bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1098/rsos.192243

Global analysis of differentially expressed genes between two Japonica rice varieties induced by low temperature during the booting stage by RNA-Seq
Cited by: 9
Author(s): Zhenhua Guo, Lijun Cai, Chuanxue Liu, Chao Huang, Zhiqiang Chen, Guoqing Pan, Tao Guo
Software Mentions: 1
Published: over 6 years ago

10.1186/s12935-020-01295-8

Construction of a metastasis-associated ceRNA network reveals a prognostic signature in lung cancer
Cited by: 22
Author(s): Qing Cao, Zewen Dong, Shuzhen Liu, Guoyan An, Bianbian Yan, Lei Lei
Software Mentions: 1
Published: over 6 years ago

10.1098/rsos.181869

Collembola interact with mycorrhizal fungi in modifying oak morphology, C and N incorporation and transcriptomics
Cited by: 12
Author(s): Marcel Graf, Markus Bönn, Lasse Feldhahn, Florence Kurth, Thorsten E. E. Grams, Sylvie Herrmann, Mika Tarkka, François Buscot, Stefan Scheu
Software Mentions: 1
Published: over 7 years ago

10.1098/rsos.180413

Identification and characterization of circular RNAs in Qinchuan cattle testis
Cited by: 40
Author(s): Yuan Gao, Mingli Wu, Yanhui Fan, Shipeng Li, Zhenyu Lai, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Hong Chen, Ruihua Dang
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-31719-5

Changes in circRNA expression profiles related to the antagonistic effects of Escherichia coli F17 in lamb spleens
Cited by: 9
Author(s): Chengyan Jin, Jianjun Bao, Yue Wang, Wei-Hao Chen, Shuangxia Zou, Tianyi Wu, Lihong Wang, Xiaoyang Lv, Wen Gao, Buzhong Wang, Guoqiang Zhu, Guojun Dai, Dongfang Shi, Wei Sun
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19092837

Guanidinoacetic Acid Regulates Myogenic Differentiation and Muscle Growth Through miR-133a-3p and miR-1a-3p Co-mediated Akt/mTOR/S6K Signaling Pathway
Cited by: 35
Author(s): Yujie Wang, Jideng Ma, Wanling Qiu, Jinwei Zhang, Siyuan Feng, Xiankun Zhou, Xun Wang, Long Jin, Keren Long, Lingyan Liu, Weihang Xiao, Qianzi Tang, Li Zhu, Yanzhi Jiang, Xuewei Li, Mingzhou Li
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-33100-y

Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota
Cited by: 49
Author(s): Alessandro Tanca, Marcello Abbondio, Antonio Palomba, Cristina Fraumene, Fabio Marongiu, Mauro Serra, Daniela Pagnozzi, Ezio Laconi, Sergio Uzzau
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-33597-3

Comparative transcriptomic analysis reveals common molecular factors responsive to heat and drought stress in Agrostis stolonifera
Cited by: 30
Author(s): Yi Xu, Bingru Huang
Software Mentions: 1
Published: about 8 years ago

10.1080/15476286.2020.1727694

Transcriptional profiling of human macrophages during infection withBordetella pertussis
Cited by: 13
Author(s): Denisa Petráčková, Mariam R. Farman, Fabian Amman, Irena Linhartová, Ana Dienstbier, Dilip Kumar, Jakub Držmíšek, Ivo L. Hofacker, Marı́a Eugenia Rodrı́guez, Branislav Večerek
Software Mentions: 1
Published: over 6 years ago

10.1098/rspb.2017.1393

Rapid functional and evolutionary changes follow gene duplication in yeast
Cited by: 26
Author(s): Samina Naseeb, Ryan M. Ames, Daniela Delneri, Simon C. Lovell
Software Mentions: 1
Published: about 9 years ago

