bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3390/plants9101334

Transcriptome-Based Analysis of Phosphite-Induced Resistance against Pathogens in Rice
Cited by: 4
Author(s): Yuqing Huang, Shengguan Cai, Guoping Zhang, Songlin Ruan
Software Mentions: 1
Published: about 6 years ago

10.3390/plants10020357

Main Molecular Pathways Associated with Copper Tolerance Response in Imperata cylindrica by de novo Transcriptome Assembly
Cited by: 5
Author(s): Catalina Vidal, Giovanni Larama, Aníbal Riveros, Claudio Meneses, Pablo Cornejo
Software Mentions: 1
Published: almost 6 years ago

10.18632/aging.103910

Prolonged treatment with Y-27632 promotes the senescence of primary human dermal fibroblasts by increasing the expression of IGFBP-5 and transforming them into a CAF-like phenotype
Cited by: 7
Author(s): Xiangyong Li, Qian Zhou, Shuangshuang Wang, Ping Wang, Juan Li, Zhiwei Xie, Chang Liu, Jie Wen, Xunwei Wu
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-019-5740-z

A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency
Cited by: 23
Author(s): Stafford Vigors, John V. O’Doherty, Kenneth Bryan, T. Sweeney
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-98905-w

Cas9-mediated genome editing reveals a significant contribution of calcium signaling pathways to anhydrobiosis in Pv11 cells
Cited by: 5
Author(s): Yugo Miyata, Hiroto Fuse, Shoko Tokumoto, Yusuke Hiki, Ruslan Deviatiiarov, Yuki Yoshida, Takahiro Yamada, Richard Cornette, Oleg Gusev, Elena Shagimardanova, Akira Funahashi, Takahiro Kikawada
Software Mentions: 1
Published: about 5 years ago

10.1007/s11103-019-00853-7

Functional and molecular characterization of the conserved Arabidopsis PUMILIO protein, APUM9
Cited by: 12
Author(s): Tünde Nyikó, Andor Auber, Etienne Bucher
Software Mentions: 1
Published: over 7 years ago

10.18632/aging.101421

Involvement of SPATA31 copy number variable genes in human lifespan
Cited by: 7
Author(s): Cemalettin Bekpen, Chen Xie, Almut Nebel, Diethard Tautz
Software Mentions: 1
Published: over 8 years ago

10.1186/s13007-016-0141-7

Infiltration-RNAseq: transcriptome profiling of Agrobacterium-mediated infiltration of transcription factors to discover gene function and expression networks in plants
Cited by: 23
Author(s): Donna M. Bond, Nick W. Albert, Robyn H Lee, Gareth Benjamin Gillard, Chris M. Brown, Roger P. Hellens, Richard C. Macknight
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-020-07279-2

Physiological and transcriptomic analyses reveal the roles of secondary metabolism in the adaptive responses of Stylosanthes to manganese toxicity
Cited by: 13
Author(s): Yidan Jia, Xinyong Li, Qin Liu, Xuan Hu, Jifu Li, Rongshu Dong, Pandao Liu, Guodao Liu, Lijuan Luo, Zhijian Chen
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41392-020-0122-1

D609 protects retinal pigmented epithelium as a potential therapy for age-related macular degeneration
Cited by: 14
Author(s): Bowen Wang, Li Wang, Sijie Gu, Yankun Yu, Haoyue Huang, Kunlun Mo, He Xu, Fanzhu Zeng, Yunfeng Xiao, Lulu Peng, Chunqiao Liu, Nan Cao, Yizhi Liu, Jing Yuan, Hong Ouyang
Software Mentions: 1
Published: over 6 years ago

10.1111/tpj.13639

Metabolite profiling of non‐sterile rhizosphere soil
Cited by: 121
Author(s): Pierre Pétriacq, Alex Williams, T. E. Anne Cotton, Alexander E. McFarlane, Stephen A. Rolfe, Jurriaan Ton
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-016-2866-0

Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster
Cited by: 28
Author(s): Korbinian von Heckel, Wolfgang Stephan, Stephan Hütter
Software Mentions: 1
Published: over 10 years ago

10.1038/s41392-021-00575-7

RNA-induced liquid phase separation of SARS-CoV-2 nucleocapsid protein facilitates NF-κB hyper-activation and inflammation
Cited by: 74
Author(s): Yiming Wu, Ling Ma, Sihui Cai, Zhen Zhuang, Zhiyao Zhao, Shouheng Jin, Weidong Xie, Lingli Zhou, Lei Zhang, Jincun Zhao, Jun Cui
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5690-5

Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss
Cited by: 13
Author(s): Hao Ma, Kyle E. Martin, Doug Dixon, Alvaro G. Hernandez, Gregory M. Weber
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22042181

Altered Expression of OsAAP3 Influences Rice Lesion Mimic and Leaf Senescence by Regulating Arginine Transport and Nitric Oxide Pathway
Cited by: 12
Author(s): Qilang Wei, Zhenwei Yan, Yifan Xiong, Zhongming Fang
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.66240

AAV-Txnip prolongs cone survival and vision in mouse models of retinitis pigmentosa
Cited by: 23
Author(s): Y. Y. Xue, Sean K. Wang, Parimal Rana, Emma R. West, Christin M Hong, Helian Feng, David M. Wu, Constance L. Cepko
Software Mentions: 1
Published: over 5 years ago

10.1111/tpj.12835

Highly specific gene silencing in a monocot species by artificial micro<scp>RNA</scp>s derived from chimeric mi<scp>RNA</scp> precursors
Cited by: 39
Author(s): Alberto Carbonell, Noah Fahlgren, Skyler Mitchell, Kevin L. Cox, Kevin C. Reilly, Todd C. Mockler, James C. Carrington
Software Mentions: 1
Published: over 11 years ago

10.1038/s41392-021-00716-y

Decreased inhibition of exosomal miRNAs on SARS-CoV-2 replication underlies poor outcomes in elderly people and diabetic patients
Cited by: 40
Author(s): Han Li, Xiao Zhu, Xiaming Jiang, Jingwei Guo, Zheng Fu, Zhen Zhou, Ping Yang, Hongyuan Guo, Xu Guo, Gaoli Liang, Ping Zeng, Gengfu Xiao, Jie Ma, Xin Yin, Leike Zhang, Chao Yan, Chenyu Zhang
Software Mentions: 1
Published: over 5 years ago

10.18632/aging.101683

Higher gene expression stability during aging in long-lived giant mole-rats than in short-lived rats
Cited by: 14
Author(s): Arne Sahm, Martin Bens, Yoshiyuki Henning, Christiane Vole, Marco Groth, Matthias Schwab, Steve Hoffmann, Matthias Platzer, Karol Szafranski, Philip Dammann
Software Mentions: 1
Published: almost 8 years ago

10.1111/tpj.14508

Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions
Cited by: 30
Author(s): Michela Cecchin, Luca Marcolungo, Marzia Rossato, Laura Girolomoni, Emanuela Cosentino, Stéphan Cuiné, Yonghua Li‐Beisson, Massimo Delledonne, Matteo Ballottari
Software Mentions: 1
Published: about 7 years ago

10.18632/aging.101471

Chronic vitamin D insufficiency impairs physical performance in C57BL/6J mice
Cited by: 14
Author(s): Kenneth L. Seldeen, Manhui Pang, Merced M Leiker, Jonathan Bard, Maria Rodríguez-Gonzalez, Mireya Hernandez, Zachary Sheridan, Norma J. Nowak, Bruce R. Troen
Software Mentions: 1
Published: over 8 years ago

10.1186/s13395-021-00273-6

The pan HDAC inhibitor Givinostat improves muscle function and histological parameters in two Duchenne muscular dystrophy murine models expressing different haplotypes of the LTBP4 gene
Cited by: 13
Author(s): Simonetta Andrea Licandro, Luca Crippa, Roberta Pomarico, Rita Perego, Gianluca Fossati, Flavio Leoni, Christian Steinkühler
Software Mentions: 1
Published: over 5 years ago

10.1111/tpj.14435

Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication
Cited by: 41
Author(s): Muriel Gros-Balthazard, Guillaume Besnard, Gautier Sarah, Yan Holtz, Julie Leclercq, Sylvain Santoni, Daniel Wegmann, Sylvain Glémin, Bouchaïb Khadari
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-3696-4

Comparative transcriptomics of mountain pine beetle pheromone-biosynthetic tissues and functional analysis of CYP6DE3
Cited by: 26
Author(s): Jeffrey A. Nadeau, Julia Petereit, Richard L. Tillett, Ki‐Hong Jung, Misha Fotoohi, Marina MacLean, Sharon M. Young, Karen Schlauch, Gary J. Blomquist, Claus Tittiger
Software Mentions: 1
Published: over 9 years ago

10.1016/j.stemcr.2019.03.006

Pathological ASXL1 Mutations and Protein Variants Impair Neural Crest Development
Cited by: 15
Author(s): Friederike Matheus, Ejona Rusha, Rizwan Rehimi, Lena Molitor, Anna Pertek, Miha Modic, Regina Feederle, Andrew Flatley, Elisabeth Kremmer, Arie Geerlof, Valentyna M. Rishko, Álvaro Rada-Iglesias, Micha Drukker
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-015-1867-8

RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection
Cited by: 39
Author(s): Esther Wilk, Ashutosh Kumar Pandey, Sarah R. Leist, Bastian Hatesuer, Matthias Preuße, Claudia Pommerenke, Junxi Wang, Klaus Schughart
Software Mentions: 1
Published: about 11 years ago

10.1002/pld3.14

ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1 ) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice (O. sativa )
Cited by: 24
Author(s): Juan David Arbelaez, Lyza Maron, Timothy O. Jobe, Miguel A. Piñeros, Adam N. Famoso, Ana Rita Rebelo, Namrata Singh, Qiyue Ma, Zhangjun Fei, Leon V. Kochian, Susan R. McCouch
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-021-07856-z

Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance
Cited by: 9
Author(s): Ke Chen, Yajun Peng, Liang Zhang, Long Wang, Donghai Mao, Zixiang Zhao, Lianyang Bai, Lifeng Wang
Software Mentions: 1
Published: over 5 years ago

10.1002/pld3.101

Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA‐dominated PHAS loci
Cited by: 14
Author(s): Seth Polydore, Alice Lunardon, Michael J. Axtell
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.stemcr.2020.05.003

Pro-maturational Effects of Human iPSC-Derived Cortical Astrocytes upon iPSC-Derived Cortical Neurons
Cited by: 38
Author(s): Anne Hedegaard, Jimena Monzón‐Sandoval, Sarah E. Newey, Emma Whiteley, Caleb Webber, Colin J. Akerman
Software Mentions: 1
Published: over 6 years ago

10.1111/pbi.13455

A 1.7‐Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach
Cited by: 38
Author(s): Hui Zhou, Ruijuan Ma, Lei Gao, Jinyun Zhang, Aidi Zhang, Xiujun Zhang, Fei Ren, Weihan Zhang, Liao Liao, Qingsong Yang, Shengli Xu, Collins Ogutu, Jianbo Zhao, Mingliang Yu, Quan Jiang, Schuyler S. Korban, Yuepeng Han
Software Mentions: 1
Published: about 6 years ago

10.1111/pbi.13566

Repressed OsMESL expression triggers reactive oxygen species‐mediated broad‐spectrum disease resistance in rice
Cited by: 16
Author(s): Bin Hu, Yong Zhou, Zaihui Zhou, Bo Sun, Fei Zhou, Changxi Yin, Weihua Ma
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-4773-z

Characterization of microRNA and mRNA expression profiles in skin tissue between early-feathering and late-feathering chickens
Cited by: 9
Author(s): Guijun Fang, Xiaoyun Jia, Hua Li, Shuo Tan, Qinghua Nie, Hui Yu, Ying Yang
Software Mentions: 1
Published: over 8 years ago

10.1016/j.stemcr.2021.07.021

Generation of pancreatic progenitors from human pluripotent stem cells by small molecules
Cited by: 14
Author(s): Yuqian Jiang, Chuanxin Chen, Lauren N. Randolph, Songtao Ye, Xin Zhang, Xiaoping Bao, Xiaojun Lian
Software Mentions: 1
Published: about 5 years ago

10.1016/j.scr.2020.101931

Hypermethylation and reduced expression of Gtl2, Rian and Mirg at the Dlk1-Dio3 imprinted locus as a marker for poor developmental potential of mouse embryonic stem cells
Cited by: 2
Author(s): Maria Schacker, Ying Cheng, Mélanie Eckersley-Maslin, Richard Michael Snaith, William H. Colledge
Software Mentions: 1
Published: about 6 years ago

10.1186/s13287-019-1155-7

Platelet-rich plasma improves therapeutic effects of menstrual blood-derived stromal cells in rat model of intrauterine adhesion
Cited by: 65
Author(s): Siwen Zhang, Pingping Li, Zhengwei Yuan, Jichun Tan
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-021-07561-x

Methamphetamine-induced changes in myocardial gene transcription are sex-dependent
Cited by: 5
Author(s): Hasitha Chavva, Daniel A. Brazeau, James Denvir, Donald A. Primerano, Jun Fan, Sarah L. Seeley, Boyd R. Rorabaugh
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-5240-6

Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
Cited by: 8
Author(s): Jessica Vannina Fay, Chris Watkins, Ram Krishna Shrestha, Sergio Litwiñiuk, Liliana Noelia Talavera Stéfani, Cristian Antonio Rojas, Carina F. Argüelles, Julian A. Ferreras, Mario Cáccamo, Marcos Mateo Miretti
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13287-019-1306-x

lncRNA-mRNA expression profiles and functional networks of mesenchymal stromal cells involved in monocyte regulation
Cited by: 5
Author(s): Ming Li, Zhongyu Xie, Zhaopeng Cai, Fang Su, Guoyan Zheng, Jinteng Li, Shan Wang, Shuizhong Cen, Wenjie Liu, Simin Tang, Guiwen Ye, Zhaofeng Li, Rujia Mi, Yiqian Pan, Peng Wang, Yanfeng Wu, Huiyong Shen
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.44328

Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1
Cited by: 41
Author(s): Hsin-I Jen, Matthew C. Hill, Litao Tao, Kuanwei Sheng, Wenjian Cao, Hongyuan Zhang, Haoze V Yu, Juan Llamas, Chenghang Zong, James F. Martin, Neil Segil, Andrew K. Groves
Software Mentions: 1
Published: over 7 years ago

10.1186/s12863-017-0499-1

Transcriptome profiling of Arabian horse blood during training regimens
Cited by: 21
Author(s): Katarzyna Ropka‐Molik, Monika Stefaniuk‐Szmukier, Kacper Żukowski, Katarzyna Piórkowska, Artur Gurgul, Monika Bugno‐Poniewierska
Software Mentions: 1
Published: over 9 years ago

10.1128/mBio.01253-16

Genetic Dissection of the Type VI Secretion System in Acinetobacter and Identification of a Novel Peptidoglycan Hydrolase, TagX, Required for Its Biogenesis
Cited by: 82
Author(s): Brent S. Weber, Seth W. Hennon, Meredith S. Wright, Nichollas E. Scott, Véronique de Berardinis, Leonard J. Foster, Juan A. Ayala, Mark D. Adams, Mario F. Feldman
Software Mentions: 1
Published: about 10 years ago

10.1186/s12863-019-0794-0

Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork
Cited by: 6
Author(s): Xueyan Zhao, Cheng Wang, Yanping Wang, Haichao Lin, Huaizhong Wang, Hongmei Hu, Jiying Wang
Software Mentions: 1
Published: almost 7 years ago

10.1111/pbi.13114

BBX16, a B‐box protein, positively regulates light‐induced anthocyanin accumulation by activating MYB10 in red pear
Cited by: 164
Author(s): Songling Bai, Ruiyan Tao, Yinxin Tang, Lei Yin, Yihan Ma, Junbei Ni, Xue Yan, Qinsong Yang, Zhongying Wu, Yanwei Zeng, Yuanwen Teng
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.02193-16

Transcriptome Remodeling of Acinetobacter baumannii during Infection and Treatment
Cited by: 32
Author(s): Meredith S. Wright, Michael Jacobs, Robert A. Bonomo, Mark D. Adams
Software Mentions: 1
Published: over 9 years ago

10.1111/pbi.13487

Installation of C 4 photosynthetic pathway enzymes in rice using a single construct
Cited by: 64
Author(s): Maria Ermakova, Stéphanie Arrivault, R. Giuliani, Florence R. Danila, Hugo Alonso-Cantabrana, Daniela Vlad, Hirofumi Ishihara, Regina Feil, Manuela Guenther, Gian Luca Borghi, Sarah Covshoff, Martha Ludwig, Asaph B. Cousins, Jane A. Langdale, Steven L. Kelly, John E. Lunn, Mark Stitt, Susanne von Caemmerer, Robert T. Furbank
Software Mentions: 1
Published: about 6 years ago

10.1111/pbi.13286

Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed
Cited by: 16
Author(s): Haixiao Hu, Juan J. Gutiérrez-González, Xinfang Liu, Trevor H. Yeats, David F. Garvin, Owen A. Hoekenga, Mark E. Sorrells, Michael A. Gore, Jean‐Luc Jannink
Software Mentions: 1
Published: almost 7 years ago

10.1128/mBio.00730-17

RIP-Seq Suggests Translational Regulation by L7Ae in Archaea
Cited by: 19
Author(s): Michael Daume, Michaël Uhl, Rolf Backofen, Lennart Randau
Software Mentions: 1
Published: about 9 years ago

10.1007/s00425-020-03536-6

Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus
Cited by: 19
Author(s): Longfei Jia, Junsheng Wang, Rui Wang, Mouzheng Duan, Cailin Qiao, Xue Chen, Genshan Ma, Xin-Tong Zhou, Meichen Zhu, Fuyu Jing, Shengsen Zhang, Cunmin Qu, Jiana Li
Software Mentions: 1
Published: almost 6 years ago

