bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1042/BSR20210051

GCH1-regulated miRNAs are potential targets for microglial activation in neuropathic pain
Cited by: 9
Author(s): Shu Fang Jia, Guowu Chen, Yanhu Liang, Xiao Liang, Chun Meng
Software Mentions: 1
Published: about 3 years ago

10.1186/1471-2164-15-S5-S3

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Cited by: 18
Author(s): Lijun Liu, Victor Missirian, Matthew S. Zinkgraf, Andrew Groover, Vladimir Filkov
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2018.00299

Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse
Cited by: 22
Author(s): Diego Javier Jiménez, Maryam Chaib De Mares, Joana Falcão Salles
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-46696-6

De novo assembly of the Platycladus orientalis (L.) Franco transcriptome provides insight into the development and pollination mechanism of female cone based on RNA-Seq data
Cited by: 4
Author(s): Wei Zhou, Qi Chen, Xiaobing Wang, Tyler O. Hughes, Jing Liu, Xin Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-46886-2

RNA sequencing analysis revealed the induction of CCL3 expression in human intracranial aneurysms
Cited by: 15
Author(s): Tomohiro Aoki, Hirokazu Koseki, Haruka Miyata, Masayoshi Itoh, Hideya Kawaji, Kazuyasu Takizawa, Akitsugu Kawashima, Hiroshi Ujiié, Takashi Higa, Kenzo Minamimura, Toshikazu Kimura, Hidetoshi Kasuya, Kazuhiko Nozaki, Akio Morita, Hirotoshi Sano, Shuh Narumiya
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-46981-4

Analysis of lncRNA-miRNA-mRNA Interactions in Hyper-proliferative Human Pulmonary Arterial Smooth Muscle Cells
Cited by: 9
Author(s): Mahendran Chinnappan, Sumedha Gunewardena, Prabhakar Chalise, Navneet K. Dhillon
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2016.00880

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms
Cited by: 41
Author(s): Rachel E. Diner, Sarah M. Schwenck, John P. McCrow, Hong Zheng, Andrew E. Allen
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms20174117

Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)
Cited by: 17
Author(s): Yu Ge, Zhihao Cheng, Xiongyuan Si, Wei Ma, Lin Tan, Xiaoping Zang, Bin Wu, Zining Xu, Nan Wang, Zhaoxi Zhou, Xiao Lin, Xiangshu Dong, Rulin Zhan
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms20194933

Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
Cited by: 13
Author(s): Nilay Mitash, Fangping Mu, Joshua E Donovan, Michael M. Myerburg, Sarangarajan Ranganathan, Catherine M. Greene, Agnieszka Swiatecka‐Urban
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-47016-8

Wx: a neural network-based feature selection algorithm for transcriptomic data
Cited by: 12
Author(s): Sung Soo Park, Bonggun Shin, Won Sang Shim, Yuni Choi, Kilsoo Kang, Keunsoo Kang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5671-8

Disruption of the pleiotropic gene scoC causes transcriptomic and phenotypical changes in Bacillus pumilus BA06
Cited by: 4
Author(s): Han Liang, Yongcheng Liu, Cuicui Miao, Feng Hong
Software Mentions: 1
Published: over 5 years ago

10.1155/2020/9502560

The YTH Domain Family of N6-Methyladenosine “Readers” in the Diagnosis and Prognosis of Colonic Adenocarcinoma
Cited by: 17
Author(s): Dian Xu, Jun Shao, Huan Song, Jianming Wang
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2017.01266

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere
Cited by: 54
Author(s): Ubiana C. Silva, Julliane Dutra Medeiros, Laura Hora Rios Leite, Daniel Morais, Sara Cuadros-Orellana, Carlos A. S. Oliveira, U. G. de P. Lana, E. A. Gomes, Vera Lúcia dos Santos
Software Mentions: 1
Published: over 7 years ago

10.1128/mSphere.00620-19

Global Transcriptomic Analysis of the Candida albicans Response to Treatment with a Novel Inhibitor of Filamentation
Cited by: 16
Author(s): Jesús A. Romo, Hao Zhang, Hong Cai, David Kadosh, Julia Koehler, Stephen P. Saville, Yufeng Wang, José L. Lopez-Ribot
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2019.02452

Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities
Cited by: 10
Author(s): Qin Ma, Heike Bücking, Jose L. Gonzalez-Hernandez, Senthil Subramanian
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms20205172

Novel Pituitary Actions of Epidermal Growth Factor: Receptor Specificity and Signal Transduction for UTS1, EGR1, and MMP13 Regulation by EGF
Cited by: 5
Author(s): Qiongyao Hu, Shaohua Xu, Ya Cheng, Jingyi Jia, Lingling Zhou, Guangfu Hu
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0035961

Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens
Cited by: 38
Author(s): Li Xiao, Liechi Zhang, Yang Ge, Honglin Zhu, Yulong He
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-016-3019-1

Gene expression and metabolism preceding soft scald, a chilling injury of ‘Honeycrisp’ apple fruit
Cited by: 26
Author(s): Rachel Leisso, Nigel E. Gapper, James P. Mattheis, Nathanael Sullivan, Christopher B. Watkins, James J. Giovannoni, Robert J. Schaffer, Jason W. Johnston, Ines Hanrahan, Maarten Hertog, Bart Nicolaı̈, David R. Rudell
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms20205069

Renal Artery Stenosis Alters Gene Expression in Swine Scattered Tubular-Like Cells
Cited by: 7
Author(s): Arash Aghajani Nargesi, Xiang Yang Zhu, Yuanhang Liu, Hui Tang, Kyra L. Jordan, Lilach O. Lerman, Alfonso Eirin
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-13-524

SERE: Single-parameter quality control and sample comparison for RNA-Seq
Cited by: 113
Author(s): Stefan K Schulze, Rahul Kanwar, Meike Gölzenleuchter, Terry M. Therneau, Andreas S. Beutler
Software Mentions: 1
Published: about 12 years ago

10.1038/s41598-019-47739-8

The role of ESCO2, SALL4 and TBX5 genes in the susceptibility to thalidomide teratogenesis
Cited by: 11
Author(s): João Luiz Ellera Gomes, Thayne Woycinck Kowalski, Lucas Rosa Fraga, Gabriel S. Macedo, Maria Teresa Vieira Sanseverino, Lavínia Schüler‐Faccini, Fernanda S.L. Vianna
Software Mentions: 1
Published: over 5 years ago

10.1098/rsob.200413

Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer
Cited by: 14
Author(s): Yuichiro Hara, Reira Shibahara, Koyuki Kondo, Wataru Abe, Takekazu Kunieda
Software Mentions: 1
Published: over 3 years ago

10.1099/acmi.0.000127

Using next-generation sequencing of microRNAs to identify host and/or pathogen nucleic acid signatures in samples from children with biliary atresia – a pilot study
Cited by: 3
Author(s): M. J. H. Smith, Mark Zuckerman, Apsara Kandanearatchi, Richard J. Thompson, Mark Davenport
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2021.651744

Growth on Formic Acid Is Dependent on Intracellular pH Homeostasis for the Thermoacidophilic Methanotroph Methylacidiphilum sp. RTK17.1
Cited by: 11
Author(s): Carlo R. Carere, Kiel Hards, Kathryn Wigley, Luke Carman, Karen M. Houghton, Gregory M. Cook, Matthew B. Stott
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.5681

De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis
Cited by: 19
Author(s): Li Li, Mimi Li, Xiwu Qi, Tang Xingli, Yunshan Zhou
Software Mentions: 1
Published: about 6 years ago

10.1186/s12934-020-01503-0

Effect of overexpression of SNF1 on the transcriptional and metabolic landscape of baker’s yeast under freezing stress
Cited by: 10
Author(s): Meng Kai Lü, Yang Xu, Xue Lin, Huan-Yuan Jiang, Xiaoping Hu, Sixin Liu
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-020-07000-3

Integrative analysis of circRNAs, miRNAs, and mRNAs profiles to reveal ceRNAs networks in chicken intramuscular and abdominal adipogenesis
Cited by: 24
Author(s): Meng Zhang, Yu Han, Yanhui Zhai, Xiangfei Ma, Xinglan An, Sheng Zhang, Ziyi Li
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2016.00078

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae
Cited by: 31
Author(s): Xiao-Yan Yang, Kui He, Gaofei Du, Xiaohui Wu, Guangchuang Yu, Yunlong Pan, Gong Zhang, Xia Sun, Qing‐Yu He
Software Mentions: 1
Published: almost 9 years ago

