bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12864-015-1626-x

Characterizing the neurotranscriptomic states in alternative stress coping styles
Cited by: 37
Author(s): Ryan Y. Wong, Melissa S. Lamm, John Godwin
Software Mentions: 3
Published: about 11 years ago

Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci
Cited by: 21
Author(s): Enoch Ng’oma, Marco Groth, Roberto Ripa, Matthias Platzer, Alessandro Cellerino
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-017-3592-y

A reference gene set for sex pheromone biosynthesis and degradation genes from the diamondback moth, Plutella xylostella, based on genome and transcriptome digital gene expression analyses
Cited by: 46
Author(s): Peng He, Yun‐Fei Zhang, Duan‐Yang Hong, Jun Wang, Xingliang Wang, Ling-Hua Zuo, Xianfu Tang, Weiming Xu, Ming He
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-16-S6-S2

FunPat: function-based pattern analysis on RNA-seq time series data
Cited by: 56
Author(s): Tiziana Sanavia, Francesca Finotello, Barbara Di Camillo
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-021-07655-6

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Cited by: 9
Author(s): Virginia Mwape, Fredrick M. Mobegi, Roshan Regmi, Toby E. Newman, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2995-5

RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.)
Cited by: 57
Author(s): Kazuma Suzuki, Tomohiro Suzuki, Takashi Nakatsuka, Hideo Dohra, Masumi Yamagishi, Kohei Matsuyama, Hideyuki Matsuura
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-016-3356-0

The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions
Cited by: 17
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Ekaterina Proshkina, А. С. Белый, Alexander Fedintsev, Svetlana Zhikrivetskaya, Zulfiya G. Guvatova, А. Ф. Садритдинова, А. В. Снежкина, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-5210-z

Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce
Cited by: 14
Author(s): Edita Jurak, Hitoshi Suzuki, Gijs van Erven, Julie-Anne Gandier, Pauline Wong, Kin Chan, Chi-Yip Ho, Yunchen Gong, Elisabeth R. M. Tillier, Marie‐Noëlle Rosso, Mirjam A. Kabel, Shingo Miyauchi, Emma R. Master
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-019-6340-7

The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers
Cited by: 11
Author(s): Xiaohong Ou, Shipeng Li, Peiran Liao, Xiuming Cui, Binglian Zheng, Ye Yang, Dahui Liu, Yun Zheng
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5618-0

Effect of paleopolyploidy and allopolyploidy on gene expression in banana
Cited by: 20
Author(s): Alberto Cenci, Yann Hueber, Yasmín Zorrilla-Fontanesi, Jelle van Wesemael, Ewaut Kissel, Marie Gislard, Julie Sardos, Rony Swennen, Nicolás Roux, Sébastien Carpentier, Mathieu Rouard
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-13-596

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells
Cited by: 1
Author(s): Maria Bro Kloster, Anders Ellern Bilgrau, María Rodrigo-Domingo, Kim Steve Bergkvist, Alexander Schmitz, Mads Sønderkær, Julie Støve Bødker, Steffen Falgreen, Mette Nyegaard, Hans Erik Johnsen, Kåre Lehmann Nielsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 3
Published: almost 14 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

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: almost 14 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: over 8 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: over 5 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: almost 11 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

10.1186/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: over 5 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: 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: 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: 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/s12870-018-1601-1

Transcriptomic signature reveals mechanism of flower bud distortion in witches’-broom disease of soybean (Glycine max)
Cited by: 10
Author(s): Sarika Jaiswal, P. V. Jadhav, Rahul Singh Jasrotia, P. B. Kale, Snehal Krishna Kad, M. P. Moharil, M. S. Dudhare, Jashminkumar Kheni, A. G. Deshmukh, S. S. Mane, R. S. Nandanwar, Suprasanna Penna, J. G. Manjaya, Mir Asif Iquebal, R. S. Tomar, Prashant G. Kawar, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-019-1902-z