10.18632/aging.103539

The circular RNA circEIF3M promotes breast cancer progression by promoting cyclin D1 expression
Cited by: 12
Author(s): Xiujuan Li, Zhao-Jun Ren, Yufeng Yao, Jun Bao, Qiao Ye
Software Mentions: 1
Published: over 6 years ago

10.1186/s12862-018-1132-2

RNA sequencing of early round goby embryos reveals that maternal experiences can shape the maternal RNA contribution in a wild vertebrate
Cited by: 16
Author(s): Irene Adrian‐Kalchhauser, Jean‐Claude Walser, Michaela Schwaiger, Patricia Burkhardt‐Holm
Software Mentions: 1
Published: over 8 years ago

10.1128/mBio.01678-17

Human Placental Syncytiotrophoblasts Restrict Toxoplasma gondii Attachment and Replication and Respond to Infection by Producing Immunomodulatory Chemokines
Cited by: 48
Author(s): Stephanie E. Ander, Elizabeth N. Rudzki, Nitin Arora, Yoel Sadovsky, Carolyn B. Coyne, Jon P. Boyle
Software Mentions: 1
Published: over 8 years ago

10.1007/s00425-021-03735-9

Methyl jasmonate elicits distinctive hydrolyzable tannin, flavonoid, and phyto-oxylipin responses in pomegranate (Punica granatum L.) leaves
Cited by: 5
Author(s): Liming Chang, Sheng Wu, Li Tian
Software Mentions: 1
Published: about 5 years ago

10.1128/mBio.02430-17

Physiological Effect of XoxG(4) on Lanthanide-Dependent Methanotrophy
Cited by: 42
Author(s): Yue Zheng, Jing Huang, Feng Zhao, Ludmila Chistoserdova
Software Mentions: 1
Published: over 8 years ago

10.14814/phy2.14396

Sexual dimorphism in cardiac transcriptome associated with a troponin C murine model of hypertrophic cardiomyopathy
Cited by: 10
Author(s): Karissa M. Dieseldorff Jones, Cynthia Vied, Isela Valera, P. Bryant Chase, Michelle S. Parvatiyar, José R. Pinto
Software Mentions: 1
Published: over 6 years ago

10.1186/s12862-016-0683-3

Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis
Cited by: 57
Author(s): Leslie S. Babonis, Mark Q. Martindale, Joseph F. Ryan
Software Mentions: 1
Published: over 10 years ago

10.1128/mBio.01222-18

Avian Influenza Virus PB1 Gene in H3N2 Viruses Evolved in Humans To Reduce Interferon Inhibition by Skewing Codon Usage toward Interferon-Altered tRNA Pools
Cited by: 24
Author(s): Bartram L Smith, Guifang Chen, Claus O. Wilke, Robert M. Krug
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms21249399

Small Noncoding RNA Signatures for Determining the Developmental Potential of an Embryo at the Morula Stage
Cited by: 19
Author(s): Timofeeva A.V. Timofeeva, Yulia S. Drapkina, Ivan S. Fedorov, Vitaliy Chagovets, Н. П. Макарова, Maria A. Shamina, Kalinina E.A. Kalinina, Г. Т. Сухих
Software Mentions: 1
Published: almost 6 years ago

10.1128/mBio.01347-18

Investigating the Campylobacter jejuni Transcriptional Response to Host Intestinal Extracts Reveals the Involvement of a Widely Conserved Iron Uptake System
Cited by: 20
Author(s): Martha M. Liu, Christine J. Boinett, Anson Chan, Julian Parkhill, M.E.P. Murphy, Erin C. Gaynor
Software Mentions: 1
Published: about 8 years ago

10.7554/eLife.58213

IL18 signaling promotes homing of mature Tregs into the thymus
Cited by: 21
Author(s): Cristina Peligero-Cruz, Tal Givony, Arnau Sebé-Pedrós, Jan Dobeš, Noam Kadouri, Shir Nevo, Francesco Roncato, Ronen Alon, Yael Goldfarb, Jakub Abramson
Software Mentions: 1
Published: over 6 years ago

10.14814/phy2.14997

Sex‐dependent acrolein sensitivity in mice is associated with differential lung cell, protein, and transcript changes
Cited by: 1
Author(s): Kiflai Bein, Rahel L. Birru, Heather Wells, Theodore P. Larkin, Tengziyi Ge, George D. Leikauf
Software Mentions: 1
Published: about 5 years ago

