bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/srep37082

Doxycycline, metronidazole and isotretinoin: Do they modify microRNA/mRNA expression profiles and function in murine T-cells?
Cited by: 19
Author(s): Eugenia Becker, Susan Bengs, Sirisha Aluri, Lennart Opitz, Kirstin Atrott, Claudia Stanzel, Pedro A. Ruiz-Castro, Gerhard Rogler, Isabelle Frey-Wagner
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12885-021-08345-y

Persistent Newcastle disease virus infection in bladder cancer cells is associated with putative pro-survival and anti-viral transcriptomic changes
Cited by: 6
Author(s): Lee-Chin Chan, Jeevanathan Kalyanasundram, Sze-Wei Leong, Mas Jaffri Masarudin, Abhi Veerakumarasivam, Khatijah Yusoff, Soon Choy Chan, Suet Lin Chia
Software Mentions: 1
Published: over 5 years ago

10.1038/srep37158

Identification of aberrant tRNA-halves expression patterns in clear cell renal cell carcinoma
Cited by: 57
Author(s): Malin Nientiedt, Mario C. Deng, Doris Schmidt, Sven Perner, Stefan Müller, Jörg Ellinger
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep37821

Long intergenic non-coding RNA expression signature in human breast cancer
Cited by: 25
Author(s): Yan Feng Zhang, Erin K. Wagner, Xingyi Guo, Isaac May, Qiuyin Cai, Zheng Wang, Chunyan He, Jirong Long
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep39109

Identification of Development-Related Genes in the Ovaries of Adult Harmonia axyridis (Pallas) Lady Beetles Using a Time- Series Analysis by RNA-seq
Cited by: 10
Author(s): Wei Du, Fanrong Zeng
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep39395

Localisation and origin of the bacteriochlorophyll-derived photosensitizer in the retina of the deep-sea dragon fish Malacosteus niger
Cited by: 10
Author(s): R. H. Douglas, Martin J. Genner, Alan G. Hudson, Julian C. Partridge, H Wagner
Software Mentions: 1
Published: almost 10 years ago

10.7554/eLife.65735

circPTPN12/miR-21–5 p/∆Np63α pathway contributes to human endometrial fibrosis
Cited by: 17
Author(s): Minmin Song, Guangfeng Zhao, Haixiang Sun, Simin Yao, Zhenhua Zhou, Pengju Jiang, Qianwen Wu, Hui Zhu, Huiyan Wang, Chenyan Dai, Jingmei Wang, Ruotian Li, Yun Cao, Haining Lv, Dan Liŭ, Jianwu Dai, Yan Zhou, Yali Hu
Software Mentions: 1
Published: over 5 years ago

10.1038/srep40472

De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters
Cited by: 16
Author(s): Katharine E. McCann, David M. Sinkiewicz, Alisa Norvelle, Kim L. Huhman
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep41661

Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro
Cited by: 36
Author(s): Dahai Zheng, Boon Seng Soh, Yin Lu, Guangan Hu, Yi‐Ping Phoebe Chen, Hyungwon Choi, Jongyoon Han, Vincent T. K. Chow, Jianzhu Chen
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep43062

Targeted RP9 ablation and mutagenesis in mouse photoreceptor cells by CRISPR-Cas9
Cited by: 16
Author(s): Ji‐Neng Lv, Gao-Hui Zhou, Xuejiao Chen, Hui Chen, Kun Wu, Lan Xiang, Xin‐Lan Lei, Xiao Zhang, Ronghan Wu, Zi‐Bing Jin
Software Mentions: 1
Published: over 9 years ago

10.1038/srep43023

Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen
Cited by: 32
Author(s): David J. Oliver, Hao Jiang, Piaomu Liu, Alexander V. Gasparian, Ellen Gardiner, Samuel Lee, Adrián Zenteno, Lillian O. Perinskaya, Mengqian Chen, Phillip Buckhaults, Eugenia V. Broude, Michael D. Wyatt, Homayoun Valafar, Edsel A. Peña, Michael Shtutman
Software Mentions: 1
Published: over 9 years ago