Transcriptomic response in symptomless roots of clubroot infected kohlrabi (Brassica oleracea var. gongylodes) mirrors resistant plants
Cited by: 29
Author(s): Stefan Ciaghi, Arne Schwelm, Sigrid Neuhauser
Software Mentions: 3
Published: about 7 years ago

10.1186/1753-6561-5-S7-P20

Detection of genes involved in bud phenology in sessile oak (Quercus petraeaMatt. Liebl) combining digital expression analysis and Q-PCR
Cited by: 3
Author(s): S. Ueno, Christophe Klopp, Céline Noirot, Valérie Léger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12918-018-0637-z

Systems biology analysis reveals new insights into invasive lung cancer
Cited by: 2
Author(s): Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera, Mary Qu Yang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12917-017-1279-x

RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars
Cited by: 14
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Frøydis Deinboll Myromslien, Dag Inge Våge, Else‐Berit Stenseth, Teklu T Zeremichael, Eli Grindflek
Software Mentions: 3
Published: over 8 years ago

10.1186/1746-6148-10-146

Effect of photoperiod on the feline adipose transcriptome as assessed by RNA sequencing
Cited by: 5
Author(s): Akira Mori, Kelly Kappen, A. C. Dilger, Kelly S. Swanson
Software Mentions: 3
Published: about 12 years ago

10.1093/bioinformatics/btv425

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Cited by: 72
Author(s): Marek Gierliński, Christian Callebaut, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
Software Mentions: 3
Published: about 11 years ago

10.1093/bioinformatics/btv209

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test
Cited by: 39
Author(s): Emmanuel Dimont, Jiantao Shi, Rory Kirchner, Winston Hide
Software Mentions: 3
Published: over 11 years ago

10.1093/bioinformatics/btt650

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Cited by: 246
Author(s): Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chávez
Software Mentions: 3
Published: almost 13 years ago

10.1093/bioinformatics/btw585

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Cited by: 124
Author(s): Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
Software Mentions: 3
Published: almost 10 years ago

10.1242/bio.039917

Characterization and comparative analyses of transcriptomes of cloned and in vivo fertilized porcine pre-implantation embryos
Cited by: 7
Author(s): Xiaoyan He, Cheng Tan, Zicong Li, Chengfa Zhao, Junsong Shi, Rong Zhou, Xingwang Wang, Gelong Jiang, Guangyan Cai, Dewu Liu, Zhenfang Wu
Software Mentions: 3
Published: over 7 years ago

10.1242/bio.031245

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation
Cited by: 18
Author(s): Jian Xu, Benjamin L. Kidder
Software Mentions: 3
Published: over 8 years ago

10.1186/1480-9222-15-4

Next generation sequencing in cancer research and clinical application
Cited by: 104
Author(s): Derek Shyr, Qi Liu
Software Mentions: 3
Published: over 13 years ago

10.3390/biology10080726

Integrated Analysis of lncRNA and mRNA in Subcutaneous Adipose Tissue of Ningxiang Pig
Cited by: 7
Author(s): Yan Gong, Jun He, Biao Li, Yu Xiao, Qinghua Zeng, Kang Xu, Yehui Duan, Jun He, Haiming Ma
Software Mentions: 3
Published: about 5 years ago

10.3390/biology10090885

Metabolic Regulation of Sugar Assimilation for Lipid Production in Aspergillus oryzae BCC7051 through Comparative Transcriptome Perspective
Cited by: 5
Author(s): Tayvich Vorapreeda, Bhimabol Khongto, Chinae Thammarongtham, Tanawut Srisuk, Kobkul Laoteng
Software Mentions: 3
Published: almost 5 years ago

10.1155/2019/7376034

Identification of Potential Biomarkers and Survival Analysis for Head and Neck Squamous Cell Carcinoma Using Bioinformatics Strategy: A Study Based on TCGA and GEO Datasets
Cited by: 37
Author(s): Yujie Shen, Jinhui Liu, Liqing Zhang, Shikun Dong, Jiacheng Zhang, Yaqin Liu, Han Zhou, Wei Dong
Software Mentions: 3
Published: about 7 years ago

