bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s13072-021-00405-8

Altered hypothalamic DNA methylation and stress-induced hyperactivity following early life stress
Cited by: 5
Author(s): Eamon Fitzgerald, Matthew C. Sinton, Sara Wernig-Zorc, Nicholas M. Morton, Megan C. Holmes, James P. Boardman, Amanda J. Drake
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-019-0580-x

A comprehensive genome-wide profiling comparison between HBV and HCV infected hepatocellular carcinoma
Cited by: 21
Author(s): Suofeng Sun, Yuan Li, Sun‐Young Han, Huiying Jia, Xiuling Li, Xiaofang Li
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-017-4170-z

Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda
Cited by: 35
Author(s): Karina Lucas Silva‐Brandão, Renato J. Horikoshi, Daniel Bernardi, Celso Omoto, Antônio Figueira, Marcelo Mendes Brandão
Software Mentions: 3
Published: about 9 years ago

10.1186/s12920-019-0548-x

Placental microRNAs in pregnancies with early onset intrauterine growth restriction and preeclampsia: potential impact on gene expression and pathophysiology
Cited by: 72
Author(s): Zain Awamleh, Gregory B. Gloor, V. K. M. Han
Software Mentions: 3
Published: over 7 years ago

10.1186/s13072-018-0187-z

Deletion of HP1γ in cardiac myocytes affects H4K20me3 levels but does not impact cardiac growth
Cited by: 12
Author(s): Kyohei Oyama, Danny El‐Nachef, Fang Chen, Hidemi Kajimoto, Jeremy Brown, Prim B. Singh, W. Robb MacLellan
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-016-2376-0

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum
Cited by: 19
Author(s): Stanford Kwenda, Vladimir Gorshkov, Aiyagari Ramesh, Sanushka Naidoo, Enrico Rubagotti, Paul R. J. Birch, Lucy N. Moleleki
Software Mentions: 3
Published: almost 11 years ago

10.3390/plants10040787

Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum
Cited by: 6
Author(s): Christian Siadjeu, Eike Mayland‐Quellhorst, Shruti Pande, Sascha Laubinger, Dirk C. Albach
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-019-0308-3

Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types
Cited by: 4
Author(s): Lila Rieber, Shaun Mahony
Software Mentions: 3
Published: about 7 years ago

10.3390/plants9111522

Screening of Salt Stress Responsive Genes in Brachypodium distachyon (L.) Beauv. by Transcriptome Analysis
Cited by: 6
Author(s): Xiaocheng Guo, Qingjun Wang, Yuan Liu, Xuejie Zhang, Luoyan Zhang, Shoujin Fan
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12920-019-0565-9

Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs
Cited by: 2
Author(s): Hua Zhong, Mingzhou Song
Software Mentions: 3
Published: almost 7 years ago

10.1093/gbe/evv117

Variation in the X:Autosome Distribution of Male-Biased Genes amongDrosophila melanogasterTissues and Its Relationship with Dosage Compensation
Cited by: 28
Author(s): Ann Kathrin Huylmans, John Parsch
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-019-5745-7

Cold acclimation triggers major transcriptional changes in Drosophila suzukii
Cited by: 29
Author(s): Thomas Enriquez, Hervé Colinet
Software Mentions: 3
Published: over 7 years ago

10.1186/s13007-018-0337-0

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants
Cited by: 81
Author(s): Fu Yuan Zhu, Mo Xian Chen, Nenghui Ye, Wang Min Qiao, Bei Gao, Wai Ki Law, Yuan Tian, Dong Zhang, Di Zhang, Tie Yuan Liu, Qi Hu, Yun Cao, Ze Zhuo Su, Jianhua Zhang, Ying Gao Liu
Software Mentions: 3
Published: about 8 years ago

10.1111/tpj.14632

Translational regulation contributes to the elevated CO 2 response in two Solanum species
Cited by: 12
Author(s): Sharon B. Gray, Joel Rodríguez-Medina, Samuel Rusoff, Ted Toal, Kaisa Kajala, Daniel E. Runcie, Siobhán M. Brady
Software Mentions: 3
Published: almost 7 years ago