10.1186/s12885-019-5671-8

CRKL regulates alternative splicing of cancer-related genes in cervical cancer samples and HeLa cell
Cited by: 24
Author(s): Qingling Song, Fengtao Yi, Yuhong Zhang, Daniel K. Jun Li, Yaxun Wei, Han Yu, Yi Zhang
Software Mentions: 1
Published: over 7 years ago

10.1038/srep45295

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum
Cited by: 41
Author(s): Pradeep Singh, Gagandeep Singh, Abhishek Bhandawat, Gopal Singh, Rajni Parmar, Romit Seth, Ram Kumar Sharma
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-24509-6

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages
Cited by: 69
Author(s): Sugata Roy, Sebastian Schmeier, Bogumił Kaczkowski, Peter Arner, Tanvir Alam, Mumin Ozturk, Ousman Tamgue, Suraj P. Parihar, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Reto Guler, Vladimir B. Bajic, Frank Brombacher, Harukazu Suzuki
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25611-5

Ca2+ imaging and gene expression profiling of Lonicera Confusa in response to calcium-rich environment
Cited by: 10
Author(s): Wenwen Jin, Yan Long, Chunhua Fu, Libin Zhang, Jun Xiang, Baoshan Wang, Maoteng Li
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25103-6

Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis
Cited by: 35
Author(s): Lingbin Liu, Qihai Xiao, Elizabeth R. Gilbert, Zhifu Cui, Xiaoling Zhao, Yan Wang, Huadong Yin, Diyan Li, Haihan Zhang, Qing Zhu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25516-3

Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer
Cited by: 18
Author(s): Kanokwan Srirattana, Justin C. St. John
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-24999-4

A Meloidogyne incognita effector MiISE5 suppresses programmed cell death to promote parasitism in host plant
Cited by: 18
Author(s): Qianqian Shi, Zhenchuan Mao, Xi Zhang, Xiaoping Zhang, Yunsheng Wang, Jian Ling, Runmao Lin, Denghui Li, Xincong Kang, Wenxian Sun, Bingyan Xie
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-017-3251-3

Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients
Cited by: 16
Author(s): Thomas Urup, Line Mærsk Staunstrup, Signe Regner Michaelsen, Kristoffer Vitting-Seerup, Marc Bennedbæk, Anders Toft, Lars Rønn Olsen, Lars Jønson, Shohreh Issazadeh‐Navikas, Helle Broholm, Petra Hamerlik, Hans Skovgaard Poulsen, Ulrik Lassen
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-26738-1

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells
Cited by: 18
Author(s): Agnes P. Chan, Yongwook Choi, Lauren Brinkac, R. Krishnakumar, Jessica DePew, Maria Kim, Mary Hinkle, Emil Lesho, Derrick E. Fouts
Software Mentions: 1
Published: over 8 years ago

10.1186/s13568-020-01076-6

Comprehensive transcriptomic and proteomic analyses of antroquinonol biosynthetic genes and enzymes in Antrodia camphorata
Cited by: 4
Author(s): Xiaofeng Liu, Yongjun Xia, Yao Zhang, Caiyun Yang, Zhiqiang Xiong, Xin Song, Lianzhong Ai
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.46012

CCN1 interlinks integrin and hippo pathway to autoregulate tip cell activity
Cited by: 34
Author(s): Myo-Hyeon Park, Ae kyung Kim, Sarala Manandhar, Su-Young Oh, Gil-Jin Jang, Kang Li, Dongwon Lee, Do Young Hyeon, Sunhee Lee, Hye-Eun Lee, Tae‐Lin Huh, Sang Heon Suh, Daehee Hwang, Kyunghee Byun, Hae-Chul Park, You Mie Lee
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-27628-2

Molecular chaperoning helps safeguarding mitochondrial integrity and motor functions in the Sahara silver ant Cataglyphis bombycina
Cited by: 12
Author(s): Quentin Willot, Patrick Mardulyn, Matthieu Defrance, Cyril Gueydan, Serge Aron
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-27527-6

