bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-017-07798-1

Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
Cited by: 15
Author(s): Hamid Hussain, Iqbal Zahid, Mohamed N. Seleem, Deyu Huang, Adeel Sattar, Haihong Hao, Yuan Zhang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0157173

Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis
Cited by: 13
Author(s): Hongxia Jiang, Xilian Li, Yuhang Sun, Fujun Hou, Yufei Zhang, Fēi Li, Zhenxin Gu, Xiaolin Liu
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-017-10272-7

HIV-1 envelope glycoprotein stimulates viral transcription and increases the infectivity of the progeny virus through the manipulation of cellular machinery
Cited by: 10
Author(s): Xiaozhuo Ran, Zhujun Ao, Adriana Trajtman, Wayne Xu, Gary P. Kobinger, Yoav Keynan, Xiaojian Yao
Software Mentions: 1
Published: about 9 years ago

10.1016/j.isci.2021.102217

Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle
Cited by: 16
Author(s): Riku Egami, Toshiya Kokaji, Atsushi Hatano, Katsuyuki Yugi, Masatoshi Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Saori Uematsu, Akira Terakawa, Yongping Bai, Yun-long Pan, Toshikazu Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Konishi, Yutaka Suzuki, Masaki Matsumoto, Keiichi I. Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-09617-z

A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus
Cited by: 33
Author(s): Teddy Amuge, David Kenneth Berger, Manpreet S. Katari, Alexander Andrew Myburg, S. L. Goldman, Morag Ferguson
Software Mentions: 1
Published: about 9 years ago

10.3389/fimmu.2021.729776

The Molecular Mechanism of Multiple Organ Dysfunction and Targeted Intervention of COVID-19 Based on Time-Order Transcriptomic Analysis
Cited by: 15
Author(s): Miao Zou, Xiaoyun Su, Luoying Wang, Xingcheng Yi, Yue Qiu, Xirui Yin, Xuan Zhou, Xinhui Niu, Liuli Wang, Manman Su
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.103139

Long non-coding RNA CCAT1 promotes colorectal cancer progression by regulating miR-181a-5p expression
Cited by: 30
Author(s): Anquan Shang, Weiwei Wang, Chenzheng Gu, Wei Chen, Wenying Lu, Zujun Sun, Dong Liu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-10349-3

IRF2BP2-deficient microglia block the anxiolytic effect of enhanced postnatal care
Cited by: 14
Author(s): Aswin Hari, Shelly A. Cruz, Zhaohong Qin, Pascal Couture, Ragnar O. Vilmundarson, Hua Huang, Alexandre F.R. Stewart, Hsiao‐Huei Chen
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-14-864

A detailed gene expression study of the Miscanthusgenus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes
Cited by: 28
Author(s): Adam Barling, Kankshita Swaminathan, Therese Mitros, Brandon T. James, Juliette Morris, Ornella Ngamboma, Mark E. Hall, Jessica Kirkpatrick, Magdy S. Alabady, Ashley K. Spence, Matthew E. Hudson, Daniel S. Rokhsar, Stephen P. Moose
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-017-08854-6

Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses)
Cited by: 46
Author(s): Sha Tang, Lin Li, Yongqiang Wang, Qiannan Chen, Wenying Zhang, Guanqing Jia, Hui Zhi, Bin Zhao, Xianmin Diao
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-10098-3

Meta-signature of human endometrial receptivity: a meta-analysis and validation study of transcriptomic biomarkers
Cited by: 163
Author(s): Signe Altmäe, Mariann Koel, Urmo Võsa, Priit Adler, Marina Suhorutšenko, Triin Laisk-Podar, Viktorija Kukushkina, Merli Saare, Agne Velthut-Meikas, Kaarel Krjutškov, Lusine Aghajanova, P. G. L. Lalitkumar, Kristina Gemzell‐Danielsson, Linda C. Giudice, Carlos Simón, Andres Salumets
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-016-2962-1