10.3390/ijms20235893

An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability
Cited by: 39
Author(s): Xin Wei, Lina Zhang, Wenzhong Zhang, Jiping Gao, Jun Yi, Xiaoxi Zhen, Min Du, Yanze Zhao, Liqiang Chen
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2016.01545

New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae
Cited by: 18
Author(s): Ramón González, Pilar Morales, Jordi Tronchoni, Gustavo Cordero-Bueso, Enrico Vaudano, Manuel Quirós, Maïté Novo, Rafael Torres‐Pérez, Eva Valero
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.4140

Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
Cited by: 18
Author(s): Jinge Ma, Linmiao Li, Haiying Jiang, Xiujuan Zhang, Juan Li, Guanyu Li, Lihong Yuan, Jun Wu, Jinping Chen
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2017.00180

Critical Issues in Mycobiota Analysis
Cited by: 63
Author(s): Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R. Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G. Thallinger, Gregor Gorkiewicz
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-019-48806-w

Comparative transcriptome and metabolite profiling of four tissues from Alisma orientale (Sam.) Juzep reveals its inflorescence developmental and medicinal characteristics
Cited by: 4
Author(s): Wenjin Lin, Fengling Sun, Yamin Zhang, Xinlan Xu, Xuehua Lu, Lisha Li, Ruihua Xu
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-3644-3

High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production
Cited by: 20
Author(s): Nan Wu, Qing Zhu, Binlong Chen, Jian Gao, Zhongxian Xu, Diyan Li
Software Mentions: 1
Published: over 7 years ago

10.18632/aging.100895

The effects of graded levels of calorie restriction: VI. Impact of short-term graded calorie restriction on transcriptomic responses of the hypothalamic hunger and circadian signaling pathways
Cited by: 24
Author(s): Davina Derous, Sharon E. Mitchell, Cara L Green, Luonan Chen, Jing–Dong Jackie Han, Yingchun Wang, Daniel E. L. Promislow, David Lusseau, John R. Speakman, Alex Douglas
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.00356

Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity
Cited by: 12
Author(s): Jonna Teikari, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0217507

A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing
Cited by: 17
Author(s): Anson T. Ku, Naveen Ravi, Minjun Yang, Mikael Evander, Thomas Laurell, Hans Lilja, Yvonne Ceder
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2021.615893

Transcriptome Profiling Reveals a Novel Mechanism of Antiviral Immunity Upon Sacbrood Virus Infection in Honey Bee Larvae (Apis cerana)
Cited by: 10
Author(s): Yanjun Guo, Zhengyi Zhang, Mingsheng Zhuang, Liuhao Wang, Kai Li, Jun Yao, Huipeng Yang, Jiaxing Huang, Ya Hao, Ying Fan, Hira Mannan, Jie Wu, Yanping Chen, Jilian Li
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.00150

Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Cited by: 35
Author(s): Murugesan Sivaranjani, Katarzyna Leskinen, Chairmandurai Aravindraja, Päivi Saavalainen, Shunmugiah Karutha Pandian, Mikael Skurnik, Arumugam Veera Ravi
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12934-021-01603-5

Site-directed mutagenesis of the quorum-sensing transcriptional regulator SinR affects the biosynthesis of menaquinone in Bacillus subtilis
Cited by: 10
Author(s): Jiang Wu, Wei Li, Su Zhao, Qian Senhe, Wang Zhou, Mengjie Zhou, Wenchao Hu, Jian Wang, Liu-xiu Hu, Yan Liu, Zhenglian Xue
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.9849

Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat
Cited by: 0
Author(s): Junhao Huang, Lesha Zhang, Yang Fang, Wan Jiang, Juan Du, Jiaquan Zhu, Min Hu, Bing Shen
Software Mentions: 1
Published: about 4 years ago

10.18632/oncotarget.17321

Inhibition of stress-inducible HSP70 impairs mitochondrial proteostasis and function
Cited by: 31
Author(s): Julia I-Ju Leu, Thibaut Barnoud, Gao Zhang, Tian Tian, Zhi Wei, Meenhard Herlyn, Maureen E. Murphy, Donna L. George
Software Mentions: 1
Published: over 7 years ago