10.1098/rspb.2017.0360

Unravelling the relationship between the tsetse fly and its obligate symbiont Wigglesworthia : transcriptomic and metabolomic landscapes reveal highly integrated physiological networks
Cited by: 50
Author(s): Xiao‐Li Bing, Geoffrey M. Attardo, Aurélien Vigneron, Emre Aksoy, Francesca Scolari, Anna R. Malacrida, Brian L. Weiss, Serap Aksoy
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-33899-6

Small non-coding RNA landscape of extracellular vesicles from human stem cells
Cited by: 50
Author(s): Sippy Kaur, Ahmed G. Abu-Shahba, Riku O. Paananen, Heidi Hongisto, Hanna Hiidenmaa, Heli Skottman, Riitta Seppänen‐Kaijansinkko, Bettina Mannerström
Software Mentions: 1
Published: about 8 years ago

10.1098/rspb.2014.2519

Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs
Cited by: 39
Author(s): Jan de Vries, Christian Woehle, Gregor Christa, Heike Wägele, Aloysius G.M. Tielens, Peter Jahns, Sven B. Gould
Software Mentions: 1
Published: over 11 years ago

10.3390/ijms19102858

Identification of Endogenous Control miRNAs for RT-qPCR in T-Cell Acute Lymphoblastic Leukemia
Cited by: 30
Author(s): Monika Drobna, Bronisława Szarzyńska‐Zawadzka, Patrycja Daca-Roszak, Maria Kosmalska, Roman Jaksik, Michał Witt, Małgorzata Dawidowska
Software Mentions: 1
Published: about 8 years ago

10.3390/polym12040937

Performance of a Biodegradable Composite with Hydroxyapatite as a Scaffold in Pulp Tissue Repair
Cited by: 14
Author(s): Masakazu Okamoto, Shigeto Matsumoto, Ayato Sugiyama, Kei Kanie, Masakatsu Watanabe, Haozhang Huang, Muslim Ali, Yuki Ito, Jiro Miura, Yujiro Hirose, Koichiro Uto, Mitsuhiro Ebara, Ryuji Kato, Aika Yamawaki-Ogata, Yuji Narita, Shigetada Kawabata, Yusuke Takahashi, Mikako Hayashi
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-34256-3

Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling
Cited by: 13
Author(s): Riccardo Lorrai, Francesco Gandolfi, Alessandra Boccaccini, Veronica Ruta, Marco Possenti, Anna Tramontano, Paolo Costantino, Rosalba Lepore, Paola Vittorioso
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-34333-7

Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species
Cited by: 7
Author(s): Hui Wang, Hanbo Zhao, Xiaobin Huang, Keping Sun, Feng Jiang
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19103083

Comprehensive Analysis of MicroRNA–Messenger RNA from White Yak Testis Reveals the Differentially Expressed Molecules Involved in Development and Reproduction
Cited by: 18
Author(s): Quanwei Zhang, Qi Wang, Yong Zhang, Cheng ShuRu, Junjie Hu, Youji Ma, Xingxu Zhao
Software Mentions: 1
Published: about 8 years ago

10.3390/nu12020511

Short-Term Caloric Restriction Attenuates Obesity-Induced Pro-inflammatory Response in Male Rhesus Macaques
Cited by: 4
Author(s): Hollis Wright, Mithila Handu, Allen Jankeel, Ilhem Messaoudi, Oleg Varlamov
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1009030

A human secretome library screen reveals a role for Peptidoglycan Recognition Protein 1 in Lyme borreliosis
Cited by: 9
Author(s): Akash Gupta, Gunjan Arora, Connor Rosen, Zachary A. Kloos, Yongguo Cao, Jiří Černý, Andaleeb Sajid, Dieuwertje Hoornstra, Maryna Golovchenko, Nataliia Rudenko, Ulrike G. Munderloh, Joppe W. Hovius, Carmen J. Booth, Christine Jacobs‐Wagner, Noah W. Palm, Aaron M. Ring, Erol Fikrig
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.ppat.1007388