Comparative miRNAome analysis revealed different miRNA expression profiles in bovine sera and exosomes
Cited by: 45
Author(s): Ke Zhao, Guanxiang Liang, Xinwei Sun, Le Luo Guan
Software Mentions: 1
Published: about 10 years ago

10.3389/fimmu.2016.00670

Regulation of Marginal Zone B-Cell Differentiation by MicroRNA-146a
Cited by: 22
Author(s): Jennifer K. King, Nolan Ung, May Paing, Jorge R. Contreras, Michael O. Alberti, Thilini R. Fernando, Kelvin Zhang, Matteo Pellegrini, Dinesh S. Rao
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-5305-6

Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis
Cited by: 40
Author(s): Yingdan Yuan, Maoyun Yu, Zhaohui Jia, Xue’er Song, Yongchao Liang, Jinchi Zhang
Software Mentions: 1
Published: almost 8 years ago

10.3389/fimmu.2020.592569

Helpless Priming Sends CD8+ T Cells on the Road to Exhaustion
Cited by: 23
Author(s): Julia Busselaar, Sun Tian, Hans van Eenennaam, Jannie Borst
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-019-6367-9

Genetic deletion of Sphk2 confers protection against Pseudomonas aeruginosa mediated differential expression of genes related to virulent infection and inflammation in mouse lung
Cited by: 11
Author(s): David L. Ebenezer, Panfeng Fu, Yashaswin Krishnan, Mark Maienschein‐Cline, Hong Hu, Su-Young Jung, Ravi Madduri, Zarema Arbieva, Anantha Harijith, Viswanathan Natarajan
Software Mentions: 1
Published: almost 7 years ago

10.1155/2021/4754454

Propofol Suppresses Microglia Inflammation by Targeting TGM2/NF-κB Signaling
Cited by: 5
Author(s): Yuanyuan Hou, Xi Xiao, Wei Yu, Shijie Qi
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.100895

The effects of graded levels of calorie restriction: VI. Impact of short-term graded calorie restriction on transcriptomic responses of the hypothalamic hunger and circadian signaling pathways
Cited by: 24
Author(s): Davina Derous, Sharon E. Mitchell, Cara L Green, Luonan Chen, Jing–Dong Jackie Han, Yingchun Wang, Daniel E. L. Promislow, David Lusseau, John R. Speakman, Alex Douglas
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-017-09554-x

LSD1 modulates the non-canonical integrin β3 signaling pathway in non-small cell lung carcinoma cells
Cited by: 12
Author(s): So‐Young Lim, Iris Macheleidt, Priya Dalvi, Stephan Schäfer, Martin Kerick, Luka Ozretić, Sandra Ortiz-Cuarán, Julie George, Sabine Merkelbach‐Bruse, Jürgen Wolf, Bernd Timmermann, Roman K. Thomas, Michal R. Schweiger, Reinhard Buettner, Margarete Odenthal
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-10742-y

RNA-seq analysis of apical meristem reveals integrative regulatory network of ROS and chilling potentially related to flowering in Litchi chinensis
Cited by: 12
Author(s): Xingyu Lu, Jingjing Li, Houbin Chen, Jiaqi Hu, Pengxu Liu, Biyan Zhou
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-021-82509-5

Long non-coding RNAs as novel therapeutic targets in juvenile myelomonocytic leukemia
Cited by: 7
Author(s): Mattias Hofmans, Tim Lammens, Barbara Depreter, Ying Wu, Miriam Erlacher, Aurélie Cayé, Hélène Cavé, Christian Flotho, Valérie de Haas, Charlotte M. Niemeyer, Jan Starý, Filip Van Nieuwerburgh, Dieter Deforce, Wouter Van Loocke, Pieter Van Vlierberghe, Jan Philippé, Barbara De Moerloose
Software Mentions: 1
Published: over 5 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