Presymptomatic change in microRNAs modulates Tau pathology
Cited by: 6
Author(s): Salil Sharma, Inès Khadimallah, Adam Williamson Corya, Yousuf Ali, Xi Rao, Yunlong Liu, Hui Lü
Software Mentions: 1
Published: over 8 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

10.1038/s41598-018-28297-x

Pirfenidone decreases mesothelioma cell proliferation and migration via inhibition of ERK and AKT and regulates mesothelioma tumor microenvironment in vivo
Cited by: 31
Author(s): Chang Li, Veronika Rezov, Emmi I. Joensuu, Ville Vartiainen, Mikko Rönty, Miao Yin, Marjukka Myllärniemi, Katri Koli
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-28916-7

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets
Cited by: 41
Author(s): Pablo Ivan Pereira Ramos, Darío Augusto Fernández Do Porto, Esteban Lanzarotti, Ezequiel Sosa, Germán Burguener, Agustín Pardo, Cecília C. Klein, Marie‐France Sagot, Ana Tereza Ribeiro de Vasconcelos, Ana Cristina Gales, Marcelo A. Martí, Adrián Turjanski, Marisa Fabiana Nicolás
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-29662-6

An integrative omics approach to unravel toxicity mechanisms of environmental chemicals: effects of a formulated herbicide
Cited by: 22
Author(s): Tiago Simões, Sara C. Novais, Tiago Natal-da-Luz, Bart Devreese, Tjalf de Boer, Dick Roelofs, José Paulo Sousa, Nico M. van Straalen, Marco F.L. Lemos
Software Mentions: 1
Published: over 8 years ago

10.1155/2020/8847226

A Prognostic 14-Gene Expression Signature for Lung Adenocarcinoma: A Study Based on TCGA Data Mining
Cited by: 4
Author(s): Jie Liu, Shiqiang Hou, Jinyi Wang, Zhengjun Chai, Xuan Hong, Tian Zhao, Zheng Sun, Liandi Bai, Hongyan Gao, Jing Gao, Guohan Chen
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-018-30147-9

Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau
Cited by: 8
Author(s): Yanyan Guo, Yongqiang Zhang, Guoqiang Zhang, Laiqiang Huang, Zhong‐Jian Liu
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-30262-7

Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng
Cited by: 35
Author(s): Kyo Bin Kang, Murukarthick Jayakodi, Yun Sun Lee, Van Binh Nguyen, Hyun-Seung Park, Hyun Jo Koo, Ik‐Young Choi, Dae Hyun Kim, You Jin Chung, Byeol Ryu, Dong Hoon Lee, Sang Hyun Sung, Tae-Jin Yang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-31592-2

Expression profiling of ubiquitin-related genes in LKB1 mutant lung adenocarcinoma
Cited by: 3
Author(s): Guanghui Wang, Fenglong Bie, Xiao Qu, Xudong Yang, Shaorui Liu, Yu Wang, Can Huang, Kai Wang, Jiajun Du
Software Mentions: 1
Published: about 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

10.1038/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

10.7554/eLife.59469

Adrenergic activation modulates the signal from the Reissner fiber to cerebrospinal fluid-contacting neurons during development
Cited by: 20
Author(s): Yasmine Cantaut-Belarif, Adeline Orts-Del’Immagine, Margot Penru, Guillaume Pézeron, Claire Wyart, Pierre-Luc Bardet
Software Mentions: 1
Published: about 6 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

10.1038/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

10.1038/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

10.1186/s12915-017-0354-x

MicroRNA miR-29 controls a compensatory response to limit neuronal iron accumulation during adult life and aging
Cited by: 70
Author(s): Roberto Ripa, Adam Antebi, Marco Terrigno, Luca Pandolfini, Aurora Savino, Valeria Arcucci, Marco Groth, Eva Terzibasi Tozzini, Mario Baumgart, Alessandro Cellerino
Software Mentions: 1
Published: over 9 years ago