Zinc-dependent substrate-level phosphorylation powers Salmonella growth under nitrosative stress of the innate host response
Cited by: 20
Author(s): Liam F. Fitzsimmons, Lin Liu, Steffen Porwollik, Sangeeta Chakraborty, Prerak Desai, Timothy Tapscott, Calvin A. Henard, Michael McClelland, Andrés Vázquez‐Torres
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-34575-5

Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis
Cited by: 38
Author(s): Ikuko Yuyama, Masakazu Ishikawa, Masahiro Nozawa, Masa‐aki Yoshida, Kazuho Ikeo
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-35531-z

The presence of extracellular microRNAs in the media of cultured Drosophila cells
Cited by: 14
Author(s): Stijn Van den Brande, M. J. M. Gijbels, Niels Wynant, Dulce Santos, Lina Mingels, Yannick Gansemans, Filip Van Nieuwerburgh, Jozef Vanden Broeck
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-36376-2

Transcriptome analysis of Aeromonas hydrophila infected hybrid sturgeon (Huso dauricus×Acipenser schrenckii)
Cited by: 20
Author(s): Nan Jiang, Yuding Fan, Yong Zhou, Weiling Wang, Jie Ma, Lingbing Zeng
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-37177-3

The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome
Cited by: 15
Author(s): Heidi H. Pak, Nicole E. Cummings, Cara L Green, Jacqueline A. Brinkman, Deyang Yu, Jay L. Tomasiewicz, Shany E. Yang, Colin Boyle, Elizabeth N. Konon, Irene M. Ong, Dudley W. Lamming
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.ppat.1007221

An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model
Cited by: 20
Author(s): James C. Romero-Masters, Makoto Ohashi, Reza Djavadian, Mark R. Eichelberg, Mitchell Hayes, Jillian A. Bristol, Shidong Ma, Erik A. Ranheim, Jenny E. Gumperz, Eric Johannsen, Shannon C. Kenney
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19103170

De Novo Transcriptome Sequencing Analysis of Goose (Anser anser) Embryonic Skin and the Identification of Genes Related to Feather Follicle Morphogenesis at Three Stages of Development
Cited by: 15
Author(s): Chang Liu, Cornelius Tlotliso Sello, Yanbo Sun, Yifang Zhou, Hongtao Lu, Yuanyuan Sui, Jingtao Hu, Chi Xu, Yue Sun, Jing Liu, Shengyi Li, Yiming Zhang, Kaiyan Zhang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.ppat.1006847

Comparative transcriptomics reveals CrebA as a novel regulator of infection tolerance in D. melanogaster
Cited by: 100
Author(s): Katia Troha, Joo Hyun Im, Jonathan Revah, Brian P. Lazzaro, Nicolas Buchon
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1006097

Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis
Cited by: 40
Author(s): Melania Abrahamian, Audrey M. V. Ah‐Fong, Carol Davis, Kalina Andreeva, Howard S. Judelson
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-018-36726-0

Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues
Cited by: 17
Author(s): Songqian Huang, Yūki Ichikawa, Yoji Igarashi, Kazutoshi Yoshitake, Shigeharu Kinoshita, Fumito Omori, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shuichi Asakawa
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-35891-6

De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms
Cited by: 34
Author(s): Muhammad Sarwar, Zarnab Ahmad, Bushra Rashid, Sahar Hassan, Per L. Gregersen, Maria De la O. Leyva, István Nagy, Torben Asp, Tayyab Husnain
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-37422-9

Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa
Cited by: 51
Author(s): Won Ju Hwang, Sang Sun Yoon
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.ppat.1005697

The WOPR Protein Ros1 Is a Master Regulator of Sporogenesis and Late Effector Gene Expression in the Maize Pathogen Ustilago maydis
Cited by: 63
Author(s): Marie Tollot, Assmann Daniela, Christian Becker, Janine Altmüller, Julien Y. Dutheil, Carl‐Eric Wegner, Regine Kahmann
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.ppat.1005160