10.1093/gbe/evu199

Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production
Cited by: 39
Author(s): Dana J. Wohlbach, Nikolay Rovinskiy, Jeffrey A. Lewis, Maria Sardi, Wendy Schackwitz, Joel Martin, Shweta Deshpande, Christopher Daum, Anna Lipzen, Trey K. Sato, Audrey P. Gasch
Software Mentions: 3
Published: about 12 years ago

10.1002/pld3.99

Field‐grown soybean transcriptome shows diurnal patterns in photosynthesis‐related processes
Cited by: 10
Author(s): Anna M. Locke, Rebecca Slattery, Donald R. Ort
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12920-021-00985-0

Label propagation-based semi-supervised feature selection on decoding clinical phenotypes with RNA-seq data
Cited by: 2
Author(s): Xue Jiang, Miao Chen, Weichen Song, Guan Ning Lin
Software Mentions: 3
Published: over 5 years ago

10.1186/1755-8794-6-S2-S1

Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening
Cited by: 7
Author(s): Mark A. van de Wiel, Renée X. de Menezes, Ellen Siebring-van Olst, Victor W. van Beusechem
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12864-017-4285-2

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis
Cited by: 15
Author(s): Dietrich Trümbach, Susanne Pfeiffer, Manuel Poppe, Hagen Scherb, Sebastian Doll, Wolfgang Wurst, Joel Schick
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13059-021-02439-3

Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Cited by: 23
Author(s): Evangelos D. Karousis, Foivos Gypas, Mihaela Zavolan, Oliver Mühlemann
Software Mentions: 3
Published: about 5 years ago

10.1093/gbe/evu200

Comparative Transcriptomics in East African Cichlids Reveals Sex- and Species-Specific Expression and New Candidates for Sex Differentiation in Fishes
Cited by: 49
Author(s): Astrid Böhne, Thierry Sengstag, Walter Salzburger
Software Mentions: 3
Published: about 12 years ago

10.1186/s13073-015-0208-5

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance
Cited by: 74
Author(s): William R. Swindell, Henriette A. Remmer, Mrinal K. Sarkar, Xianying Xing, Drew H. Barnes, Liza Wolterink, John J. Voorhees, Rajan P. Nair, Andrew Johnston, James T. Elder, Jóhann E. Guðjónsson
Software Mentions: 3
Published: over 11 years ago

10.1186/s12920-021-00975-2

Identification and validation of signal recognition particle 14 as a prognostic biomarker predicting overall survival in patients with acute myeloid leukemia
Cited by: 3
Author(s): Lingling Shi, Rui Huang, Yongrong Lai
Software Mentions: 3
Published: over 5 years ago

10.1111/pbi.13249

Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis
Cited by: 54
Author(s): Yingfan Cai, Xiaoyan Cai, Qinglian Wang, Wang Ping, Yu Zhang, Chaowei Cai, Yanchao Xu, Kunbo Wang, Zhongli Zhou, Chenxiao Wang, Shuaipeng Geng, Bo Li, Qi Dong, Yuqing Hou, Heng Wang, Peng Ai, Zhen Liu, Feifei Yi, Minshan Sun, Gary An, Jieru Cheng, Yuanyuan Zhang, Qian Shi, Yuanhui Xie, Xiaojian Shi, Ying Chang, Feifei Huang, Yun Chen, Shimiao Hong, Lingyu Mi, Quan Sun, Lin Zhang, Baoliang Zhou, Renhai Peng, Xiao Zhang, Fang Liu
Software Mentions: 3
Published: about 7 years ago

10.1111/pbi.13007

A Ma10 gene encoding P‐type <scp>ATP</scp>ase is involved in fruit organic acid accumulation in apple
Cited by: 54
Author(s): Baiquan Ma, Liao Liao, Ting Fang, Qian Peng, Collins Ogutu, Hui Zhou, Fengwang Ma, Yuepeng Han
Software Mentions: 3
Published: about 8 years ago