10.14814/phy2.14381

Altered proteomics profile in the amnion of patients with oligohydramnios
Cited by: 2
Author(s): Cecilia Y. Cheung, Robert A. Brace
Software Mentions: 1
Published: almost 7 years ago

10.1128/mBio.01276-18

Arylvinylpiperazine Amides, a New Class of Potent Inhibitors Targeting QcrB of Mycobacterium tuberculosis
Cited by: 50
Author(s): Caroline S. Foo, Andréanne Lupien, Maryline Kienle, Anthony Vocat, Andrej Benjak, Raphael Sommer, Dirk A. Lamprecht, Adrie J. C. Steyn, Kévin Pethe, Jérémie Piton, Karl‐Heinz Altmann, Stewart T. Cole
Software Mentions: 1
Published: about 8 years ago

10.1186/s12862-020-01622-7

Chloroplast (Cp) Transcriptome of P. davidiana Dode×P. bolleana Lauch provides insight into the Cp drought response and Populus Cp phylogeny
Cited by: 4
Author(s): Xin Zhang, Chao Gu, Tianxu Zhang, Botong Tong, Heng Zhang, Yong-Pei Wu, Chuanping Yang
Software Mentions: 1
Published: over 6 years ago

10.1098/rstb.2019.0194

Temporary adhesion of the proseriate flatworm Minona ileanae
Cited by: 14
Author(s): Robert Pjeta, Julia Wunderer, Philip Bertemes, T. Hofer, Willi Salvenmoser, Birgit Lengerer, Stefan Coassin, Gertraud Erhart, Christian Beisel, Daniel Sobral, Leopold Kremser, Herbert Lindner, Marco Curini‐Galletti, Claus‐Peter Stelzer, Michael W. Hess, Peter Ladurner
Software Mentions: 1
Published: about 7 years ago

10.1128/mBio.02189-18

Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member
Cited by: 34
Author(s): Bela Hausmann, Claus Pelikan, Thomas Rattei, Alexander Loy, Michael Pester
Software Mentions: 1
Published: over 7 years ago

10.3390/pharmaceutics13091415

Cannabidiol Effectively Promoted Cell Death in Bladder Cancer and the Improved Intravesical Adhesion Drugs Delivery Strategy Could Be Better Used for Treatment
Cited by: 9
Author(s): Shanshan Chen, Changping Deng, Wenyun Zheng, Shihui Li, Yuping Liu, Tong Zhang, Chen Zhang, Yunhui Fu, Hui Miao, Fuzheng Ren, Xiaochun Ma
Software Mentions: 1
Published: about 5 years ago

10.3390/pharmaceutics12100967

Non-Human Primate Blood–Brain Barrier and In Vitro Brain Endothelium: From Transcriptome to the Establishment of a New Model
Cited by: 10
Author(s): Catarina Chaves, Tuan-Minh Do, Céline Cegarra, Valérie Roudières, Sandrine Tolou, Gilbert Thill, Corinne Rocher, Michel Didier, Dominique Lesuisse
Software Mentions: 1
Published: about 6 years ago

10.1186/s12862-021-01818-5

Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle
Cited by: 1
Author(s): Adrielle Ayumi de Vasconcelos, Juliana José, Paulo M. Tokimatu, Antônio Pedro Camargo, Paulo José Pereira Lima Teixeira, Daniela P. T. Thomazella, Paula Favoretti Vital do Prado, Gabriel Lorencini Fiorin, Juliana Leles Costa, Antônio Figueira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Renata Moro Baroni
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.6541

Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)
Cited by: 4
Author(s): Moisés A. Bernal, Groves Dixon, Mikhail V. Matz, Luiz A. Rocha
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00273-19

Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
Cited by: 23
Author(s): Kelley Hurst-Hess, Ratna Biswas, Yong Yang, Paulami Rudra, Erica Lasek‐Nesselquist, Phalguni Ghosh
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.02469-18

Antibody Treatment against Angiopoietin-Like 4 Reduces Pulmonary Edema and Injury in Secondary Pneumococcal Pneumonia
Cited by: 19
Author(s): Liang Li, Benjamin Jie Wei Foo, Ka Wai Kwok, Noriho Sakamoto, Hiroshi Mukae, Koichi Izumikawa, Stéphane Mandard, Jean‐Pierre Quenot, Laurent Lagrost, Wooi Keong Teh, Gurjeet S. Kohli, Pengcheng Zhu, Hyungwon Choi, Martin L. Buist, Ju Ee Seet, Liang Yang, Fang He, Vincent T. K. Chow, Nguan Soon Tan
Software Mentions: 1
Published: over 7 years ago