The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation
Cited by: 76
Author(s): Dan Drecktrah, Meghan Lybecker, Niko Popitsch, Philipp Rescheneder, Laura S. Hall, D. Scott Samuels
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.ppat.1004994

IFNγ and IL-12 Restrict Th2 Responses during Helminth/Plasmodium Co-Infection and Promote IFNγ from Th2 Cells
Cited by: 41
Author(s): Stephanie M. Coomes, Victoria S. Pelly, Yashaswini Kannan, Isobel Okoye, Stephanie Czieso, Lewis J. Entwistle, Jimena Perez-Lloret, Nikolay P. Nikolov, Alexandre J. Potocnik, Judit Bíró, Jean Langhorne, Mark S. Wilson
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-018-37763-5

Leukocyte expression profiles reveal gene sets with prognostic value for seizure-free outcome following stereotactic laser amygdalohippocampotomy
Cited by: 2
Author(s): Ryan Sprissler, Robert W. Bina, Willard S. Kasoff, Marlys H. Witte, Michael Bernas, C. Walter, David M. Labiner, Branden Lau, Michael F. Hammer, Martin E. Weinand
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37609-0

Genetic regulatory mechanisms in human osteoclasts suggest a role for the STMP1 and DCSTAMP genes in Paget’s disease of bone
Cited by: 20
Author(s): Benjamin H. Mullin, Kun Zhu, Suzanne J. Brown, Shelby Mullin, Jennifer Tickner, Nathan J. Pavlos, Frank Dudbridge, Jiake Xu, John P. Walsh, Scott G. Wilson
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.ppat.1004443

Expression Profiling during Arabidopsis/Downy Mildew Interaction Reveals a Highly-Expressed Effector That Attenuates Responses to Salicylic Acid
Cited by: 85
Author(s): Shuji Asai, Ghanasyam Rallapalli, Sophie J. M. Piquerez, Marie‐Cécile Caillaud, Oliver J. Furzer, Naveed Ishaque, Lennart Wirthmueller, Georgina Fabro, Ken Shirasu, Jonathan D. G. Jones
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.ppat.1003186

Epstein - Barr Virus Transforming Protein LMP-1 Alters B Cells Gene Expression by Promoting Accumulation of the Oncoprotein ΔNp73α
Cited by: 19
Author(s): Rosita Accardi, Ikbal Fathallah, Henri Gruffat, Giuseppe Mariggiò, Florence Le Calvez-Kelm, Catherine Voegele, Birke Bartosch, Héctor Hernandez-Vargas, James McKay, Bakary S. Sylla, Évelyne Manet, Massimo Tommasino
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.ppat.1002470

Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma
Cited by: 281
Author(s): Elaine M. Morazzani, Michael R. Wiley, Marta G. Murreddu, Zach N. Adelman, K.M. Myles
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-018-37755-5

Reference assembly and gene expression analysis of Apostichopus japonicus larval development
Cited by: 9
Author(s): Alexey V. Boyko, Alexander S. Girich, М. Г. Елисейкина, С. И. Масленников, Igor Yu. Dolmatov
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-38368-8

Higher abundance of enterovirus A species in the gut of children with islet autoimmunity
Cited by: 31
Author(s): Ki Wook Kim, Jessica L. Horton, Chi Nam Ignatius Pang, Komal Jain, Preston Leung, Sonia R Isaacs, Rowena A. Bull, Fabio Luciani, Marc R. Wilkins, Jacki Catteau, W. Ian Lipkin, William D. Rawlinson, Thomas Briese, Maria E. Craig
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms19103180

iTRAQ-Based Proteomic Analysis of Ogura-CMS Cabbage and Its Maintainer Line
Cited by: 12
Author(s): Fengqing Han, Xiaoli Zhang, Limei Yang, Mu Zhuang, Yangyong Zhang, Zhansheng Li, Zhiyuan Fang, Honghao Lv
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-019-38628-1