10.1111/pbi.12910

Up‐regulation of Gh<scp>TT</scp>2‐3A in cotton fibres during secondary wall thickening results in brown fibres with improved quality
Cited by: 45
Author(s): Qian Yan, Yi Wang, Qian Li, Zhengsheng Zhang, Hui Ding, Yue Zhang, Housheng Liu, Ming Luo, Dexin Liu, Song Wu, Haifeng Liu, Dan Yao, Xufen Ouyang, Yaohua Li, Xin Li, Yan Pei, Yazhong Xiao
Software Mentions: 3
Published: over 8 years ago

10.1002/ece3.5181

Differential gene expression in relation to mating system in Peromyscine rodents
Cited by: 2
Author(s): Jesyka Meléndez‐Rosa, Ke Bi, Eileen A. Lacey
Software Mentions: 3
Published: over 7 years ago

10.1002/ece3.5956

Transcriptomic regulation of seasonal coat color change in hares
Cited by: 13
Author(s): Mafalda S. Ferreira, Paulo C. Alves, Colin M. Callahan, Iwona Giska, Liliana Farelo, Hannes Jenny, L. Scott Mills, Klaus Hackländer, Jeffrey M. Good, José Melo‐Ferreira
Software Mentions: 3
Published: almost 7 years ago

10.14814/phy2.14482

Modifying nutritional substrates induces macrovesicular lipid droplet accumulation and metabolic alterations in a cellular model of hepatic steatosis
Cited by: 5
Author(s): Pippa J. Gunn, Camilla Pramfalk, Val Millar, Thomas Cornfield, Matthew Hutchinson, Elspeth Johnson, Shilpa R. Nagarajan, Perla Troncoso‐Rey, Richard Mithen, Katherine E. Pinnick, Μαρία Τράκα, Charlotte Green, Leanne Hodson
Software Mentions: 3
Published: over 6 years ago

10.1002/ece3.6688

Examining the molecular mechanisms contributing to the success of an invasive species across different ecosystems
Cited by: 0
Author(s): Sarah K. Lamar, Ian Beddows, Charlyn Partridge
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-021-07560-y

Factors affecting the rapid changes of protein under short-term heat stress
Cited by: 4
Author(s): Bingjin Wu, Jian-Wen Qiao, Xiaoming Wang, Manshuang Liu, Shengbao Xu, Dianjun Sun
Software Mentions: 3
Published: over 5 years ago

10.1002/ece3.6377

Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii
Cited by: 4
Author(s): Xianqiong Zhong, Max Lundberg, Lars Råberg
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-020-02164-3

Tissue-specific usage of transposable element-derived promoters in mouse development
Cited by: 48
Author(s): Benpeng Miao, Shuhua Fu, Cheng Lyu, Paul Gontarz, Ting Wang, Bo Zhang
Software Mentions: 3
Published: about 6 years ago

10.1152/physiolgenomics.00123.2014

Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout
Cited by: 14
Author(s): Tamsyn M. Uren Webster, Janice A. Shears, Karen Moore, Eduarda M. Santos
Software Mentions: 3
Published: about 11 years ago

10.1002/prp2.386

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes
Cited by: 16
Author(s): Brandon T. Gufford, Jason Robarge, Michael T. Eadon, Hongyu Gao, Hai Lin, Yunlong Liu, Zeruesenay Desta, Todd C. Skaar
Software Mentions: 3
Published: over 8 years ago

10.3390/ph14010041

Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients
Cited by: 4
Author(s): Hana Votavová, Zuzana Urbanová, David Kundrát, Michaela Dostálová Merkerová, Martin Vostrý, Monika Hruba, Jaroslav Čermák, Monika Beličková
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-020-02150-9

A novel antiviral lncRNA, EDAL, shields a T309 O-GlcNAcylation site to promote EZH2 lysosomal degradation
Cited by: 34
Author(s): Baokun Sui, Dong Chen, Wei Liu, Qiong Wu, Bin Tian, Yingying Li, Jing Hou, Shiyong Liu, Juan Xie, Hao Jiang, Zhidan Luo, Lei Lv, Fei Huang, Ruiming Li, Chengguang Zhang, Yuling Tian, Min Cui, Ming Zhou, Huanchun Chen, Zhen F. Fu, Yi Zhang, Ling Zhao
Software Mentions: 3
Published: about 6 years ago