10.1155/2017/2421459

Prediction and Validation of Hub Genes Associated with Colorectal Cancer by Integrating PPI Network and Gene Expression Data
Cited by: 19
Author(s): Yong Xiong, Wenxian You, Rong Wang, Linglong Peng, Zhongxue Fu
Software Mentions: 3
Published: over 9 years ago

10.1155/2021/5589101

Weighted Gene Coexpression Network Analysis to Construct Competitive Endogenous RNA Network in Chromogenic Renal Cell Carcinoma
Cited by: 1
Author(s): Yon-Bo Chen, Liang Gao, Jindong Zhang, Jiang Guo, Ping-Hong You, Liang-you Tang, Ying-Wen Liu
Software Mentions: 3
Published: about 5 years ago

10.3390/md19080429

RKC-B1 Blocks Activation of NF-κB and NLRP3 Signaling Pathways to Suppress Neuroinflammation in LPS-Stimulated Mice
Cited by: 3
Author(s): Man Liu, Yinglin Yang, Shanshan Zhang, Dong-Ni Liu, Lian-Hua Fang, Guanhua Du, Yue-Hua Wang
Software Mentions: 3
Published: about 5 years ago

10.3390/medicines6030071

Effect of Sulforaphane and 5-Aza-2’-Deoxycytidine on Melanoma Cell Growth
Cited by: 5
Author(s): Tung-Chin Chiang, Brian Koss, L. Joseph Su, Charity L. Washam, Stephanie D. Byrum, Aaron J. Storey, Alan J. Tackett
Software Mentions: 3
Published: about 7 years ago

10.1590/0074-02760190378

Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium
Cited by: 3
Author(s): Thaís Cunha de Sousa Cardoso, Carlos Bruno de Araújo, Laysa Gomes Portilho, Luiz Guilherme Alves Mendes, Tamires Caixeta Alves, Gustavo Caetano Silva, Thales Henrique Cherubino Ribeiro, Peterson Elizandro Gandolfi, Enyara Rezende Morais, Laurence Rodrigues do Amaral, Matheus de Souza Gomes
Software Mentions: 3
Published: over 6 years ago

10.3390/metabo11060369

Plant Transcriptome Reprograming and Bacterial Extracellular Metabolites Underlying Tomato Drought Resistance Triggered by a Beneficial Soil Bacteria
Cited by: 17
Author(s): Rafael J. L. Morcillo, Juan Ignacio Vílchez, Song Zhang, Rajesh Kaushal, Danxia He, Hailing Zi, Renyi Liu, Karsten Niehaus, Avtar K. Handa, Huiming Zhang
Software Mentions: 3
Published: about 5 years ago

10.1099/mgen.0.000104

Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
Cited by: 16
Author(s): Kelly C. Rice, Matthew E. Turner, O’neshia V. Carney, Tongjun Gu, Sang‐Joon Ahn
Software Mentions: 3
Published: over 9 years ago

10.1002/mbo3.565

Transcriptome analysis and anaerobic C4‐dicarboxylate transport in Actinobacillus succinogenes
Cited by: 8
Author(s): Mi Na Rhie, Byeonghyeok Park, Hyeok Jin Ko, In Geol Choi, Ok Bin Kim
Software Mentions: 3
Published: over 8 years ago

10.1002/mbo3.494

wblE2 transcription factor in Streptomyces griseus S4‐7 plays an important role in plant protection
Cited by: 7
Author(s): Hyun Ji Cho, Young Chul Kwon, Da-Ran Kim, Gyeongjun Cho, Seong Won Hong, Dong-Won Bae, Youn‐Sig Kwak
Software Mentions: 3
Published: over 9 years ago

10.1186/s40168-021-01049-2

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field
Cited by: 41
Author(s): Selma Cadot, Hang Guan, Moritz Bigalke, Jean‐Claude Walser, Georg Jander, Matthias Erb, Marcel G. A. van der Heijden, Klaus Schlaeppi
Software Mentions: 3
Published: over 5 years ago