10.18632/aging.103205

Chestnut polysaccharides benefit spermatogenesis through improvement in the expression of important genes
Cited by: 10
Author(s): Shuai Yu, Yong Zhao, Fa‐Li Zhang, Ya-Qi Li, Wei Shen, Zhongyi Sun
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21249550

Cellular, Extracellular and Extracellular Vesicular miRNA Profiles of Pre-Ovulatory Follicles Indicate Signaling Disturbances in Polycystic Ovaries
Cited by: 16
Author(s): Ilmatar Rooda, Mohammad Mehedi Hasan, Kristine Roos, Janeli Viil, Aneta Andronowska, Olli‐Pekka Smolander, Ülle Jaakma, Andres Salumets, Alireza Fazeli, Agne Velthut-Meikas
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.6710

Automated analysis of small RNA datasets with RAPID
Cited by: 8
Author(s): Sivarajan Karunanithi, Martín Simón, Marcel H. Schulz
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.2119

Integrated microRNA, gene expression and transcription factors signature in papillary thyroid cancer with lymph node metastasis
Cited by: 30
Author(s): Nurul Syakima Ab Mutalib, Sri Noraima Othman, Azliana Mohamad Yusof, Shahrun Niza Abdullah Suhaimi, Rohaizak Muhammad, A. Rahman A. Jamal
Software Mentions: 1
Published: over 10 years ago

10.1186/s12861-020-00219-z

Identification of vital candidate microRNA/mRNA pairs regulating ovule development using high-throughput sequencing in hazel
Cited by: 11
Author(s): Jianfeng Liu, Qizheng Luo, Xingzheng Zhang, Qiang Zhang, Yufei Cheng
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.8624

Identification and validation of potential key long noncoding RNAs in sorafenib-resistant hepatocellular carcinoma cells
Cited by: 2
Author(s): Manya Wu, Xiaofeng Shen, Yanping Tang, Caifu Zhou, Haixia Li, Xi Luo
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.6425

Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis
Cited by: 24
Author(s): Yang Fang, Pingping Wang, Lin Xia, Suwen Bai, Yonggang Shen, Qing Li, Yang Wang, Jiaquan Zhu, Juan Du, Bing Shen
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.02253-19

A rhlI 5′ UTR-Derived sRNA Regulates RhlR-Dependent Quorum Sensing in Pseudomonas aeruginosa
Cited by: 34
Author(s): Maureen K. Thomason, Maya Voichek, Daniel Dar, Victoria Addis, David J. FitzGerald, Susan Gottesman, Rotem Sorek, E. Peter Greenberg
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.12133

Transcriptome and structure analysis in root of Casuarina equisetifolia under NaCl treatment
Cited by: 6
Author(s): Yujiao Wang, Jin Zhang, Qiu Zhenfei, Bingshan Zeng, Yong Zhang, Xiaoping Wang, Jun Chen, Zhong Chen, Renhua Deng, Chunjie Fan
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.11506

Transcriptome analysis of Sonneratia caseolaris seedlings under chilling stress
Cited by: 6
Author(s): Yong Yang, Chunfang Zheng, Cairong Zhong, Tianxi Lu, Juma Gul, Xiang Jin, Ying Zhang, Qiang Liu
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.9994

Potential role of cellular miRNAs in coronavirus-host interplay
Cited by: 64
Author(s): Stepan Nersisyan, Narek Engibaryan, Aleksandra Gorbonos, Ksenia Kirdey, Alexey Makhonin, Alexander G. Tonevitsky
Software Mentions: 1
Published: about 6 years ago

10.1128/mBio.02774-19

The Staphylococcus aureus Transcriptome during Cystic Fibrosis Lung Infection
Cited by: 35
Author(s): Carolyn B. Ibberson, Marvin Whiteley
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.8054

Ciglitazone—a human PPARγ agonist—disrupts dorsoventral patterning in zebrafish
Cited by: 7
Author(s): Vanessa Cheng, Subham Dasgupta, Aalekhya Reddam, David C. Volz
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.6629

Evidence for an oncogenic role of HOXC6 in human non-small cell lung cancer
Cited by: 10
Author(s): Yuting Yang, Xiaoping Tang, Xueqin Song, Li Tang, Yong Cao, Xu Liu, Xiaoyan Wang, Yan Li, Minglan Yu, Haisu Wan, Feng Chen
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.02788-19

Diversity in Natural Transformation Frequencies and Regulation across Vibrio Species
Cited by: 25
Author(s): Chelsea A. Simpson, Ram Podicheti, Douglas B. Rusch, Ankur B. Dalia, Julia C. van Kessel
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.5782