10.1186/s12920-019-0551-2

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines
Cited by: 28
Author(s): Xing Yi Woo, Anuj Srivastava, Joel H. Graber, Vinod Kumar Yadav, Vishal Kumar Sarsani, Al Simons, Glen L. Beane, Stephen C. Grubb, Guruprasad Ananda, Rangjiao Liu, Grace A. Stafford, Jeffrey H. Chuang, Susan D. Airhart, R. Krishna Murthy Karuturi, Joshy George, Carol J. Bult
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.3773

Canopy soil bacterial communities altered by severing host tree limbs
Cited by: 9
Author(s): Cody R. Dangerfield, Nalini M. Nadkarni, William J. Brazelton
Software Mentions: 3
Published: about 9 years ago

10.1186/s12920-021-00878-2

Expression and gene regulatory network of SNHG1 in hepatocellular carcinoma
Cited by: 4
Author(s): Chaoran Zheng, Shicheng Yu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13072-017-0158-9

Genome-wide profiling of transcribed enhancers during macrophage activation
Cited by: 21
Author(s): Elena Denisenko, Reto Guler, Musa M. Mhlanga, Harukazu Suzuki, Frank Brombacher, Sebastian Schmeier
Software Mentions: 3
Published: about 9 years ago

10.1186/s13059-020-02110-3

Cis and trans effects differentially contribute to the evolution of promoters and enhancers
Cited by: 26
Author(s): Kaia Mattioli, Winona Oliveros, Chiara Gerhardinger, Daniel Andergassen, Philipp G. Maass, John L. Rinn, Marta Melé
Software Mentions: 3
Published: about 6 years ago

10.1186/s12920-020-0700-7

Transcriptome analysis of HPV-induced warts and healthy skin in humans
Cited by: 13
Author(s): Laith N. AL-Eitan, Amneh H. Tarkhan, Mansour A. Alghamdi, Firas Al‐Qarqaz, Hadeel Alkofahi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-020-00756-3

Analysis of exosomal circRNAs upon irradiation in pancreatic cancer cell repopulation
Cited by: 16
Author(s): Yiyun Chen, Mier Jiang, Ling Tian
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4675-0

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
Cited by: 31
Author(s): Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Sharon Benjamini, Shoval Miyara, M. Ruzal, Manfred Grabherr, Nima Rafati, Anna Maja Molin, Ken Pendavis, Shane C. Burgess, Leif Andersson, Miriam Friedman‐Einat
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-020-02046-8

MAUDE: inferring expression changes in sorting-based CRISPR screens
Cited by: 14
Author(s): Carl G. de Boer, John J. Ray, Nir Hacohen, Aviv Regev
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.8260

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
Cited by: 4
Author(s): Necla Koçhan, G. Yazgı Tütüncü, Gordon K. Smyth, Luke C. Gandolfo, Göknur Giner
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13059-020-01972-x

A benchmark of algorithms for the analysis of pooled CRISPR screens
Cited by: 38
Author(s): Sunil Bodapati, Timothy Daley, Xueqiu Lin, James Zou, Lei Qi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-5017-y

Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves
Cited by: 6
Author(s): Zhixiong He, Albert J. Fischer, Yang Song, M.A. Steele, Le Luo Guan
Software Mentions: 3
Published: about 8 years ago

10.1186/s13059-019-1876-z

Non-coding RNAs underlie genetic predisposition to breast cancer
Cited by: 18
Author(s): Mahdi Moradi Marjaneh, Jonathan Beesley, Tracy A. O’Mara, Pamela Mukhopadhyay, Lambros T. Koufariotis, Stephen H. Kazakoff, Nehal Hussein, Laura Fachal, Nenad Bartoniček, Kristine M. Hillman, Susanne Kaufmann, Haran Sivakumaran, Chanel E. Smart, Amy E. McCart Reed, Kaltin Ferguson, Jodi M. Saunus, Sunil R. Lakhani, Daniel R. Barnes, Antonis C. Antoniou, Marcel E. Dinger, Nicola Waddell, Douglas F. Easton, Alison M. Dunning, Georgia Chenevix-Trench, Stacey L. Edwards, Juliet D. French
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-016-3168-2

