj, Antoni Domagała, Marta Siernicka, Agnieszka Zagożdżon, Paweł Siedlecki, Monika Kniotek, Patrick C. O’Leary, Jakub Goła̧b, Radosław Zagożdżon
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41416-021-01441-7

Essential role of the histone lysine demethylase KDM4A in the biology of malignant pleural mesothelioma (MPM)
Cited by: 4
Author(s): Moshe Lapidot, Abigail Case, Ellen Weisberg, Chengcheng Meng, Sarah R. Walker, Swati Garg, Wei Ni, Klaus Podar, Yin P. Hung, Ruben D. Carrasco, Aine Knott, Prafulla C. Gokhale, Sunil Sharma, Alex Pozhitkov, Prakash Kulkarni, David A. Frank, Ravi Salgia, James D. Griffin, Srinivas Vinod Saladi, Raphael Bueno, Martin Sattler
Software Mentions: 1
Published: about 5 years ago

10.1038/s41413-018-0037-4

Characterization of a novel murine Sost ERT2 Cre model targeting osteocytes
Cited by: 19
Author(s): Daniel Maurel, Tsutomu Matsumoto, Julian Vallejo, Mark Johnson, Sarah L. Dallas, Yukiko Kitase, Marco Brotto, Michael Wacker, Marie A. Harris, S. E. Harris, Lynda F. Bonewald
Software Mentions: 1
Published: over 7 years ago

10.1186/s13068-015-0245-8

Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) II: transcriptome alterations of pathways involved in carbohydrate metabolism and endogenous hormone crosstalk
Cited by: 46
Author(s): Yang Liu, Yang Fang, Mengjun Huang, Yanling Jin, Jiaolong Sun, Tao Xiang, Guohua Zhang, Kai He, Yun Zhao, Hai Zhao
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-017-3961-6

Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi–SlPH tomato line with reduced fruit acidity and higher pH
Cited by: 9
Author(s): Shiri Barad, Noa Sela, Amit Dubey, Dilip Kumar, Neta Luria, Dana Ment, Shahar Cohen, Arthur A. Schaffer, Dov Prusky
Software Mentions: 1
Published: about 9 years ago

10.3390/ijms21124252

Micro-Transcriptome Analysis Reveals Immune-Related MicroRNA Regulatory Networks of Paralichthys olivaceus Induced by Vibrio anguillarum Infection
Cited by: 11
Author(s): Xianhui Ning, Li Sun
Software Mentions: 1
Published: about 6 years ago

10.1128/mSystems.00819-20

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy
Cited by: 16
Author(s): Jiawei He, Xu‐jie Zhou, Yafeng Li, Yan-Na Wang, Lijun Liu, Sufang Shi, Xu Xin, Rongshan Li, Mario Falchi, Jicheng Lv, Hong Zhang
Software Mentions: 1
Published: over 5 years ago

10.1186/s13068-019-1377-z

Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris
Cited by: 7
Author(s): Xihao Liao, Jing Zhao, Shuli Liang, Jingjie Jin, Li Cheng, Ruiming Xiao, Lu Li, Meijin Guo, Gong Zhang, Ying Lin
Software Mentions: 1
Published: over 7 years ago

10.1186/s13068-015-0203-5

Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009
Cited by: 34
Author(s): Magdalena Całusińska, Christopher Hamilton, Pieter Monsieurs, Grégory Mathy, Natalie Leys, Fabrice Franck, Bernard Joris, Philippe Thonart, Serge Hiligsmann, Annick Wilmotte
Software Mentions: 1
Published: over 11 years ago

10.1186/gb-2013-14-12-r149

Staged miRNA re-regulation patterns during reprogramming
Cited by: 16
Author(s): Christine Henzler, Zhonghan Li, Jason Dang, Mary Luz Arcila, Hongjun Zhou, Jingya Liu, Kung Yen Chang, Danielle S. Bassett, Tariq M. Rana, Kenneth S. Kosik
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2010-11-3-r25

A scaling normalization method for differential expression analysis of RNA-seq data
Cited by: 5,530
Author(s): Mark D. Robinson, Alicia Oshlack
Software Mentions: 1
Published: over 16 years ago