10.1186/s40478-020-01099-x

Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer’s disease
Cited by: 116
Author(s): Akira Sobue, Okiru Komine, Yuichiro Hara, Fumito Endo, Hideaki Mizoguchi, Seiji Watanabe, Shigeo Murayama, Takashi Saito, Takaomi C. Saido, Naruhiko Sahara, Makoto Higuchi, Tomoo Ogi, Koji Yamanaka
Software Mentions: 1
Published: almost 6 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

10.1186/s12859-019-3247-x

A protocol to evaluate RNA sequencing normalization methods
Cited by: 64
Author(s): Zachary B. Abrams, Travis Johnson, Kun Huang, Philip R. O. Payne, Kevin R. Coombes
Software Mentions: 1
Published: almost 7 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

10.1186/s12859-016-0926-8

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack
Cited by: 2
Author(s): Renée X. de Menezes, Leila Mohammadi, Jelle J. Goeman, Judith M. Boer
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-15-116

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs
Cited by: 36
Author(s): Mark A. van de Wiel, Maarten Neerincx, Tineke E. Buffart, Daoud Sie, Henk M.W. Verheul
Software Mentions: 1
Published: over 12 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

10.1038/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

10.1186/1471-2105-14-110

Differential expression analysis for paired RNA-seq data
Cited by: 18
Author(s): Lisa Chung, John Ferguson, Wei Zheng, Feng Qian, Vincent M. Bruno, Ruth R. Montgomery, Hongyu Zhao
Software Mentions: 1
Published: over 13 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

10.1186/1471-2105-15-S17-S2

Identification of genes and pathways involved in kidney renal clear cell carcinoma
Cited by: 45
Author(s): William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen, Liangjiang Wang, Dong Xu, Hamid R. Arabnia, Weida Tong, Mary Qu Yang
Software Mentions: 1
Published: almost 12 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

10.1186/1471-2105-11-564

Empirical bayes analysis of sequencing-based transcriptional profiling without replicates
Cited by: 45
Author(s): Zhijin Wu, Bethany D. Jenkins, Tatiana A. Rynearson, Sonya T. Dyhrman, Mak A. Saito, Melissa L. Mercier, LeAnn P. Whitney
Software Mentions: 1
Published: almost 16 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

10.18632/aging.102332

Loss of FoxA2 accelerates neoplastic changes in the intrahepatic bile duct partly via the MAPK signaling pathway
Cited by: 5
Author(s): Jian Shen, Yongjie Zhou, Xiaoyun Zhang, Wei Peng, Chihan Peng, Qiang Zhou, Chuan Li, Tianfu Wen, Yujun Shi
Software Mentions: 1
Published: almost 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

10.18632/aging.103189

A three-lncRNA signature predicts clinical outcomes in low-grade glioma patients after radiotherapy
Cited by: 17
Author(s): Wanzun Lin, Ze‐Ning Huang, Yanyan Xu, Xiaochuan Chen, Ting Chen, Yuling Ye, Jianming Ding, Zhangjie Chen, Long Chen, Xianxin Qiu, Sufang Qiu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-021-04201-9

Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development
Cited by: 0
Author(s): Thomas E. Bartlett
Software Mentions: 1
Published: over 5 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

10.1186/s12859-019-3144-3

ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data
Cited by: 7
Author(s): Matúš Medo, Daniel M. Aebersold, Michaela Medová
Software Mentions: 1
Published: almost 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

10.1155/2021/8846951

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

10.7554/eLife.28415

Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions
Cited by: 54
Author(s): Jason A. Morrison, Rebecca McLennan, Lauren A. Wolfe, Madelaine Gogol, Samuel R. Meier, Mary Cathleen McKinney, Jessica M. Teddy, Laura Holmes, Craig L. Semerad, Andrew Box, Hua Li, Kathryn Hall, Anoja Perera, Paul M. Kulesa
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12859-017-1745-2