Novel equine tissue miRNAs and breed-related miRNA expressed in serum
Cited by: 27
Author(s): Alicja Pacholewska, Núria Mach, Xavier Mata, Anne Vaiman, Laurent Schibler, Éric Barrey, V. Gerber
Software Mentions: 3
Published: about 10 years ago

10.7717/peerj.10576

A novel similarity score based on gene ranks to reveal genetic relationships among diseases
Cited by: 3
Author(s): Dongmei Luo, Chengdong Zhang, Liwan Fu, Yuening Zhang, Yue‐Qing Hu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-6514-3

Transcriptomics supports local sensory regulation in the antenna of the kissing-bug Rhodnius prolixus
Cited by: 21
Author(s): José Manuel Latorre-Estivalis, Marcos Sterkel, Sheila Ons, Marcelo G. Lorenzo
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.8930

Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma
Cited by: 24
Author(s): Xi Ma, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4900-x

Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae)
Cited by: 24
Author(s): Zhiqiang Tian, Lina Sun, Yanyan Li, Linfa Quan, Huaijiang Zhang, Wentao Yan, Qiang Yue, Qiu GuiSheng
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-019-1873-2

The majority of A-to-I RNA editing is not required for mammalian homeostasis
Cited by: 55
Author(s): Alistair M. Chalk, Scott Taylor, Jacki Heraud-Farlow, Carl R. Walkley
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.5443

Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus albaL.)
Cited by: 20
Author(s): Dujun Wang, Li Zhao, Dan Wang, Jia Liu, Xin Yu, Yuan Wei, Zhen Ouyang
Software Mentions: 3
Published: about 8 years ago

10.1186/s13059-018-1531-0

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops
Cited by: 54
Author(s): Yu Guo, Andrew A. Perez, Dennis J. Hazelett, Gerhard A. Coetzee, Suhn Kyong Rhie, Peggy J. Farnham
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-020-07050-7

RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake
Cited by: 2
Author(s): Xiaofeng Guo, Xiaoling Gao, Brendan T. Keenan, Jane M. Zhu, Dimitra Sarantopoulou, Jie Liu, Raymond J. Galante, Gregory R. Grant, Allan I. Pack
Software Mentions: 3
Published: about 6 years ago

10.1016/j.ebiom.2018.02.017

Reciprocal modulation of mesenchymal stem cells and tumor cells promotes lung cancer metastasis
Cited by: 45
Author(s): Giulia Fregni, Mathieu Quinodoz, Emely Möller, Joanna A. Vuille, Sabine Galland, Carlo Fusco, Patricia Martin, Igor Letovanec, Paolo Provero, Carlo Rivolta, Nicolò Riggi, Ivan Stamenkovic
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-07277-4

Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
Cited by: 13
Author(s): Ning Li, Ziwei Meng, Tao Mei, Yueyuan Wang, Yulan Zhang, Shufen Li, Wu‐Jun Gao, Chuan‐Liang Deng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-017-1222-2

Translational contributions to tissue specificity in rhythmic and constitutive gene expression
Cited by: 49
Author(s): Violeta Castelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich, David Gatfield
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.8088

Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic spongeIsodictyasp.
Cited by: 11
Author(s): Marcelo González-Aravena, Nathan J. Kenny, Magdalena Osorio, Alejandro Font, Ana Riesgo, César Cárdenas
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-5325-2

Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.
Cited by: 12
Author(s): Junqiang Guo, Qingyi Wang, Li Liu, Shuchao Ren, Shipeng Li, Peiran Liao, Zhigang Zhao, Chenyu Lu, Bingbing Jiang, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.3389

Modeling thecis-regulatory modules of genes expressed in developmental stages ofDrosophila melanogaster
Cited by: 2
Author(s): Yosvany López, Alexis Vandenbon, Akinao Nose, Kenta Nakai
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-017-1301-4

Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis
Cited by: 60
Author(s): Jacki Heraud-Farlow, Alistair M. Chalk, Sandra Linder, Qin Li, Scott Taylor, Joshua M. White, Lokman Pang, Brian Liddicoat, Ankita Gupte, Carl R. Walkley
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-015-2068-1

A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication
Cited by: 15
Author(s): Pedro Rodenas-Cuadrado, Xiaowei Sylvia Chen, Lutz Wiegrebe, Uwe Firzlaff, Sonja C. Vernes
Software Mentions: 3
Published: about 11 years ago

10.1155/2020/9369341

Nine Genes Mediate the Therapeutic Effects of Iodine-131 Radiotherapy in Thyroid Carcinoma Patients
Cited by: 6
Author(s): Shuwen Han, Yang Xi, Miao Da, Jingying Xu, Zhuang Jing, Gao Wei-li
Software Mentions: 3
Published: over 6 years ago

10.1111/acel.13232

Autophagy‐Sirt3 axis decelerates hematopoietic aging
Cited by: 21
Author(s): Yixuan Fang, Ni An, Lingjiang Zhu, Yue Gu, Jiawei Qian, Gaoyue Jiang, Ruijin Zhao, Wei Wen, Li Xu, Gaochuan Zhang, Xingyun Yao, Na Yuan, Suping Zhang, Yun Zhao, Jianrong Wang
Software Mentions: 3
Published: about 6 years ago

10.1007/s00125-017-4500-3

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes
Cited by: 121
Author(s): Michele Solimena, Anke M. Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno‐Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B. Wollheim, Gustavo Baretton, Raphaël Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer‐Puttlitz, Ugo Boggi, Hans‐Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xénarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A. Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti
Software Mentions: 3
Published: almost 9 years ago

10.1242/dev.199628

LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells
Cited by: 8
Author(s): Juli Liu, Sheng Liu, Lei Han, Sheng Yi, Yucheng Zhang, Il-man Kim, Jun Wan, Lei Yang
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.3631

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
Cited by: 34
Author(s): Van L.T. Hoang, Lisa Tom, Xiu-Cheng Quek, Jean-Marie Tan, Elizabeth Payne, Lynlee L. Lin, Sudipta Sinnya, Anthony P. Raphael, Duncan Lambie, Ian H. Frazer, Marcel E. Dinger, H. Peter Soyer, Tarl W. Prow
Software Mentions: 3
Published: about 9 years ago

10.7717/peerj.8592

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
Cited by: 2
Author(s): Allen Hubbard, Matthew Bomhoff, Carl J. Schmidt
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-020-3446-5

Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice
Cited by: 8
Author(s): Anna M. Nia, Tianlong Chen, Brooke L. Barnette, Kamil Khanipov, Robert L. Ullrich, Suresh K. Bhavnani
Software Mentions: 3
Published: over 6 years ago

10.1111/acel.13357

Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions
Cited by: 8
Author(s): Xiao Dong, Shixiang Sun, Lei Zhang, Seung-Soo Kim, Zhidong Tu, Cristina Montagna, Alexander Y. Maslov, Yousin Suh, Tao Wang, Judith Campisi, Jan Vijg
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.3640

Expression differences inAphidius ervi(Hymenoptera: Braconidae) females reared on different aphid host species
Cited by: 11
Author(s): Gabriel I. Ballesteros, Juergen Gadau, Fabrice Legeai, Angélica González-González, Blas Lavandero, Jean Simon, Christian C. Figueroa
Software Mentions: 3
Published: about 9 years ago

10.7717/peerj.2834

Transcriptome analysis of the oriental melon (Cucumis meloL. var.makuwa) during fruit development
Cited by: 26
Author(s): Ah-Young Shin, Yongmin Kim, Namjin Koo, Su‐Min Lee, Seok-Hyeon Nahm, Suk‐Yoon Kwon
Software Mentions: 3
Published: almost 10 years ago