10.1042/BSR20203804

Integrated analysis of ceRNA network and tumor-infiltrating immune cells in esophageal cancer
Cited by: 5
Author(s): Yuhua Chen, Hao Zhou, Zhendong Wang, Zhanghao Huang, Jinjie Wang, Miaosen Zheng, Xuejun Ni, Lei Liu
Software Mentions: 1
Published: over 3 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: almost 8 years ago

10.1186/s12864-015-1420-9

Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration
Cited by: 21
Author(s): Yang Dong, Fangyin Dai, Yandong Ren, Hui Liu, Lei Chen, Pengcheng Yang, Yanping Liu, Xin Li, Wen Wang, Hui Xiang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0004634

Analysis on Gene Expression Profile in Oncospheres and Early Stage Metacestodes from Echinococcus multilocularis
Cited by: 28
Author(s): Fuqiang Huang, Zhisheng Dang, Yutaka Suzuki, T Horiuchi, Kinpei Yagi, Hirokazu Kouguchi, Takao Irie, Kyeong-Soon Kim, Yuzaburo Oku
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.46551

NRG1 is a critical regulator of differentiation in TP63-driven squamous cell carcinoma
Cited by: 9
Author(s): Ganapati V. Hegde, Cecile de la Cruz, Jennifer M. Giltnane, Lisa Crocker, Avinashnarayan Venkatanarayan, Gabriele Schaefer, Debra Dunlap, Joerg D. Hoeck, Robert Piskol, Florian Gnad, Zora Modrušan, Frédéric J. de Sauvage, Christian W. Siebel, Erica Jackson
Software Mentions: 1
Published: over 5 years ago

10.1186/s12967-018-1637-x

Molecular network-based identification of competing endogenous RNAs and mRNA signatures that predict survival in prostate cancer
Cited by: 36
Author(s): Ning Xu, Yupeng Wu, Hubin Yin, Xue-Yi Xue, Xin Gou
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2018.01643

Long-Term Land Use Affects Phosphorus Speciation and the Composition of Phosphorus Cycling Genes in Agricultural Soils
Cited by: 54
Author(s): Liu Jin, Barbara J. Cade-Menun, Jianjun Yang, Yongfeng Hu, Corey W. Liu, Julien Tremblay, Kerry LaForge, Michael P. Schellenberg, Chantal Hamel, Luke D. Bainard
Software Mentions: 1
Published: over 6 years ago

10.1515/med-2020-0190

Identification of four genes associated with cutaneous metastatic melanoma
Cited by: 7
Author(s): Ji Chen, Yuming Li, Kai Yang, Yumei Gao, Yan Sha, Dong Xiao, Xiaohong Liang, Zhongqin Cheng
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-018-5209-5

Intramuscular preadipocytes impede differentiation and promote lipid deposition of muscle satellite cells in chickens
Cited by: 25
Author(s): Liping Guo, Huanxian Cui, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng, Yuming Guo, Jie Wen
Software Mentions: 1
Published: almost 6 years ago

10.18632/oncotarget.17506

A five-long non-coding RNA signature to improve prognosis prediction of clear cell renal cell carcinoma
Cited by: 27
Author(s): Da Shi, Qinghua Qu, Qimeng Chang, Yilin Wang, Yan Gui, Dong Dong
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2018.00859

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8
Cited by: 62
Author(s): Helen L. Hayden, Keith W. Savin, Jenny Wadeson, Vadakattu V. S. R. Gupta, Pauline M. Mele
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-13-285

Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis
Cited by: 32
Author(s): Robert S. Cornman, Anna Bennett, K. Daniel Murray, Jay D. Evans, Christine G. Elsik, Kate Aronstein
Software Mentions: 1
Published: over 12 years ago

10.3389/fmicb.2018.01765

Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose
Cited by: 18
Author(s): Sabrina Giaretta, Laura Treu, Veronica Vendramin, Vinícius da Silva Duarte, Armin Tarrah, Stefano Campanaro, Viviana Corich
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21010159

Transcriptome Response to Drought, Rehydration and Re-Dehydration in Potato
Cited by: 47
Author(s): Yongkun Chen, Canhui Li, Jing Yi, Yang Yu, Chunxia Lei, Ming Gong
Software Mentions: 1
Published: almost 5 years ago