Metabolic adaptation of adherent-invasive Escherichia coli to exposure to bile salts
Cited by: 38
Author(s): Julien Delmas, Lucie Gibold, Tiphanie Faïs, Sylvine Batista, Martin Leremboure, Clara Sinel, Emilie Vazeille, Vincent Cattoir, Anthony Buisson, Nicolas Barnich, Guillaume Dalmasso, Richard Bonnet
Software Mentions: 1
Published: over 7 years ago

10.1186/s13058-018-1059-y

Metastatic breast cancer cells overexpress and secrete miR-218 to regulate type I collagen deposition by osteoblasts
Cited by: 53
Author(s): Xuxiang Liu, Minghui Cao, Melanie R. Palomares, Xiwei Wu, Arthur Li, Yan Wei, Miranda Fong, Wing-Chung Chan, Shizhen Emily Wang
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19113412

Transcriptomic Analysis of Betula halophila in Response to Salt Stress
Cited by: 17
Author(s): Fenjuan Shao, Lisha Zhang, Iain W. Wilson, Deyou Qiu
Software Mentions: 1
Published: almost 8 years ago

10.1093/jxb/eraa581

Restriction of cytosolic sucrose hydrolysis profoundly alters development, metabolism, and gene expression in Arabidopsis roots
Cited by: 12
Author(s): Cristina Pignocchi, Alexander Ivakov, Regina Feil, Martin Trick, Marilyn J. Pike, Trevor L. Wang, John E. Lunn, Alison M. Smith
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-39273-4

A RNA sequencing-based six-gene signature for survival prediction in patients with glioblastoma
Cited by: 41
Author(s): Shuguang Zuo, Xinhong Zhang, Liping Wang
Software Mentions: 1
Published: over 7 years ago

10.1093/jxb/eraa221

Responses of mature symbiotic nodules to the whole-plant systemic nitrogen signaling
Cited by: 17
Author(s): Ilana Lambert, Marjorie Pervent, Antoine Le Quéré, Gilles Clément, Marc Tauzin, Dany Séverac, Claire Benezech, Pascal Tillard, Marie‐Laure Martin‐Magniette, Stefano Colella, Marc Lepetit
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-39100-w

Early responses given distinct tactics to infection of Peronophythora litchii in susceptible and resistant litchi cultivar
Cited by: 10
Author(s): Jun Sun, Liangjing Cao, L Huanling, Wenbin Guo, Shujun Wang, Fang Li, Xuefeng Zou, Jiabao Wang
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms19123735

Comparative Transcriptome Analysis between a Resistant and a Susceptible Wild Tomato Accession in Response to Phytophthora parasitica
Cited by: 25
Author(s): Zunaira Afzal Naveed, Gul Shad Ali
Software Mentions: 1
Published: almost 8 years ago

10.1093/jxb/erz533

ATBS1-INTERACTING FACTOR 2 negatively regulates dark- and brassinosteroid-induced leaf senescence through interactions with INDUCER OF CBF EXPRESSION 1
Cited by: 19
Author(s): Yonggyun Kim, Park Min Su, Shin Dm, Giang Pham, Yong-Jin Jeong, Kim Sh
Software Mentions: 1
Published: almost 7 years ago

10.1093/jxb/ery189

Differential response to heat stress in outer and inner onion bulb scales
Cited by: 13
Author(s): Ortal Galsurker, Adi Doron‐Faigenboim, Paula Teper‐Bamnolker, Avinoam Daus, Amnon Lers, Dani Eshel
Software Mentions: 1
Published: over 8 years ago

10.1093/jxb/ery077

GCN5 contributes to stem cuticular wax biosynthesis by histone acetylation of CER3 in Arabidopsis
Cited by: 34
Author(s): Tianya Wang, Jiewen Xing, Xinye Liu, Yingyin Yao, Zhaorong Hu, Huiru Peng, Mingming Xin, Dao‐Xiu Zhou, Yirong Zhang, Zhongfu Ni
Software Mentions: 1
Published: over 8 years ago