10.1186/s40168-021-01117-7

Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Cited by: 23
Author(s): Wisnu Adi Wicaksono, Tomislav Cernava, Christian Berg, Gabriele Berg
Software Mentions: 3
Published: about 5 years ago

10.3390/microorganisms9020452

Supernatants of Bifidobacterium longum and Lactobacillus plantarum Strains Exhibited Antioxidative Effects on A7R5 Cells
Cited by: 11
Author(s): Yusheng Wang, Zhifeng Fang, Qixiao Zhai, Shumao Cui, Jianxin Zhao, Hao Zhang, Wenwei Liu
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms7040096

Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii
Cited by: 27
Author(s): Senjie Lin, Liying Yu, Huan Zhang
Software Mentions: 3
Published: over 7 years ago

10.3390/microorganisms8020244

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
Cited by: 5
Author(s): Ohana Y.A. Costa, Marcelo M. Zerillo, Daniela Zühlke, Anna M. Kielak, Agata Pijl, Katharina Riedel, Eiko E. Kuramae
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms8040609

Incidental Prophylactic Appendectomy Is Associated with a Profound Microbial Dysbiosis in the Long-Term
Cited by: 13
Author(s): Lidia Sánchez-Alcoholado, José Carlos Fernández‐García, Carolina Gutiérrez-Repiso, María Rosa Bernal-López, Luis Ocaña-Wilhelmi, Eduardo Garcı́a-Fuentes, Isabel Moreno-Indias, Francisco J. Tinahones
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms8071012

Transcriptomic and Ultrastructural Signatures of K+-Induced Aggregation in Phytophthora parasitica Zoospores
Cited by: 7
Author(s): Ilaria Bassani, Corinne Rancurel, Sophie Pagnotta, François Orange, Nicolas Pons, Kévin Lebrigand, Franck Panabières, Laurent Counillon, Xavier Noblin, Eric Galiana
Software Mentions: 3
Published: about 6 years ago

10.3390/microorganisms8122007

Impact of Helicobacter pylori Infection and Its Major Virulence Factor CagA on DNA Damage Repair
Cited by: 7
Author(s): Eleftherios Kontizas, Spyros Tastsoglou, Timokratis Karamitros, Yiannis Karayiannis, Panagoula Κollia, Artemis G. Hatzigeorgiou, Dionyssios N. Sgouras
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms9020370

Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model
Cited by: 12
Author(s): Hyunjoon Park, Soyoung Yeo, Seok‐Won Kang, Chul Sung Huh
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms8111793

Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model
Cited by: 10
Author(s): Jinxin Zhao, Yan Zhu, Ji-Ru Han, Yu Wei Lin, Michael Aichem, Jiping Wang, Ke Chen, Tony Velkov, Falk Schreiber, Jian Li
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13229-019-0285-1

RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation
Cited by: 13
Author(s): Ayden Saffari, Matt Arno, Eric Nasser, Angelica Ronald, Chloe Wong, Leonard C Schalkwyk, Jonathan Mill, Frank Dudbridge, Emma L. Meaburn
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13229-018-0219-3

Role of miR-146a in neural stem cell differentiation and neural lineage determination: relevance for neurodevelopmental disorders
Cited by: 57
Author(s): Lam Son Nguyen, Julien Fregeac, Christine Bôle‐Feysot, Nicolas Cagnard, Anand M. Iyer, Jasper J. Anink, Eleonora Aronica, Olivier Alibeu, Patrick Nitschké, Laurence Colleaux
Software Mentions: 3
Published: about 8 years ago

10.1186/s13229-020-0318-9

Transcriptomics of Gabra4 knockout mice reveals common NMDAR pathways underlying autism, memory, and epilepsy
Cited by: 19
Author(s): Cui-Xia Fan, Yue Gao, Guanmei Liang, Lang Huang, Jing Wang, Xiaoxue Yang, Yi‐Wu Shi, Ursula C. Dräger, Ming Zhong, Tianming Gao, Xinping Yang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13229-019-0311-3

TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling
Cited by: 27
Author(s): Pauline Martín, Vilas Wagh, Surya A. Reis, Serkan Erdin, Roberta L. Beauchamp, Ghalib Shaikh, Michael E. Talkowski, Elizabeth A. Thiele, Steven D. Sheridan, Stephen J. Haggarty, Vijaya Ramesh
Software Mentions: 3
Published: over 6 years ago

10.1093/molbev/msy217

Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes
Cited by: 24
Author(s): Darren J. Parker, Jens Bast, Kirsten M. Jalvingh, Zoé Dumas, Marc Robinson‐Rechavi, Tanja Schwander
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13041-020-00702-5

Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq
Cited by: 17
Author(s): Lisa C. Lyons, Snehajyoti Chatterjee, Yann Vanrobaeys, Marie E. Gaine, Ted Abel
Software Mentions: 3
Published: over 5 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: almost 6 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: almost 9 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: over 5 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

10.1152/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: almost 11 years ago

10.14814/phy2.13019

Effect of energy restriction and physical exercise intervention on phenotypic flexibility as examined by transcriptomics analyses of mRNA from adipose tissue and whole body magnetic resonance imaging
Cited by: 19
Author(s): Sindre Lee, Frode Norheim, Torgrim M. Langleite, Hans Jørgen Noreng, Trygve H. Storås, Lydia A. Afman, Gary Frost, Jimmy D. Bell, E. Louise Thomas, Kristoffer Jensen Kolnes, Daniel S. Tangen, Hans Kristian Stadheim, Gregor D. Gilfillan, Hanne Løvdal Gulseth, Kåre I. Birkeland, Jørgen Jensen, Christian A. Drevon, Torgeir Holen
Software Mentions: 3
Published: almost 10 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: about 6 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

10.1111/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: almost 8 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: almost 7 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: over 7 years ago

10.1002/pld3.240

Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater
Cited by: 10
Author(s): Rejbana Alam, Maureen Hummel, Euson Yeung, Anna M. Locke, John Carlos I. Ignacio, Miriam D. Baltazar, Zhenyu Jia, Ismail Am, Endang M. Septiningsih, Julia Bailey‐Serres
Software Mentions: 3
Published: about 6 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: over 6 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

10.3390/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

10.3390/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

10.3390/plants9010060

Analysis of Small RNAs of Barley Genotypes Associated with Resistance to Barley Yellow Dwarf Virus
Cited by: 8
Author(s): Jana Jarošová, Kundan Singh, J. Chrpová, Jiban Kumar Kundu
Software Mentions: 3
Published: over 6 years ago

10.3390/plants10071407

The Modification of Plant Cell Wall Polysaccharides in Potato Plants during Pectobacterium atrosepticum-Caused Infection
Cited by: 7
Author(s): Vladimir Gorshkov, Ivan Tsers, Bakhtiyar Islamov, Marina Ageeva, Natalia Gogoleva, Polina Mikshina, Olga Parfirova, Olga Gogoleva, Olga Petrova, Т. А. Горшкова, Alexander A. Kamnev
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pbio.1002500

Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia
Cited by: 50
Author(s): Xiaozhu Wang, John H. Werren, Andrew G. Clark
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pbio.2000731

Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway
Cited by: 35
Author(s): Clare E. Weeden, Yunshun Chen, Bettzy Stephen, Yifang Hu, Georg Ramm, Kate D. Sutherland, Gordon K. Smyth, Marie Liesse Asselin-Labat
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pbio.2002887

Systematic analysis of transcription start sites in avian development
Cited by: 33
Author(s): Marina Lizio, Ruslan Deviatiiarov, Hiroki Nagai, Laura Galán, Peter Arner, Masayoshi Itoh, Timo Lassmann, Takeya Kasukawa, Akira Hasegawa, María A. Ros, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Hideya Kawaji, Oleg Gusev, Guojun Sheng
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pbio.3000225

Tubulin mRNA stability is sensitive to change in microtubule dynamics caused by multiple physiological and toxic cues
Cited by: 43
Author(s): Ivana Gasic, Sarah A. Boswell, Timothy J. Mitchison
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1003501