10.1111/acel.13420

Circulating microRNA profile in humans and mice with congenital GH deficiency
Cited by: 6
Author(s): Tatiana D. Saccon, Augusto Schneider, Cindi G. Marinho, Allancer D C Nunes, Sarah Noureddine, Joseph M. Dhahbi, Yury O. Nunez Lopez, Gage LeMunyan, Roberto Salvatori, Carla R. P. Oliveira, Alécia A Oliveira-Santos, Nicolas Musi, Andrzej Bartke, Manuel H. Aguiar‐Oliveira, Michał M. Masternak
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-014-0567-z

The draft genome of Primula veris yields insights into the molecular basis of heterostyly
Cited by: 90
Author(s): Michael Nowak, Giancarlo Russo, Ralph Schlapbach, Cuong Nguyen Huu, Michael Lenhard, Elena Conti
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-021-07367-x

The semi-dwarfing gene Rht-dp from dwarf polish wheat (Triticum polonicum L.) is the "Green Revolution” gene Rht-B1b
Cited by: 12
Author(s): Songyue Chai, Yao Qin, Xu Zhang, Xue Xiao, Xing Fan, Jian Zeng, Sha Li, Houyang Kang, Haiqin Zhang, Jun Li, Yong‐Hong Zhou, Yi Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-016-0883-6

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Cited by: 156
Author(s): Anna Vlasova, Salvador Capella-Gutiérrez, Martha Rendón-Anaya, Miguel Ángel Hernández‐Oñate, André E. Minoche, Ionas Erb, Francisco Câmara, Pablo Prieto Barja, André Corvelo, Walter Sanseverino, Gastón Westergaard, Juliane C. Dohm, George J. Pappas, Soledad Saburido-Álvarez, Darek Kedra, Irene González González, Luca Cozzuto, Jèssica Gómez-Garrido, María A. Aguilar-Morón, Núria Andreu, O. Mario Aguilar, Jordi García-Más, Maik Zehnsdorf, Martı́n Vázquez, Alfonso Delgado‐Salinas, Luis Delaye, Ernesto Lowy, Alejandro Mentaberry, Rosana Pereira Vianello-Brondani, José Luis Garcı́a, Tyler Alioto, Federico Sánchez, Heinz Himmelbauer, Marta Santalla, Cédric Notredame, Toni Gabaldón, Alfredo Herrera-Estrella, Roderic Guigó
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-018-4488-1

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes
Cited by: 38
Author(s): Mahsa Khorramdelazad, Ido Bar, Paul Whatmore, Gabrielle Smetham, Vijay Bhaaskaria, Yuedong Yang, Shahla Hosseini Bai, Nitin Mantri, Yaoqi Zhou, Rebecca Ford
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.12091

Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation
Cited by: 0
Author(s): Wenyan Kang, Liqing Du, Qianyu Liang, Rui Zhang, Chunxu Lv, Shaohua Ge
Software Mentions: 3
Published: about 5 years ago

10.1186/gb-2012-13-11-r102

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Cited by: 63
Author(s): Ana C. Marques, Jennifer Y. Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P. Ponting
Software Mentions: 3
Published: almost 15 years ago

10.3390/dj7020058

Effect of Dietary Fiber on the Composition of the Murine Dental Microbiome
Cited by: 10
Author(s): Lea M. Sedghi, Craig Byron, Ryan deM. Jennings, George E. Chlipala, Stefan J. Green, Laura Silo-Suh
Software Mentions: 3
Published: over 7 years ago

10.1093/database/baz086

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms
Cited by: 12
Author(s): Jochen T. Bick, Shuqin Zeng, Mark D. Robinson, Susanne E. Ulbrich, Stefan Bauersachs
Software Mentions: 3
Published: almost 8 years ago

10.1186/gb-2010-11-10-r106

Differential expression analysis for sequence count data
Cited by: 12,645
Author(s): Simon Anders, Wolfgang Huber
Software Mentions: 3
Published: about 16 years ago

10.1186/gb-2013-14-8-r89

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
Cited by: 191
Author(s): Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing‐Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
Software Mentions: 3
Published: almost 14 years ago