10.1186/s40478-018-0555-8

Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients
Cited by: 22
Author(s): Daniel A. Mordes, Mercedes Prudencio, Lindsey D. Goodman, Joseph R. Klim, Rob Moccia, Francesco Limone, Olli Pietiläinen, Kaitavjeet Chowdhary, Dennis W. Dickson, Rosa Rademakers, Nancy M. Bonini, Leonard Petrucelli, Kevin Eggan
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-11456-x

Antennal transcriptome and expression analyses of olfactory genes in the sweetpotato weevil Cylas formicarius
Cited by: 25
Author(s): Shuying Bin, Meng-Qiu Qu, Xinhua Pu, Zhongzhen Wu, Jintian Lin
Software Mentions: 1
Published: almost 9 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

10.1038/s41598-017-11588-0

Comparative transcriptome analysis of axillary buds in response to the shoot branching regulators gibberellin A3 and 6-benzyladenine in Jatropha curcas
Cited by: 36
Author(s): Jun Ni, Miaomiao Zhao, Maosheng Chen, Bang-Zhen Pan, Yongfu Tao, Zeng-Fu Xu
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-14-322

Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction
Cited by: 56
Author(s): Magda Aparecida Beneventi, Orzenil Bonfim da Silva, Maria Eugênia Lisei de Sá, Alexandre Augusto Pereira Firmino, Regina Maria Santos de Amorim, Érika Valéria Saliba Albuquerque, Maria Cristina Mattar da Silva, Joseane Padilha da Silva, Magnólia de Araújo Campos, Marcus José Conceição Lopes, Roberto Coiti Togawa, Γεώργιος Παππάς, Maria Fátima Grossi-de-Sá
Software Mentions: 1
Published: over 13 years ago

10.3389/fimmu.2019.02888

Mycobacterium abscessus—Bronchial Epithelial Cells Cross-Talk Through Type I Interferon Signaling
Cited by: 15
Author(s): Chongxu Zhang, Huda Asif, Gregory E. Holt, Anthony J. Griswold, Michael Campos, P.A. Bejarano, Nevis Fregien, Mehdi Mirsaeidi
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-2006-2

Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes
Cited by: 18
Author(s): Miriam L. Sharpe, Peter K. Dearden, Grégory Gimenez, Kurt L. Krause
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-016-3126-z

Metatranscriptome analysis reveals bacterial symbiont contributions to lower termite physiology and potential immune functions
Cited by: 27
Author(s): Brittany F. Peterson, Michael E. Scharf
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-017-10675-6

Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer
Cited by: 83
Author(s): Huân M. Ngô, Ying Zhou, Hernán Lorenzi, Kai Wang, Taek Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V. Rajagopala, Craig W. Roberts, Fiona L. Henriquez, Alexandre Montpetit, Jenefer M. Blackwell, Sarra E. Jamieson, Kelsey Wheeler, Ian J. Begeman, Carlos Andrés Naranjo Galvis, Ney Alliey‐Rodriguez, Roderick G. Davis, Liliana Soroceanu, Charles S. Cobbs, Dennis A. Steindler, Kenneth M. Boyer, A. Gwendolyn Noble, Charles N. Swisher, Peter Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, Rima McLeod
Software Mentions: 1
Published: almost 9 years ago

10.3389/fimmu.2020.01602

Systemic Sclerosis Perturbs the Architecture of the Immunome
Cited by: 10
Author(s): Bhairav Paleja, Andrea Low, Pavanish Kumar, Suzan Saidin, Ahmad Lajam, Sharifah Nur Hazirah, Camillus Chua, Lai Li Yun, Salvatore Albani
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms22137025

Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development
Cited by: 7
Author(s): Francesca Lucibelli, Maria Carmen Valoroso, Günter Theißen, Susanne Nolden, Mariana Mondragón-Palomino, Serena Aceto
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-83074-7

Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat
Cited by: 13
Author(s): Haipei Liu, Amanda J. Able, Jason A. Able
Software Mentions: 1
Published: over 5 years ago