10.18632/aging.203235

miR-30a-5p suppresses lung squamous cell carcinoma via ATG5 - mediated autophagy
Cited by: 15
Author(s): Jichen Yang, Sunyin Rao, Run Cao, Shouyong Xiao, Xin Cui, Lianhua Ye
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2014.00430

Wolbachia is not all about sex: male-feminizing Wolbachia alters the leafhopper Zyginidia pullula transcriptome in a mainly sex-independent manner
Cited by: 12
Author(s): Hosseinali Asgharian, Peter L. Chang, Peter John Mazzoglio, Ilaria Negri
Software Mentions: 1
Published: about 10 years ago

10.3390/ijms21010118

Comparative Proteomic Analysis Reveals the Regulatory Effects of H2S on Salt Tolerance of Mangrove Plant Kandelia obovata
Cited by: 36
Author(s): Yiling Liu, Zhijun Shen, Martín Simón, Huan Li, Dongna Ma, Xike Zhu
Software Mentions: 1
Published: almost 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 7 years ago

10.3389/fmicb.2019.01873

Hydrogen Oxidation Influences Glycogen Accumulation in a Verrucomicrobial Methanotroph
Cited by: 12
Author(s): Carlo R. Carere, Ben McDonald, Hanna Peach, Chris Greening, Daniel J. Gapes, Christophe Collet, Matthew B. Stott
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.01264

Yeast Assimilable Nitrogen Concentrations Influence Yeast Gene Expression and Hydrogen Sulfide Production During Cider Fermentation
Cited by: 10
Author(s): Yangbo Song, Patrick A. Gibney, Lailiang Cheng, Shuwen Liu, Gregory M. Peck
Software Mentions: 1
Published: over 4 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 5 years ago

10.1042/BSR20194432

Development of a novel prognostic signature for predicting the overall survival of bladder cancer patients
Cited by: 3
Author(s): Huamei Tang, Lijuan Kan, Tong Ou, Dayang Chen, Xiaowei Dou, Wei Wu, Xiang Ji, Mengmeng Wang, Zhi‐Hong Zong, Hongmei Mo, Xiuming Zhang, Dan Xiong
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2020.00460

Investigating the Role of FlhF Identifies Novel Interactions With Genes Involved in Flagellar Synthesis in Campylobacter jejuni
Cited by: 11
Author(s): Xiaofei Li, Fangzhe Ren, Guoqiang Cai, Pingyu Huang, Qinwen Chai, Ozan Gundogdu, Xinan Jiao, Jinlin Huang
Software Mentions: 1
Published: over 4 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: almost 9 years ago

10.3389/fmicb.2020.563139

tpo3 and dur3, Aspergillus fumigatus Plasma Membrane Regulators of Polyamines, Regulate Polyamine Homeostasis and Susceptibility to Itraconazole
Cited by: 6
Author(s): Mingcong Chen, Guowei Zhong, Sha Wang, Jun Zhu, Lei Tang, Lei Li
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-015-1750-7

RNA-sequencing elucidates the regulation of behavioural transitions associated with the mating process in honey bee queens
Cited by: 32
Author(s): Fabio Manfredini, Mark J. F. Brown, Vanina Vergoz, Benjamin P. Oldroyd
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2018.00877

Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle
Cited by: 16
Author(s): Marcos H. de Moraes, Emanuel Becerra Soto, Isaí Salas González, Prerak Desai, Chu Wu, Steffen Porwollik, Michael McClelland, Max Teplitski
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.18833

The molecular characterization of porcine egg precursor cells
Cited by: 10
Author(s): Te-Sha Tsai, Jacqueline L. Johnson, Yvonne A.R. White, Justin C. St. John
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-018-5057-3

Transcriptomic analysis of crustacean neuropeptide signaling during the moult cycle in the green shore crab, Carcinus maenas
Cited by: 51
Author(s): Andrew Oliphant, Jodi Alexander, Martin Swain, S. G. Webster, David Wilcockson
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2018.02418

Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in L. lactis SK11
Cited by: 7
Author(s): Annereinou Dijkstra, Marjo Starrenburg, Tilman Todt, Sacha A. F. T. van Hijum, Jeroen Hugenholtz, Peter A. Bron
Software Mentions: 1
Published: about 6 years ago