10.3390/pathogens9020131

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
Cited by: 9
Author(s): Julia Bespyatykh, Egor Shitikov, Dmitry Bespiatykh, Andrei Guliaev, Ksenia M. Klimina, Vladimir A. Veselovsky, Georgij Arapidi, Marine Dogonadze, Viacheslav Zhuravlev, Elena Ilina, Vadim M. Govorun
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-13-459

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
Cited by: 52
Author(s): Agnieszka Podolska, Christian Anthon, Mads Bak, Niels Tommerup, Kerstin Skovgaard, Peter M. H. Heegaard, Jan Gorodkin, Susanna Cirera, Merete Fredholm
Software Mentions: 3
Published: about 14 years ago

10.1186/s12864-019-5763-5

Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006
Cited by: 27
Author(s): Rocío M. Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramírez, Roberto Vera Alvarez, David Landsman, Leonardo Mariño-Ramírez
Software Mentions: 3
Published: over 7 years ago

10.3390/pathogens10091127

Delineating the Role of Aedes aegypti ABC Transporter Gene Family during Mosquito Development and Arboviral Infection via Transcriptome Analyses
Cited by: 8
Author(s): Vijoy Kumar, Shilpi Garg, Lalita Gupta, Kuldeep Gupta, Cheikh Tidiane Diagne, Dorothée Missé, Julien Pompon, Sanjeev Kumar, Vishal Saxena
Software Mentions: 3
Published: about 5 years ago

10.3390/pathogens8030132

Whole Transcriptome Analysis of Aedes albopictus Mosquito Head and Thorax Post-Chikungunya Virus Infection
Cited by: 9
Author(s): Ravikiran Vedururu, Matthew J. Neave, Vinod Sundaramoorthy, Diane Green, Jennifer Harper, Paul R Gorry, Jean‐Bernard Duchemin, Prasad N. Paradkar
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-11-422

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
Cited by: 677
Author(s): Thomas J. Hardcastle, Krystyna A. Kelly
Software Mentions: 3
Published: about 16 years ago

10.7717/peerj.9701

A prognostic long non-coding RNA-associated competing endogenous RNA network in head and neck squamous cell carcinoma
Cited by: 13
Author(s): Chengyao Zhang, Wei Cao, Jiawu Wang, Jiannan Liu, Jialiang Li, Hao Wu, Siyi Li, Chenping Zhang
Software Mentions: 3
Published: about 6 years ago

10.3390/pathogens10020167

Characterization of the Rhipicephalus (Boophilus) microplus Sialotranscriptome Profile in Response to Theileria equi Infection
Cited by: 5
Author(s): Patrícia Gonzaga Paulino, Gabriela Lopes Vivas Vitari, Antônio Mauro Rezende, Joana Couto, Sandra Antunes, Ana Domingos, Maristela Peckle, Carlos Luiz Massard, Flávio Marcos Gomes Araújo, Huarrisson Azevedo Santos
Software Mentions: 3
Published: over 5 years ago

10.1016/j.gdata.2015.12.027

Transcriptional profiling of the epigenetic regulator Smchd1
Cited by: 12
Author(s): Ruijie Liu, Kelan Chen, Natasha Jansz, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-016-2363-5

Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients
Cited by: 41
Author(s): Roy G. Danzmann, Andrea L. Kocmarek, Joseph D. Norman, Caird E. Rexroad, Yniv Palti
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13071-016-1341-8

Reconstruction of the insulin-like signalling pathway of Haemonchus contortus
Cited by: 14
Author(s): Namitha Mohandas, Min Hu, Andreas J. Stroehlein, Neil D. Young, Paul W. Sternberg, James B. Lok, Robin B. Gasser
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-021-07536-y

Expression characteristics of pineal miRNAs at ovine different reproductive stages and the identification of miRNAs targeting the AANAT gene
Cited by: 1
Author(s): Ran Di, Qiu Yue Liu, Shu Hui Song, Dong Tian, Jian He, Ying Ge, Xiang Yu Wang, Wen Hu, Joram M. Mwacharo, Zhang Yuan Pan, Jian Dong Wang, Qing Ma, G. L. Cao, Hui Jin, Liang Xiao, M. X. Chu
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568