10.1186/s12864-018-4646-5

Comprehensive analysis of blood cells and plasma identifies tissue-specific miRNAs as potential novel circulating biomarkers in cattle
Cited by: 22
Author(s): Jason Ioannidis, F.X. Donadeu
Software Mentions: 1
Published: over 8 years ago

10.1534/genetics.117.300103

Developmental Restriction of Retrotransposition Activated in Arabidopsis by Environmental Stress
Cited by: 21
Author(s): Hervé Gaubert, Diego H. Sánchez, Hajk-Georg Drost, Jerzy Paszkowski
Software Mentions: 1
Published: about 9 years ago

10.1590/1678-4685-GMB-2019-0377

Transcriptomic evidences of local thermal adaptation for the native fish Colossoma macropomum (Cuvier, 1818)
Cited by: 6
Author(s): Luciana Mara Fé-Gonçalves, José Deney Alves Araújo, Carlos dos Anjos dos Henrique Santos, Vera Maria Fonseca de Almeida-Val
Software Mentions: 1
Published: over 6 years ago

10.1590/1678-4685-GMB-2018-0033

De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana
Cited by: 7
Author(s): Suhong Fu, Ming Lei, Zhang YongQun, Zhaomin Deng, Jing Shi, Doudou Hao
Software Mentions: 1
Published: about 7 years ago

10.3390/genes12091437

Metformin Triggers Apoptosis and Induction of the G0/G1 Switch 2 Gene in Macrophages
Cited by: 5
Author(s): Xuming Hu, Huai‐Rong Luo, Chunfeng Dou, Xujing Chen, Yi Huang, Liping Wang, Song Xue, Zhen Sun, Shihao Chen, Qi Xu, Tuoyu Geng, Xin Zhao, Hengmi Cui
Software Mentions: 1
Published: almost 5 years ago

10.3390/genes12070985

CircVAMP3: A circRNA with a Role in Alveolar Rhabdomyosarcoma Cell Cycle Progression
Cited by: 8
Author(s): Francesca Maria Rossi, Alvaro Centrón-Broco, Dario Dattilo, Gaia Di Timoteo, Marco Guarnacci, Alessio Colantoni, Manuel Beltran Nebot, Irene Bozzoni
Software Mentions: 1
Published: about 5 years ago

10.3390/genes12060944

Expression of Wnt and TGF-Beta Pathway Components during Whole-Body Regeneration from Cell Aggregates in Demosponge Halisarca dujardinii
Cited by: 6
Author(s): Ilya Borisenko, Fyodor Bolshakov, Alexander Ereskovsky, Andrey Lavrov
Software Mentions: 1
Published: about 5 years ago

10.3390/genes12050618

Transcriptome Analysis Provides Insights into the Mechanism of Astaxanthin Enrichment in a Mutant of the Ridgetail White Prawn Exopalaemon carinicauda
Cited by: 7
Author(s): Yue Jin, Shihao Li, Yang Yu, Chengsong Zhang, Xiaojun Zhang, Fuhua Li
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12040561

Genome-Wide Transcriptional Analysis and Functional Validation Linked a Cluster of Epsilon Glutathione S-Transferases with Insecticide Resistance in the Major Malaria Vector Anopheles funestus across Africa
Cited by: 15
Author(s): Mersimine F. M. Kouamo, Sulaiman S. Ibrahim, Jack Hearn, Jacob M. Riveron, Michael O. Kusimo, Magellan Tchouakui, Ebai Terence, Williams Tchapga, Murielle J. Wondji, Helen Irving, Thaddée Boudjeko, Fabrice Fekam Boyom, Charles S. Wondji
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12030355

Decoding the Reproductive System of the Olive Fruit Fly, Bactrocera oleae
Cited by: 4
Author(s): Maria‐Eleni Gregoriou, Martin Reczko, Evdoxia G. Kakani, Konstantina T. Tsoumani, Kostas D. Mathiopoulos
Software Mentions: 1
Published: over 5 years ago

10.1186/s13059-015-0632-2

The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution
Cited by: 212
Author(s): Krystyna Cwiklinski, John P. Dalton, Philippe J. Dufresne, James La Course, Diana Williams, Jane E. Hodgkinson, Steve Paterson
Software Mentions: 1
Published: over 11 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568