10.1093/jxb/erw343

C3cotyledons are followed by C4leaves: intra-individual transcriptome analysis ofSalsola soda(Chenopodiaceae)
Cited by: 19
Author(s): Maximilian Lauterbach, Kumari Billakurthi, Gudrun Kadereit, Martha Ludwig, Peter Westhoff, Udo Gowik
Software Mentions: 1
Published: about 10 years ago

10.1186/s13058-018-0963-5

Dependence receptor UNC5A restricts luminal to basal breast cancer plasticity and metastasis
Cited by: 14
Author(s): Maria B. Padua, Poornima Bhat‐Nakshatri, Manjushree Anjanappa, Mayuri Prasad, Yangyang Hao, Xi Rao, Sheng Liu, Jun Wan, Yunlong Liu, Kyle McElyea, Max Jacobsen, George E. Sandusky, Sandra K. Althouse, Susan M. Perkins, Harikrishna Nakshatri
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-019-39852-5

Suppression of glioblastoma by a drug cocktail reprogramming tumor cells into neuronal like cells
Cited by: 19
Author(s): Lei Gao, Shichao Huang, Hong Zhang, Wei Hua, Shunmei Xin, Lin Cheng, Wuqiang Guan, Yongchun Yu, Ying Mao, Gang Pei
Software Mentions: 1
Published: over 7 years ago

10.3390/nu12103051

A Multi-Omics Approach Identifies Key Regulatory Pathways Induced by Long-Term Zinc Supplementation in Human Primary Retinal Pigment Epithelium
Cited by: 14
Author(s): Eszter Emri, Elöd Körtvely, Sascha Dammeier, Franziska Klose, David Simpson, Anneke I. den Hollander, Marius Ueffing, Imre Lengyel
Software Mentions: 1
Published: about 6 years ago

10.1093/jxb/erw391

Photosynthesis in C3–C4intermediateMoricandiaspecies
Cited by: 52
Author(s): Urte Schlüter, Andrea Bräutigam, Udo Gowik, Michael Melzer, Pascal‐Antoine Christin, Samantha Kurz, Tabea Mettler‐Altmann, Andreas P.M. Weber
Software Mentions: 1
Published: about 10 years ago

10.3390/brainsci11070913

Characterization of Early Life Stress-Affected Gut Microbiota
Cited by: 12
Author(s): Noriyoshi Usui, Hideo Matsuzaki, Shoichi Shimada
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20030539

Global Transcriptional Insights of Pollen-Pistil Interactions Commencing Self-Incompatibility and Fertilization in Tea [Camellia sinensis (L.) O. Kuntze]
Cited by: 29
Author(s): Romit Seth, Abhishek Bhandawat, Rajni Parmar, Pradeep Singh, Sanjay Kumar, Ram Kumar Sharma
Software Mentions: 1
Published: almost 8 years ago

10.1093/jxb/erx057

Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris
Cited by: 22
Author(s): James D. Stone, Pavla Koloušková, Daniel B. Sloan, Helena Štorchová
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms20040944

Insights into Body Size Evolution: A Comparative Transcriptome Study on Three Species of Asian Sisoridae Catfish
Cited by: 3
Author(s): Weixing Jiang, Yicheng Guo, Kuo-Pin Yang, Qiong Shi, Jing Yang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-40227-z

Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development
Cited by: 2
Author(s): Vikram S. Shivakumar, Gabriel Johnson, Elizabeth A. Zimmer
Software Mentions: 1
Published: over 7 years ago

10.1093/jxb/erw338

Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis
Cited by: 34
Author(s): Long Jiang, Liduan Zheng, Xiaomeng Wu, Yan-Ni Fang, Hui-Hui Jia, Zongzhou Xie, Xiuxin Deng, Wen‐Wu Guo
Software Mentions: 1
Published: about 10 years ago