TnseqDiff: identification of conditionally essential genes in transposon sequencing studies
Cited by: 35
Author(s): Lili Zhao, Mark T. Anderson, Weisheng Wu, Harry L. T. Mobley, Michael A. Bachman
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.50346

Disruption of entire Cables2 locus leads to embryonic lethality by diminished Rps21 gene expression and enhanced p53 pathway
Cited by: 2
Author(s): Tra Thi Huong Dinh, Hiroyoshi Iseki, Seiya Mizuno, Saori Iijima-Mizuno, Yoko Tanimoto, Yoko Daitoku, Kayoko Kato, Yuko Hamada, Ammar Shaker Hamed Hasan, Hayate Suzuki, Katsuyuki Murata, Masafumi Muratani, Masatsugu Ema, Jun-Dal Kim, Junji Ishida, Akiyoshi Fukamizu, Mitsuyasu Kato, Satoru Takahashi, Ken‐ichi Yagami, Valerie Wilson, Ruth M. Arkell, Fumihiro Sugiyama
Software Mentions: 1
Published: over 5 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

10.1186/1471-2105-14-357

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data
Cited by: 29
Author(s): Chung I. Li, Pei Fang Su, Yu Shyr
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0178189

Systematic genomic and translational efficiency studies of uveal melanoma
Cited by: 27
Author(s): Chelsea Place Johnson, Ivana K. Kim, Bita Esmaeli, Ali Amin‐Mansour, Daniel J. Treacy, Scott L. Carter, Eran Hodis, Nikhil Wagle, Sara Seepo, Xiaoxing Yu, Anne Marie Lane, Evangelos S. Gragoudas, Francisca Vázquez, Elizabeth Nickerson, Kristian Cibulskis, Aaron McKenna, Stacey Gabriel, Gad Getz, Eliezer M. Van Allen, Peter A.C. ’t Hoen, Levi A. Garraway, Scott E. Woodman
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0002402

Sex-Biased Expression of MicroRNAs in Schistosoma mansoni
Cited by: 59
Author(s): A. De Marco, Ana Kozomara, Jerome H. L. Hui, Aidan M. Emery, David Rollinson, Sam Griffiths-Jones, Matthew Ronshaugen
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pntd.0003975

Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax
Cited by: 31
Author(s): Andrew P. Jackson, Sophie Goyard, Dong Xia, Bernardo J. Foth, Mandy Sanders, Jonathan M. Wastling, Paola Minóprio, Matthew Berriman
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0216294

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus
Cited by: 8
Author(s): Anna Abramova, Magnus Alm Rosenblad, Anders Blomberg, Tomas Larsson
Software Mentions: 1
Published: over 7 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

10.1371/journal.pone.0200210

Transcription factor induced conversion of human fibroblasts towards the hair cell lineage
Cited by: 23
Author(s): Maria B Duran Alonso, Iris Lopez Hernandez, Miguel A. de la Fuente, Javier García‐Sancho, Fernando Giráldez, Thomas Schimmang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0165268

Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells
Cited by: 19
Author(s): Sarita Panula, Ahmed Reda, Jan-Bernd Stukenborg, Cyril Ramathal, Meena Sukhwani, Halima Albalushi, Daniel Edsgärd, Michiko Nakamura, Olle Söder, Kyle E. Orwig, Shinya Yamanaka, Renee A. Reijo Pera, Outi Hovatta
Software Mentions: 1
Published: about 10 years ago

10.1186/s12859-020-03929-0

Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach
Cited by: 5
Author(s): Mike Fang, Brian Richardson, Cheryl M. Cameron, Jean-Eudes Dazard, Mark J. Cameron
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pntd.0009377

Combined gene deletion of dihydrofolate reductase-thymidylate synthase and pteridine reductase in Leishmania infantum
Cited by: 5
Author(s): Arijit Bhattacharya, Philippe Leprohon, Marc Ouellette
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pntd.0006186

Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti
Cited by: 10
Author(s): Matthew W. Eng, Anthony Clemons, Casey Hill, Roberta Engel, David W. Severson, Susanta K. Behura
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0100477