10.1515/med-2020-0237

Key pathways in prostate cancer with SPOP mutation identified by bioinformatic analysis
Cited by: 2
Author(s): Guanxiong Ding, Jian Sun, Lianhua Jiang, Peng Gao, Qing Zhou, Jianqing Wang, Shijun Tong
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-51150-8

Depth-dependent transcriptomic response of diatoms during spring bloom in the western subarctic Pacific Ocean
Cited by: 4
Author(s): Shigekatsu Suzuki, Takafumi Kataoka, Tsuyoshi Watanabe, Haruyo Yamaguchi, Akira Kuwata, Masanobu Kawachi
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms21030817

Role of Phagocytosis in the Pro-Inflammatory Response in LDL-Induced Foam Cell Formation; a Transcriptome Analysis
Cited by: 16
Author(s): Alexander N. Orekhov, Nikita G. Nikiforov, Vasily N. Sukhorukov, M. Kubekina, Igor A. Sobenin, Wei-Kai Wu, Kathy Foxx, Sergey S. Pintus, Philip Stegmaier, Daria Stelmashenko, Alexander Kel, Alexei Gratchev, Alexandra А. Melnichenko, Reinhard Wetzker, Volha I Summerhill, Ichiro Manabe, Yumiko Oishi
Software Mentions: 1
Published: almost 5 years ago

10.1155/2021/8875971

High FAM189B Expression and Its Prognostic Value in Patients with Gastric Cancer
Cited by: 3
Author(s): Changliang Wu, Quan-Xiao Tan, Dan Liŭ, Jun-E Jiang, Ting Lu, Zu-Mei Huang, Yingjie Su
Software Mentions: 1
Published: over 3 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 10 years ago

10.3389/fmicb.2018.01565

Comparative Transcriptomics of Cold Growth and Adaptive Features of a Eury- and Steno-Psychrophile
Cited by: 31
Author(s): Isabelle Raymond-Bouchard, Julien Tremblay, Ianina Altshuler, Charles W. Greer, Lyle G. Whyte
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.14409

Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution
Cited by: 38
Author(s): Audrey P. Gasch, James Hose, Michael A. Newton, Maria Sardi, Mun Yong, Zhishi Wang
Software Mentions: 1
Published: over 8 years ago

10.1128/mSystems.00819-20

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy
Cited by: 16
Author(s): Jiawei He, Xu‐jie Zhou, Yafeng Li, Yan-Na Wang, Lijun Liu, Sufang Shi, Xu Xin, Rongshan Li, Mario Falchi, Jicheng Lv, Hong Zhang
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-019-52225-2

The Role and Therapeutic Potential of miRNAs in Colorectal Liver Metastasis
Cited by: 9
Author(s): Smiti Snigdha Sahu, Shatovisha Dey, Sarah C. Nabinger, Guanglong Jiang, Alison Bates, Hiromi Tanaka, Yunlong Liu, Janaiah Kota
Software Mentions: 1
Published: about 5 years ago

10.18632/oncotarget.18234

Cell lines generated from a chronic lymphocytic leukemia mouse model exhibit constitutive Btk and Akt signaling
Cited by: 17
Author(s): Simar Pal Singh, Saravanan Y. Pillai, Marjolein J. W. de Bruijn, Ralph Stadhouders, Odilia B. J. Corneth, Henk-Jan van den Ham, Alice F. Muggen, Wilfred F. J. van IJcken, Erik Slinger, Annemieke Kuil, Marcel Spaargaren, Arnon P. Kater, Anton W. Langerak
Software Mentions: 1
Published: over 7 years ago

10.3389/fpls.2016.01338

Identification of Candidate Anthocyanin-Related Genes by Transcriptomic Analysis of ‘Furongli’ Plum (Prunus salicina Lindl.) during Fruit Ripening Using RNA-Seq
Cited by: 46
Author(s): Zhi‐Zhen Fang, Dan‐Rong Zhou, Xinfu Ye, Cuicui Jiang, Shao‐Lin Pan
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms21030745

Divergent Regulation of Myotube Formation and Gene Expression by E2 and EPA during In-Vitro Differentiation of C2C12 Myoblasts
Cited by: 8
Author(s): Orly Lacham‐Kaplan, Donny M. Camera, John A. Hawley
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.19532