10.1093/jxb/erw131

Up-regulating the abscisic acid inactivation geneZmABA8ox1bcontributes to seed germination heterosis by promoting cell expansion
Cited by: 16
Author(s): Yangyang Li, Cheng Wang, Xinye Liu, Jian Song, Hongjian Li, Zhipeng Sui, Ming Zhang, S. S. Fang, Jinfang Chu, Mingming Xin, Chaojie Xie, Yirong Zhang, Qixin Sun, Zhongfu Ni
Software Mentions: 1
Published: over 10 years ago

10.1093/jxb/ert428

Global and local perturbation of the tomato microRNA pathway by atrans-activatedDICER-LIKE 1mutant
Cited by: 26
Author(s): Michael Kravchik, Ramanjulu Sunkar, Subha Damodharan, Ran Stav, Matat Zohar, Tal Isaacson, Tzahi Arazi
Software Mentions: 1
Published: almost 13 years ago

10.1186/s13059-019-1830-0

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses
Cited by: 152
Author(s): Ciara H. O’Flanagan, Kieran R Campbell, Allen W. Zhang, Farhia Kabeer, Jamie Lim, Justina Biele, Peter Eirew, Daniel Lai, Andrew McPherson, Esther Kong, Cherie Bates, Kelly Borkowski, Matt Wiens, Brittany Hewitson, James Hopkins, Jenifer Pham, Nicholas Ceglia, Richard A. Moore, Andrew J. Mungall, Jessica N. McAlpine, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms20061411

Map-Based Cloning, Phylogenetic, and Microsynteny Analyses of ZmMs20 Gene Regulating Male Fertility in Maize
Cited by: 22
Author(s): Yan Bo Wang, Dongcheng Liu, Youhui Tian, Wu Shu, Xianghai An, Zhenying Dong, Simiao Zhang, Jianxi Bao, Ziwen Li, Jinping Li, Xiangyuan Wan
Software Mentions: 1
Published: over 7 years ago

10.1186/s13059-015-0813-z

Erratum to: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Cited by: 11
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-019-42010-6

A Network-guided Association Mapping Approach from DNA Methylation to Disease
Cited by: 16
Author(s): Yandan Lin, De-Shuang Huang
Software Mentions: 1
Published: over 7 years ago

10.3390/brainsci9070155

Regional Analysis of the Brain Transcriptome in Mice Bred for High and Low Methamphetamine Consumption
Cited by: 16
Author(s): Robert Hitzemann, Ovidiu D. Iancu, Cheryl Reed, Harue Baba, Denesa R. Lockwood, Tamara J. Phillips
Software Mentions: 1
Published: over 7 years ago

10.1186/s13059-015-0780-4

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures
Cited by: 37
Author(s): Oksung Chung, Shil Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, JeHoon Jun, Hye-Jin Lee, Alvin Chon, Junsu Ko, Jeremy S. Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O’Brien, Andrea Manica, Jong Bhak, Woon Kee Paek
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms20081906

Comparative Transcriptomic Studies on a Cadmium Hyperaccumulator Viola baoshanensis and Its Non-Tolerant Counterpart V. inconspicua
Cited by: 19
Author(s): Haoyue Shu, Jun Zhang, Fuye Liu, Chao Bian, Jie-Liang Liang, Jiaqi Liang, Weihe Liang, Zhiliang Caleb Lin, Wen‐Sheng Shu, Jintian Li, Qiong Shi, Bin Liao
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms20092349

An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability
Cited by: 66
Author(s): Xin Wei, Lina Zhang, Wenzhong Zhang, Jiping Gao, Jun Yi, Xiaoxi Zhen, Ziang Li, Zhao Ying, Chengcheng Peng, Chen Zhao
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-42025-z

Transcriptomic analysis reveals differences in the regulation of amino acid metabolism in asexual and sexual planarians
Cited by: 11
Author(s): Kiyono Sekii, Shunta Yorimoto, Hikaru Okamoto, Nanna Nagao, Takanobu Maezawa, Yasuhisa Matsui, Katsushi Yamaguchi, Ryo Furukawa, Shuji Shigenobu, Kazuya Kobayashi
Software Mentions: 1
Published: over 7 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