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
Cited by: 75
Author(s): Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pcbi.1002968

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
Cited by: 199
Author(s): Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, J Stamatoyannopoulos, Jason Ernst, M Kellis, Bing Ren
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pcbi.1006088

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Cited by: 21
Author(s): Matthew E. MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pntd.0006410

Sialome diversity of ticks revealed by RNAseq of single tick salivary glands
Cited by: 61
Author(s): Jan Perner, Sára Kropáčková, Petr Kopáček, José M. C. Ribeiro
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pntd.0009797

A gene expression panel for estimating age in males and females of the sleeping sickness vector Glossina morsitans
Cited by: 1
Author(s): Eric R. Lucas, Alistair C. Darby, Stephen J. Torr, Martin J. Donnelly
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0161987

De Novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation Using Contrasting Genotypes
Cited by: 25
Author(s): Jeongsukhyeon Han, Senthil Kumar Thamilarasan, Sathishkumar Natarajan, Jong-In Park, Mi-Young Chung, Ill–Sup Nou
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0242970

Chronic IL-1 exposure drives LNCaP cells to evolve androgen and AR independence
Cited by: 8
Author(s): Haley Dahl, Mohammed Kanchwala, Shayna E. Thomas‐Jardin, Amrit Sandhu, Preethi Kanumuri, Afshan F. Nawas, Chao Xing, Chenchu Lin, Daniel E. Frigo, Nikkí A. Delk
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0174236

Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors
Cited by: 7
Author(s): Niels van Tol, Martijn Rolloos, Johan E. Pinas, Christiaan V. Henkel, Dieuwertje Augustijn, Paul J. J. Hooykaas, Bert J. van der Zaal
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0091041

Variation in RNA-Seq Transcriptome Profiles of Peripheral Whole Blood from Healthy Individuals with and without Globin Depletion
Cited by: 70
Author(s): Heesun Shin, Casey P. Shannon, Nick Fishbane, Jian Ruan, Mi Zhou, Robert Balshaw, J. Wilson-McManus, Raymond T. Ng, Bruce M. McManus, Scott J. Tebbutt
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0230249

Proteomic changes during experimental de- and remyelination in the corpus callosum
Cited by: 6
Author(s): Gabor T. Szilagyi, Arkadiusz Nawrocki, Krisztián Erős, J. Schmidt, Katalin Fekete, Maria L. Elkjaer, K. H. Hyrlov, Martin R. Larsen, Zsolt Illés, Ferenc Gallyas
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0162402

Comprehensive Transcriptome Analyses of the Fructose-Fed Syrian Golden Hamster Liver Provides Novel Insights into Lipid Metabolism
Cited by: 8
Author(s): Ziyang Li, Chaoliang Xiong, Suo Mo, Haiying Tian, Mengqian Yu, Tingting Mao, Qian Chen, Huai‐Rong Luo, Quan-Zhen Li, Jianxin Lü, Yi Zhao, Wei Li
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0170779

Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver
Cited by: 50
Author(s): I‐Hsuan Lin, Yifan Chen, Ming Hsu
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0184003

Honokiol induces superoxide production by targeting mitochondrial respiratory chain complex I in Candida albicans
Cited by: 38
Author(s): Libo Sun, Kai Liao, Dayong Wang
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0234029

An investigation into the beneficial effects and molecular mechanisms of humic acid on foxtail millet under drought conditions
Cited by: 8
Author(s): Jie Shen, Meijun Guo, Yuguo Wang, Xiangyang Yuan, Shuqi Dong, Xi-e Song, Peng Guo
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0180842

RNA sequencing to determine the contribution of kinase receptor transactivation to G protein coupled receptor signalling in vascular smooth muscle cells
Cited by: 15
Author(s): Danielle Kamato, Venkata Vijayanand Bhaskarala, Nitin Mantri, Tae Gyu Oh, Dora Ling, Reearna Janke, Wenhua Zheng, Peter J. Little, Narin Osman
Software Mentions: 3
Published: about 9 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568