10.1038/s41396-020-0718-z

Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms
Cited by: 12
Author(s): Rebecca E. Cooper, Carl‐Eric Wegner, Stefan Kügler, Remington X. Poulin, Nico Ueberschaar, Jens D. Wurlitzer, Daniel Stettin, Thomas Wichard, Georg Pohnert, Kirsten Küsel
Software Mentions: 1
Published: about 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

10.3389/fimmu.2020.01240

Neonatal Diet Impacts Circulatory miRNA Profile in a Porcine Model
Cited by: 4
Author(s): Laura E. Carr, Anne K. Bowlin, Ahmed A. Elolimy, Stephanie D. Byrum, Charity L. Washam, Christopher E. Randolph, Stewart L. MacLeod, Laxmi Yeruva
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-017-12025-y

Molecular dissection of transcriptional reprogramming of steviol glycosides synthesis in leaf tissue during developmental phase transitions in Stevia rebaudiana Bert
Cited by: 47
Author(s): Gopal Singh, Gagandeep Singh, Pradeep Singh, Rajni Parmar, Navgeet Paul, Radhika Vashist, Mohit Kumar Swarnkar, Ashok Kumar, Sanatsujat Singh, Anil Kumar Singh, Sanjay Kumar, Ram Kumar Sharma
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-016-2957-y

Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves
Cited by: 55
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Hua Bao, Paul Stothard, Philip Griebel, Le Luo Guan
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-021-08026-x

Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome
Cited by: 1
Author(s): Po-Shun Chuang, Satoshi Mitarai
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-019-5517-4

Gene regulation of Sclerotinia sclerotiorum during infection of Glycine max: on the road to pathogenesis
Cited by: 33
Author(s): Nathaniel M. Westrick, Ashish Ranjan, Sachin Jain, C. R. Grau, Damon Smith, Mehdi Kabbage
Software Mentions: 1
Published: over 7 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

10.3389/fimmu.2014.00396

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis
Cited by: 48
Author(s): Kirsten E. McLoughlin, Nicolas C. Nalpas, Kévin Rue-Albrecht, John A. Browne, David A. Magee, Kate E. Killick, Stephen D. E. Park, Karsten Hokamp, Kieran G. Meade, Cliona O’Farrelly, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 1
Published: about 12 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

10.18632/oncotarget.6859

Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs
Cited by: 92
Author(s): Chunjie Jiang, Yongsheng Li, Zheng Zhao, Jianping Lu, Hong Chen, Na Ding, Guangjuan Wang, Juan Xu, Xia Li
Software Mentions: 1
Published: over 10 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

10.1038/s41389-018-0089-8

MicroRNA-transcription factor network analysis reveals miRNAs cooperatively suppress RORA in oral squamous cell carcinoma
Cited by: 28
Author(s): Xueqing Zheng, Kejing Wu, Shengjie Liao, Yifan Pan, Yanan Sun, Xinming Chen, Yi Zhang, Sun-Hui Xia, Yaying Hu, Jiali Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-12875-6

Membrane Trafficking Modulation during Entamoeba Encystation
Cited by: 11
Author(s): Emily K. Herman, Maria A. Siegesmund, Michael Bottery, Ronny van Aerle, Maulood Mohammed Shather, Elisabet Caler, Joel B. Dacks, Mark van der Giezen
Software Mentions: 1
Published: almost 9 years ago

10.1186/s40478-019-0739-x

c-MYC overexpression induces choroid plexus papillomas through a T-cell mediated inflammatory mechanism
Cited by: 5
Author(s): Ashirwad Merve, Xinyu Zhang, Nicola Pomella, Serena Acquati, Joerg D. Hoeck, Anaëlle Dumas, Gabriel Rosser, Yichen Li, Jennie N. Jeyapalan, Silvia Vicenzi, Qianhai Fan, Zeng Jie Yang, Arianna Sabò, Denise Sheer, Axel Behrens, Silvia Marino
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-019-5522-7

Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO2
Cited by: 9
Author(s): Allison R. Kolbe, Anthony J. Studer, Omar E. Cornejo, Asaph B. Cousins
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-12537-7