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: almost 14 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: almost 17 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: almost 7 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: over 7 years ago

10.3390/ijms20092360

OsbZIP81, A Homologue of Arabidopsis VIP1, May Positively Regulate JA Levels by Directly Targetting the Genes in JA Signaling and Metabolism Pathway in Rice
Cited by: 22
Author(s): Defang Liu, Shaopeng Shi, Hao Zhang, Wentao Xiong, Meizhong Luo
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-85394-0

Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams
Cited by: 4
Author(s): Alexandre Leduc, Samia Chaouni, Frédéric Pouzoulet, Ludovic De Marzi, Frédérique Mégnin-Chanet, Erwan Corre, Dinu Stefan, Jean‐Louis Habrand, François Sichel, Carine Laurent
Software Mentions: 1
Published: over 5 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: about 5 years ago

10.1038/s41598-021-85480-3

Transcriptional regulation of dosage compensation in Carica papaya
Cited by: 4
Author(s): Juan Liu, Jennifer Han, Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Software Mentions: 1
Published: over 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: over 5 years ago

10.1038/s41598-021-85886-z

Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr
Cited by: 9
Author(s): Hyein Kang, Chae-Bin Lee, Sae-Hyuk Kwon, Jimin Park, Kyu-Suk Kang, Donghwan Shim
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-5128-5

Differentially expressed non-coding RNAs induced by transmissible gastroenteritis virus potentially regulate inflammation and NF-κB pathway in porcine intestinal epithelial cell line
Cited by: 37
Author(s): Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang, Dewen Tong
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-021-86465-y

Powerful p-value combination methods to detect incomplete association
Cited by: 25
Author(s): Susan A. Yoon, Bukyung Baik, Taesung Park, Dougu Nam
Software Mentions: 1
Published: over 5 years ago

10.1093/brain/awab123

Aromatic <scp>l</scp>-amino acid decarboxylase deficiency: a patient-derived neuronal model for precision therapies
Cited by: 14
Author(s): Giada Rossignoli, Karolin Krämer, Eleonora Lugarà, Haya Alrashidi, Simon Pope, Carmen De La Fuente Barrigon, Katy Barwick, Giovanni Bisello, Joanne Ng, John R. Counsell, Gabriele Lignani, Simon Heales, Mariarita Bertoldi, Serena Barral, Manju A. Kurian
Software Mentions: 1
Published: over 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: over 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

10.1155/2020/1384907

Proteome and Transcriptome Analysis of the Antioxidant Mechanism in Chicken Regulated by Eucalyptus Leaf Polyphenols Extract
Cited by: 2
Author(s): Wei Li, Zeqi He, Xiaoying Zhang, Yunjiao Chen, Jianjun Zuo, Yong Cao
Software Mentions: 1
Published: over 6 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

10.1186/s12881-019-0936-2

POLE mutations improve the prognosis of endometrial cancer via regulating cellular metabolism through AMF/AMFR signal transduction
Cited by: 19
Author(s): Yiran Li, Yiding Bian, Kai Wang, Xiaoping Wan
Software Mentions: 1
Published: almost 7 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

10.1371/journal.pone.0207050

Hypothalamic transcriptome analysis reveals the neuroendocrine mechanisms in controlling broodiness of Muscovy duck (Cairina moschata)
Cited by: 11
Author(s): Pengfei Ye, Min Li, Wang Liao, Kai Ge, Sihua Jin, Cheng Zhang, Xingyong Chen
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0242159

Variation in intrinsic resistance of pea aphids to parasitoid wasps: A transcriptomic basis
Cited by: 4
Author(s): Ailsa H. C. McLean, Benjamin J. Parker
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0192625

Transcriptome variations among human embryonic stem cell lines are associated with their differentiation propensity
Cited by: 23
Author(s): Chengbo Sun, Jiawen Zhang, Dongmin Zheng, Wang Jian, Huanming Yang, Xi Zhang
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568