Transcriptomic Analysis of Prunus domestica Undergoing Hypersensitive Response to Plum Pox Virus Infection
Cited by: 35
Author(s): Bernardo Rodamilans, David San León, Louisa Mühlberger, Thierry Candresse, M. Neumüller, Juan Carlos Oliveros, Juan Antonio Garcı́a
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0237744

Transcriptome analysis and comparison reveal divergence between the Mediterranean and the greenhouse whiteflies
Cited by: 1
Author(s): Yujun Wang, Hua-Ling Wang, Xiaowei Wang, Shu‐Sheng Liu
Software Mentions: 1
Published: about 6 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

10.1371/journal.pone.0130902

Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
Cited by: 23
Author(s): Yuanhao Zhang, Leahana Rowehl, Julia M. Krumsiek, Erika P. Orner, Nurmohammad Shaikh, Phillip I. Tarr, Erica Sodergren, George M. Weinstock, Edgar C. Boedeker, Xuejian Xiong, John Parkinson, Daniel N. Frank, Ellen Li, Grace Gathungu
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0187351

Kojic acid-mediated damage responses induce mycelial regeneration in the basidiomycete Hypsizygus marmoreus
Cited by: 10
Author(s): Jinjing Zhang, Hui Chen, Mingjie Chen, Hong Wang, Qian Wang, Xiaoxia Song, Haibo Hao, Zhen Feng
Software Mentions: 1
Published: almost 9 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

10.1371/journal.pone.0200558

FAK auto-phosphorylation site tyrosine 397 is required for development but dispensable for normal skin homeostasis
Cited by: 8
Author(s): Joel B. Heim, Cera A. McDonald, Saranya P. Wyles, Sindhuja Sominidi‐Damodaran, Edwin J. Squirewell, Ming Li, Catherine Motsonelidze, Ralph T. Böttcher, Jan van Deursen, Alexander Meves
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0159372

Antennal and Abdominal Transcriptomes Reveal Chemosensory Genes in the Asian Citrus Psyllid, Diaphorina citri
Cited by: 39
Author(s): Zhongzhen Wu, Zuyong He, Shuying Bin, Lei Chen, Qunxin Han, Jintian Lin
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0194765

IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs
Cited by: 17
Author(s): Louise Brogaard, Lars Erik Larsen, Peter M. H. Heegaard, Christian Anthon, Jan Gorodkin, Ralf Dürrwald, Kerstin Skovgaard
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0200826

BRD4 amplification facilitates an oncogenic gene expression program in high-grade serous ovarian cancer and confers sensitivity to BET inhibitors
Cited by: 43
Author(s): Garrett W. Rhyasen, Yi Yao, Jingwen Zhang, Austin Dulak, Lillian Castriotta, Kelly Jacques, Wei Zhao, Farzin Gharahdaghi, Maureen M. Hattersley, Paul Lyne, Edwin Clark, Michael Zinda, Stephen E. Fawell, Gordon B. Mills, Huawei Chen
Software Mentions: 1
Published: over 8 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

10.1371/journal.pone.0186382

Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions
Cited by: 14
Author(s): Boon Huat Cheah, Sudhir Jadhao, Madavan Vasudevan, R Wickneswari V Ratnam, Kalaivani K. Nadarajah
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0231206

Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113
Cited by: 30
Author(s): Mukesh Kumar Malviya, Changning Li, Manoj Kumar Solanki, Rajesh Kumar Singh, Reemon Htun, Pratiksha Singh, Krishan K. Verma, Li‐Tao Yang, Yang–Rui Li
Software Mentions: 1
Published: over 6 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

10.1371/journal.pone.0185595

De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes
Cited by: 15
Author(s): Ingrid Garbus, José R. Romero, Juan Pablo Selva, María Cielo Pasten, Carolina Chinestra, José Luís Carballo, Diego Zappacosta, Viviana Echenique
Software Mentions: 1
Published: almost 9 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568