Dynamic mRNA and miRNA expression analysis in response to hypoxia and reoxygenation in the blunt snout bream (Megalobrama amblycephala)
Cited by: 17
Author(s): Shengming Sun, Fujun Xuan, Xianping Ge, Jian Zhu, Wuxiao Zhang
Software Mentions: 1
Published: almost 9 years ago

10.3390/microorganisms5010003

Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae
Cited by: 8
Author(s): Ryan M. Ames
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.10654

Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis
Cited by: 9
Author(s): Chelsea Hall, Sara Camilli, Henry Dwaah, Benjamin Kornegay, Christie A. Lacy, Malcolm Hill, Andrew P. Hill
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2019.00265

Transcriptome Profiles of Human Visceral Adipocytes in Obesity and Colorectal Cancer Unravel the Effects of Body Mass Index and Polyunsaturated Fatty Acids on Genes and Biological Processes Related to Tumorigenesis
Cited by: 23
Author(s): Manuela Del Cornò, Antonella Baldassarre, Enrica Calura, Lucia Conti, Paolo Martini, Chiara Romualdi, Rosaria Varı́, Beatrice Scazzocchio, Massimo D’Archivio, Andrea Masotti, Sandra Gessani
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.1591

The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission
Cited by: 54
Author(s): Eugene V. Ryabov, Jessica Fannon, Jonathan D. Moore, Graham R. Wood, David J. Evans
Software Mentions: 1
Published: over 10 years ago

10.18632/aging.202164

SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma
Cited by: 19
Author(s): Yuting Zhan, Lei Li, Tingting Zeng, Ningning Zhou, Xin‐Yuan Guan, Yan Li
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-15-492

Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development
Cited by: 63
Author(s): David Fernando Plaza, Chi Feng Lin, Niels Sebastiaan Johannes van der Velden, Markus Aebi, Markus Künzler
Software Mentions: 1
Published: about 12 years ago

10.3389/fimmu.2021.705253

Targeted Transcriptomics of Frog Virus 3 in Infected Frog Tissues Reveal Non-Coding Regulatory Elements and microRNAs in the Ranaviral Genome and Their Potential Interaction with Host Immune Response
Cited by: 5
Author(s): Yun Tian, Collins N. Khwatenge, Jiuyi Li, Francisco De Jesús Andino, Jacques Robert, Yongming Sang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-017-14673-6

Epigenetics and adaptive phenotypic variation between habitats in an asexual snail
Cited by: 50
Author(s): Jennifer L. M. Thorson, Mark W. Smithson, Daniel Beck, Ingrid Sadler‐Riggleman, Eric Nilsson, Mark F. Dybdahl, Michael K. Skinner
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-3664-z

Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
Cited by: 16
Author(s): Antanas Spokevicius, Josquin Tibbits, Philippe Rigault, Marc-Alexandre Nolin, Caroline Müller, Andrew Merchant
Software Mentions: 1
Published: over 9 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/s12864-015-1731-x

Daytime soybean transcriptome fluctuations during water deficit stress
Cited by: 38
Author(s): Fabiana Aparecida Rodrigues, Renata Fuganti-Pagliarini, Juliana Marcolino-Gomes, Thiago Jonas Nakayama, Hugo Bruno Correa Molinari, Francisco Pereira Lobo, Frank G. Harmon, Alexandre Lima Nepomuceno
Software Mentions: 1
Published: about 11 years ago

10.3390/microorganisms8071020

Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil
Cited by: 16
Author(s): Nikola Major, Jasper Schierstaedt, Sven Jechalke, Joseph Nesme, Smiljana Goreta Ban, Marko Černe, Søren J. Sørensen, Dean Ban, Adam Schikora
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-017-14736-8

Differential gene expression of Australian Cricotopus draysoni (Diptera: Chironomidae) populations reveals seasonal association in detoxification gene regulation
Cited by: 5
Author(s): Matt N. Krosch, Litticia M. Bryant, Sue Vink
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.8609

Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation
Cited by: 4
Author(s): Wenmin Qiu, Jingen Li, Wei Yi, Fan Feng, Jing Jiang, Mingying Liu, Xiaojiao Han, Chaoguang Tian, Shihong Zhang, Renying Zhuo
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-13999-5

The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy
Cited by: 19
Author(s): Canaan Whitfield-Cargile, Noah D. Cohen, Kejun He, Ivan Ivanov, Jennifer S. Goldsby, Ana M. Chamoun‐Emanuelli, Brad R. Weeks, Laurie A. Davidson, Robert S. Chapkin
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12995-021-00332-0

Genome-wide mRNA profiling identifies the NRF2-regulated lymphocyte oxidative stress status in patients with silicosis
Cited by: 1
Author(s): Zhao Yi, Guangcui Xu, Haibin Li, Meiyu Chang, Chuan Xiong, Yingjun Tao, Yi Guan, Yuchun Li, Sanqiao Yao
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.10668

An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis
Cited by: 4
Author(s): Juan Wang, Xiongfei Wu, Yue Tu, Jianzhong Dang, Zhitao Cai, Wenjing Liao, Weili Quan, Yaxun Wei
Software Mentions: 1
Published: over 5 years ago

10.18632/aging.203235

miR-30a-5p suppresses lung squamous cell carcinoma via ATG5 - mediated autophagy
Cited by: 15
Author(s): Jichen Yang, Sunyin Rao, Run Cao, Shouyong Xiao, Xin Cui, Lianhua Ye
Software Mentions: 1
Published: about 5 years ago

10.1002/JLB.3A0120-001RRR

Monocytes differentiated into macrophages and dendritic cells in the presence of human IFN-λ3 or IFN-λ4 show distinct phenotypes
Cited by: 7
Author(s): Manjarika De, Anand Bhushan, Sreedhar Chinnaswamy
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-017-14808-9

Antibiotics induce polarization of pleural macrophages to M2-like phenotype in patients with tuberculous pleuritis
Cited by: 13
Author(s): Sisi Wang, Jian Zhang, Liyan Sui, Hao Xu, Qianling Piao, Ying Liu, Xiangping Qu, Ying Sun, Lei Song, Dan Li, Liping Peng, Shucheng Hua, Guangan Hu, Jianzhu Chen
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-14-412

Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production
Cited by: 29
Author(s): Sara J. Hanson, Claus‐Peter Stelzer, David Welch, John M. Logsdon
Software Mentions: 1
Published: about 13 years ago

10.7717/peerj.7102

Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots
Cited by: 1
Author(s): Wang Wei, Sunil Kumar Singh, Xiwen Li, Hui Sun, Yu Ye, Min Jiang, Hailing Zi, Renyi Liu, Huiming Zhang, Zhaoqing Chu
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.8776

Physiological parameters and differential expression analysis of N-phenyl-N′-[6-(2-chlorobenzothiazol)-yl] urea-induced callus of Eucalyptus urophylla × Eucalyptus grandis
Cited by: 4
Author(s): Lejun Ouyang, Zechen Wang, Limei Li, Baoling Chen
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.8379

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis
Cited by: 12
Author(s): Xuhui Tong, Han Zhang, Fang Wang, Zhengyao Xue, Jing Cao, Cheng Peng, Jianbin Guo
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-14913-9

Differential transcriptome regulation by 3,5-T2 and 3′,3,5-T3 in brain and liver uncovers novel roles for thyroid hormones in tilapia
Cited by: 16
Author(s): Arturo Olverá, Christopher J. Martyniuk, Nicolas Buisine, Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Laurent M. Sachs, Aurea Orozco
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-021-08003-4

Early life and adult stress promote sex dependent changes in hypothalamic miRNAs and environmental enrichment prevents stress-induced miRNA and gene expression changes in rats
Cited by: 7
Author(s): Lauren McKibben, Yogesh K. Dwivedi
Software Mentions: 1
Published: almost 5 years ago