Sex-biased expression between guppies varying in the presence of ornamental coloration
Cited by: 3
Author(s): Cynthia Dick, David N. Reznick, Cheryl Y. Hayashi
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.6388

Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach
Cited by: 12
Author(s): Saleembhasha Asanigari, Seema Mishra
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.8509

Integrated analysis of the roles and prognostic value of RNA binding proteins in lung adenocarcinoma
Cited by: 25
Author(s): Wei Li, Na Li, Lina Gao, Chongge You
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.2486

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
Cited by: 62
Author(s): Christian Rinke, Serene Low, Ben J. Woodcroft, Jean-Baptiste Raina, Adam Skarshewski, Xuyen H. Le, Margaret K. Butler, Roman Stocker, Justin R. Seymour, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 1
Published: about 10 years ago

10.1128/mBio.03193-19

Modulation of Symbiotic Compatibility by Rhizobial Zinc Starvation Machinery
Cited by: 10
Author(s): Pan Zhang, Biliang Zhang, Jian Jiao, Shi-Qi Dai, Wenxin Chen, Chang Fu Tian
Software Mentions: 1
Published: over 6 years ago

10.1186/s40478-017-0431-y

Altered Ca2+ homeostasis induces Calpain-Cathepsin axis activation in sporadic Creutzfeldt-Jakob disease
Cited by: 30
Author(s): Franc Llorens, Katrin Thüne, Beata Sikorska, Matthias Schmitz, Waqas Tahir, Natalia Fernández‐Borges, Maria Cramm, Nadine Gotzmann, Margarita Carmona, Nathalie Streichenberger, Uwe Michel, Saima Zafar, Anna-Lena Schuetz, Ashish Rajput, Olivier Andréoletti, Stefan Bonn, André Fischer, Paweł P. Liberski, Juan María Torres, Isidre Ferrer, Inga Zerr
Software Mentions: 1
Published: over 9 years ago

10.1128/mBio.03210-19

Multi-Omic Analyses Provide Links between Low-Dose Antibiotic Treatment and Induction of Secondary Metabolism in Burkholderia thailandensis
Cited by: 17
Author(s): Anran Li, Dainan Mao, Aya Yoshimura, Paul Rosen, Warham Lance Martin, Étienne Gallant, Martin Wühr, Mohammad R. Seyedsayamdost
Software Mentions: 1
Published: over 6 years ago

10.1128/mBio.02777-19

A Sustained Immune Response Supports Long-Term Antiviral Immune Priming in the Pacific Oyster, Crassostrea gigas
Cited by: 41
Author(s): M. Lafont, Agnès Vergnes, Jérémie Vidal-Dupiol, Julien de Lorgeril, Yannick Gueguen, Philippe Haffner, Bruno Petton, Cristian Chaparro, Célia Barrachina, D. Destoumieux-Garzón, Guillaume Mitta, Benjamin Gourbal, Caroline Montagnani
Software Mentions: 1
Published: over 6 years ago

10.1186/s12861-021-00240-w

Changes in the expression levels of elastic fibres in yak lungs at different growth stages
Cited by: 2
Author(s): Jingyi Li, Xiangqiong Meng, Lihan Wang, Hanry Yu, Honggang Yu, Qing Wei
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.9357

Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach
Cited by: 42
Author(s): Tamizhini Loganathan, Srimathy Ramachandran, Prakash Shankaran, Devipriya Nagarajan, Suma Mohan
Software Mentions: 1
Published: over 6 years ago

10.1186/s12906-019-2558-9

Antimicrobial characteristics of Berberine against prosthetic joint infection-related Staphylococcus aureus of different multi-locus sequence types
Cited by: 27
Author(s): Jiaqi Tan, Jin Wang, Chuang Yang, Chongzun Zhu, Geyong Guo, Jin Tang, Hao Shen
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00816-20

Aspergillus fumigatus Transcription Factors Involved in the Caspofungin Paradoxical Effect
Cited by: 26
Author(s): Clara Valero, Ana Cristina Colabardini, Jéssica Chiaratto, Lakhansing Pardeshi, Patrícia Alves de Castro, Jaire Alves Ferreira Filho, Lilian Pereira Silva, Marina Campos Rocha, Iran Malavazi, Jonas Henrique Costa, Taícia Pacheco Fill, Mário H. Barros, Sarah Sze Wah Wong, Vishukumar Aimanianda, Koon Ho Wong, Gustavo H. Goldman
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.6832

Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)
Cited by: 21
Author(s): Jie Li, Xinhao Liu
Software Mentions: 1
Published: over 7 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

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Papers Mentioning DESeq2 9,583