Integration of genomic, transcriptomic and functional profiles of aggressive osteosarcomas across multiple species
Cited by: 12
Author(s): Lara E. Davis, Sophia Jeng, Matthew N. Svalina, Elaine Huang, Janét Pittsenbarger, Emma L. Cantor, Noah Berlow, Bernard Séguin, Atiya Mansoor, Shannon K. McWeeney, Charles Keller
Software Mentions: 1
Published: over 7 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 3 years ago

10.18632/aging.103772

ARHGEF11 promotes proliferation and epithelial-mesenchymal transition of hepatocellular carcinoma through activation of &#x3B2;-catenin pathway
Cited by: 9
Author(s): Dingjun Hao, Zexin Zhu, Xu Lin, Xing Chen, Xuefeng Li, Tian Lan, Wei Li, Kefei Yuan, Yong Zeng
Software Mentions: 1
Published: about 4 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 11 years ago

10.1186/s12864-018-5344-z

Functional genomics of the digestive tract in broilers
Cited by: 8
Author(s): Amélie Juanchich, Christelle Hennequet-Antier, Cédric Cabau, Elisabeth Le Bihan‐Duval, M. J. Duclos, Sandrine Mignon-Grasteau, Agnès Narcy
Software Mentions: 1
Published: almost 6 years ago

10.3390/ani10030468

MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens
Cited by: 19
Author(s): Xiangfei Ma, Junwei Sun, Shuaipeng Zhu, Zhenwei Du, Donghua Li, Wenting Li, Zhuanjian Li, Yadong Tian, Xiangtao Kang, Guirong Sun
Software Mentions: 1
Published: over 4 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 10 years ago

10.3389/fpls.2016.00432

Using Transcriptomics to Identify Differential Gene Expression in Response to Salinity among Australian Phragmites australis Clones
Cited by: 18
Author(s): Gareth D. Holmes, Nathan E. Hall, Anthony R. Gendall, Paul I. Boon, Elizabeth A. James
Software Mentions: 1
Published: over 8 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: over 9 years ago

10.3389/fpls.2018.00252

The Novel Secreted Meloidogyne incognita Effector MiISE6 Targets the Host Nucleus and Facilitates Parasitism in Arabidopsis
Cited by: 27
Author(s): Qianqian Shi, Zhenchuan Mao, Xiaoping Zhang, Jian Ling, Runmao Lin, Xi Zhang, Rui Li, Yunsheng Wang, Youyou Yang, Xinyue Cheng, Bingyan Xie
Software Mentions: 1
Published: over 6 years ago

10.1515/med-2021-0276

Four long noncoding RNAs act as biomarkers in lung adenocarcinoma
Cited by: 3
Author(s): Zhihui Zhang, Liu Yang, Yujiang Li, Yingxi Wu, Xiang Li, Xu Wu
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-016-2747-6

Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression
Cited by: 11
Author(s): Vince Grolmusz, Eszter Tóth, Kornélia Baghy, István Láng, Ottó Darvasi, Ilona Kovalszky, János Matkó, Kàroly Rácz, Attila Patócs
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-014-1197-2

Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing
Cited by: 81
Author(s): Rienk A. Rienksma, María Suárez-Diez, Hans-Joachim Mollenkopf, Gregory Dolganov, Anca Dorhoi, Gary K. Schoolnik, Vítor A. P. Martins dos Santos, Stefan H. E. Kaufmann, Peter J. Schaap, Martin Gengenbacher
Software Mentions: 1
Published: almost 10 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: about 14 years ago

10.1038/s41598-019-53717-x

Differentially Expressed Genes between Carrot Petaloid Cytoplasmic Male Sterile and Maintainer during Floral Development
Cited by: 9
Author(s): Bo Liu, C. Ou, Shumin Chen, Qiongwen Cao, Zhi‐Wei Zhao, Zengjian Miao, Xiaoping Kong, Feiyun Zhuang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12967-021-02857-8

Identifying the functions of two biomarkers in human oligodendrocyte progenitor cell development
Cited by: 4
Author(s): Huixia Zhou, HE Ya, Zhaoyan Wang, Qian Wang, Caiyan Hu, Xiaohua Wang, Shan Lu, Ké Li, Ye Yang, Zuo Luan
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568