10.1002/advs.202100681

Diclofenac Resensitizes Methicillin‐Resistant Staphylococcus aureus to β‐Lactams and Prevents Implant Infections
Cited by: 23
Author(s): Shutao Zhang, Xinhua Qu, Haozheng Tang, You Wang, Hongtao Yang, Weien Yuan, Bing Yue
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-2150-8

The comprehensive immunomodulation of NeurimmiRs in haemocytes of oyster Crassostrea gigas after acetylcholine and norepinephrine stimulation
Cited by: 25
Author(s): Hao Chen, Lingling Wang, Zhi Zhou, Zujun Hou, Zhaoqun Liu, Weilin Wang, Dahai Gao, Qiang Gao, Mengqiang Wang, Linsheng Song
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-017-15699-6

Transcriptomic analysis of the regulation of stalk development in flowering Chinese cabbage (Brassica campestris) by RNA sequencing
Cited by: 17
Author(s): Xinmin Huang, Yuling Lei, Hongling Guan, Yanwei Hao, Houcheng Liu, Guangwen Sun, Riyuan Chen, Shiwei Song
Software Mentions: 1
Published: almost 9 years ago

10.3389/fmolb.2018.00079

Systematic Analysis of Gene Expression Profiles Controlled by hnRNP Q and hnRNP R, Two Closely Related Human RNA Binding Proteins Implicated in mRNA Processing Mechanisms
Cited by: 10
Author(s): Sara Cappelli, Maurizio Romano, Emanuele Buratti
Software Mentions: 1
Published: about 8 years ago

10.1007/s00239-019-09901-8

Eye Degeneration and Loss of otx5b Expression in the Cavefish Sinocyclocheilus tileihornes
Cited by: 9
Author(s): Zhuo Huang, Tom A. Titus, John H. Postlethwait, Fanwei Meng
Software Mentions: 1
Published: about 7 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: over 6 years ago

10.1186/s12864-017-4037-3

Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
Cited by: 50
Author(s): Risheng Chen, Yunfeng Cheng, Sang‐Mi Han, Ben Van Handel, Lü Dong, Xinmin Li, Xiaoqing Xie
Software Mentions: 1
Published: about 9 years ago

10.3389/fmolb.2021.587436

Comprehensive Analysis of Ferroptosis Regulators in Lung Adenocarcinomas Identifies Prognostic and Immunotherapy-Related Biomarkers
Cited by: 11
Author(s): Sijin Sun, Guo Wei, Fang Lv, Guochao Zhang, Juhong Wang, Renda Li, Fengwei Tan, Ning Li, Xue Qin, Yibo Gao, Shugeng Gao, Jie He
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-14-855

A platform independent RNA-Seq protocol for the detection of transcriptome complexity
Cited by: 6
Author(s): Claudia Calabrese, Marina Mangiulli, Caterina Manzari, Anna Maria Paluscio, Mariano Francesco Caratozzolo, Flaviana Marzano, Ivana Kurelac, Anna Maria D’Erchia, Domenica D’Elia, Flavio Licciulli, Sabino Liuni, Ernesto Picardi, Marcella Attimonelli, Giuseppe Gasparre, Anna Maria Porcelli, Graziano Pesole, Elisabetta Sbisà, Apollonia Tullo
Software Mentions: 1
Published: almost 13 years ago

10.7150/ijbs.59581

The effect of mitochondrial transplantation therapy from different gender on inhibiting cell proliferation of malignant melanoma
Cited by: 8
Author(s): Zhenyao Yu, Yixue Hou, Wei Zhou, Zizhen Zhao, Zesheng Liu, Ailing Fu
Software Mentions: 1
Published: over 5 years ago

10.3389/fmolb.2017.00057

Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14
Cited by: 34
Author(s): Georges St. Laurent, Bernd Seilheimer, Michael Tackett, Jianhua Zhou, Dmitry Shtokalo, Yuri Vyatkin, Maxim Ri, Ian Toma, Dan Jones, Timothy A. McCaffrey
Software Mentions: 1
Published: about 9 years ago

10.3389/fmolb.2021.682769

Novel Insights into the Potential Diagnostic Value of Circulating Exosomal IncRNA-Related Networks in Large Artery Atherosclerotic Stroke
Cited by: 4
Author(s): Shuai Zhang, Jing Wang, Mei Jie Qu, Kun Wang, Jun Ai, Pan Xu, Xiao Jun Zhu
Software Mentions: 1
Published: over 5 years ago

10.1007/s00109-020-01922-x

Opposite regulation of piRNAs, rRNAs and miRNAs in the blood after subarachnoid hemorrhage
Cited by: 2
Author(s): Rafał Morga, Małgorzata Borczyk, Michał Korostyński, Marcin Piechota, Dżesika Hoinkis, Sławomir Gołda, Tomasz Dziedzic, Agnieszka Słowik, Marek Moskała, Joanna Pera
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-017-4161-0

Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification
Cited by: 32
Author(s): Kevin M. Johnson, Gretchen E. Hofmann
Software Mentions: 1
Published: almost 9 years ago

10.3389/fmolb.2021.737472

Transcriptional Network Analysis Reveals the Role of miR-223-5p During Diabetic Corneal Epithelial Regeneration
Cited by: 4
Author(s): Yuan Zhang, Shengqian Dou, Xia Qi, Zhenzhen Zhang, Yujie Qiao, Yani Wang, Jin Xie, Hui Jiang, Bin Zhang, Qingjun Zhou, Qun Wang, Lixin Xie
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0245070

Transcriptomic analyses show that 24-epibrassinolide (EBR) promotes cold tolerance in cotton seedlings
Cited by: 10
Author(s): Dou Liu, Yaru Sun, Shuye Li, Changwei Ge, Qian Shen, Huaizhu Li, Wenbo Wang, Jiayi Mao, Gao Xiao, Chaoyou Pang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-82848-3

A transcriptomic view to wounding response in young Scots pine stems
Cited by: 9
Author(s): Kean‐Jin Lim, Tanja Paasela, Anni Harju, Martti Venäläinen, Lars Paulín, Petri Auvinen, Katri Kärkkäinen, Teemu H. Teeri
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-16611-y

OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells
Cited by: 10
Author(s): Runsheng He, Besa Xhabija, Batool Al‐Qanber, Benjamin L. Kidder
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pntd.0004929

The Effects of Ivermectin on Brugia malayi Females In Vitro: A Transcriptomic Approach
Cited by: 21
Author(s): Cristina Ballesteros, Lucienne Tritten, Maeghan O’Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew R. Moorhead, Steven A. Williams, Timothy G. Geary
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-017-16472-5

Identification of a histone family gene signature for predicting the prognosis of cervical cancer patients
Cited by: 42
Author(s): Xiaofang Li, Run Tian, Hugh Gao, Yongkang Yang, Bryan R.G. Williams, Michael P. Gantier, Nigel A.J. McMillan, Dakang Xu, Yiqun Hu, Yue Gao
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-16930-0

MALE STERILE6021 (MS6021) is required for the development of anther cuticle and pollen exine in maize
Cited by: 27
Author(s): Youhui Tian, Senlin Xiao, Juan Liu, Yamuna Somaratne, Hua Zhang, Mingming Wang, Huairen Zhang, Li Zhao, Huabang Chen
Software Mentions: 1
Published: almost 9 years ago

10.3389/fnmol.2018.00410

Transcriptome Profiling of Layer 5 Intratelencephalic Projection Neurons From the Mature Mouse Motor Cortex
Cited by: 7
Author(s): Alison J Clare, Robert C. Day, Ruth M. Empson, Stephanie M. Hughes
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-017-3577-x

De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes
Cited by: 24
Author(s): Stephanie C. Kerr, Federico Gaiti, Christine A. Beveridge, Miloš Tanurdžić
Software Mentions: 1
Published: over 9 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568