bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/ijms21113870

Time-course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air
Cited by: 5
Author(s): Habibu Aliyu, Teresa Mohr, Don A. Cowan, Pieter De Maayer, Anke Neumann
Software Mentions: 3
Published: about 6 years ago

10.18632/aging.101985

Prediction of competing endogenous RNA coexpression network as prognostic markers in AML
Cited by: 38
Author(s): Jun Dan Wang, Hongsheng Zhou, Xi Xiang Tu, Yi He, Qi Fa Liu, Quentin Liu, Zi Long
Software Mentions: 3
Published: about 7 years ago

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: about 5 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: about 8 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: almost 10 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: almost 8 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/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: almost 9 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

10.1038/s41598-021-94386-z

An epigenetic GPI anchor defect impairs TLR4 signaling in the B cell transdifferentiation model for primary human monocytes BLaER1
Cited by: 3
Author(s): Julia Wegner, Thomas Zillinger, Thais Marina Schlee-Guimarães, Eva Bartok, Martin Schlee
Software Mentions: 3
Published: about 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: almost 7 years ago

10.1038/s41598-021-93142-7

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
Cited by: 3
Author(s): Zoltán Maróti, Dóra Tombácz, Norbert Moldován, Gábor Torma, Victoria A Jefferson, Zsolt Csabai, Gábor Gulyás, Ákos Dörmő, Miklós Boldogkői, Tibor Kalmár, Florencia Meyer, Zsolt Boldogköi
Software Mentions: 3
Published: about 5 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/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/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: over 10 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: almost 9 years ago

10.1186/1471-2105-12-480

GC-Content Normalization for RNA-Seq Data
Cited by: 656
Author(s): Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit
Software Mentions: 3
Published: over 14 years ago

10.1186/s12885-021-08283-9

A novel treatment strategy for lapatinib resistance in a subset of HER2-amplified gastric cancer
Cited by: 8
Author(s): Gang Ning, Qihui Zhu, Wonyoung Kang, Hamin Lee, Leigh Maher, Yun Suhk Suh, Michael Michaud, Mayerlin Silva, Jee Young Kwon, Chengsheng Zhang, Charles Lee
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-018-4627-8

Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse
Cited by: 44
Author(s): Paula Fagundes de Gouvêa, Aline Vianna Bernardi, Luís Eduardo Gerolamo, Emerson de Souza Santos, Diego Mauricio Riaño‐Pachón, Sérgio Akira Uyemura, Taísa Magnani Dinamarco
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-016-3009-3

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat
Cited by: 79
Author(s): Siyuan Zhan, Yao Dong, Wei Zhao, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-15-570

Comparing reference-based RNA-Seq mapping methods for non-human primate data
Cited by: 33
Author(s): Ashlee M. Benjamin, Marshall Nichols, Thomas W. Burke, Geoffrey S. Ginsburg, Joseph E. Lucas
Software Mentions: 3
Published: over 12 years ago

10.18632/aging.104088

An eleven metabolic gene signature-based prognostic model for clear cell renal cell carcinoma
Cited by: 11
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Shaogang Wang, Jihong Liu, Tao Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-15-406

Differential gene expression between functionally specialized polyps of the colonial hydrozoan Hydractinia symbiolongicarpus (Phylum Cnidaria)
Cited by: 43
Author(s): Steven M. Sanders, Mariya Shcheglovitova, Paulyn Cartwright
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-15-1031

Differential gene expression and alternative splicing in insect immune specificity
Cited by: 38
Author(s): Carolyn Riddell, Juan David Lobaton Garces, Sally Adams, Seth M. Barribeau, David Twell, Eamonn B. Mallon
Software Mentions: 3
Published: over 11 years ago

10.18632/aging.202493

Identification of hub genes associated with adult acute myeloid leukemia progression through weighted gene co-expression network analysis
Cited by: 4
Author(s): Ruiqi Zhu, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-90412-2

Axonopathy precedes cell death in ocular damage mediated by blast exposure
Cited by: 9
Author(s): Nickolas Boehme, Adam Hedberg-Buenz, Nicole Tatro, Michael Bielecki, William C Castonguay, Todd E. Scheetz, Michael G. Anderson, Laura M. Dutca
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07516-2

Mitochondrial genotype alters the impact of rapamycin on the transcriptional response to nutrients in Drosophila
Cited by: 7
Author(s): John Santiago, Joan M. Boylan, Faye A Lemieux, Philip A. Gruppuso, Jennifer Sanders, David M. Rand
Software Mentions: 3
Published: over 5 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: about 5 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

10.1186/s12864-020-6549-5

Transcriptome profiles of Quercus rubra responding to increased O3 stress
Cited by: 10
Author(s): Nourolah Soltani, Teo Best, Dantria Grace, Christen Nelms, Ketia L. Shumaker, Jeanne Romero‐Severson, Daniela Moses, Stephan C. Schuster, Margaret Staton, John E. Carlson, Kimberly D. Gwinn
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: almost 6 years ago

10.1038/s41598-021-89207-2

Cold-induction of afadin in brown fat supports its thermogenic capacity
Cited by: 2
Author(s): Morten Lundh, Ali Altıntaş, Marco Tozzi, Odile Fabre, Tao Ma, Farnaz Shamsi, Zachary Gerhart-Hines, Romain Barrès, Yu–Hua Tseng, Brice Emanuelli
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0218858

Transcriptomes of antigen presenting cells in human thymus
Cited by: 13
Author(s): Ingvild Gabrielsen, Hanna Helgeland, Helle Akselsen, Hans Christian Dalsbotten Aass, Arvind Sundaram, Isaac Snowhite, Alberto Pugliese, Siri Tennebø Flåm, Benedicte A. Lie
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-021-07584-4

Identification of co-expression network correlated with different periods of adipogenic and osteogenic differentiation of BMSCs by weighted gene co-expression network analysis (WGCNA)
Cited by: 13
Author(s): Yu Liu, Markus Tingart, Sophie Lecouturier, Jianzhang Li, Jörg Eschweiler
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07478-5

Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs
Cited by: 13
Author(s): Christine N Goldfarb, David J. Waxman
Software Mentions: 3
Published: over 5 years ago

10.3390/nu10081069

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice
Cited by: 28
Author(s): Simon Ghaly, Nadeem O. Kaakoush, Frances Lloyd, Lavinia Gordon, Cynthia Forest, Ian C. Lawrance, Prue H. Hart
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-020-6477-4

Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during 17alpha-methyltestosterone-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)
Cited by: 12
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-019-6327-4

Molecular subtyping improves prognostication of Stage 2 colorectal cancer
Cited by: 13
Author(s): Rachel Purcell, Sebastian Schmeier, Yee Chen Lau, John F. Pearson, F. A. Frizelle
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-021-08634-6

Overexpression of UBE2C in esophageal squamous cell carcinoma tissues and molecular analysis
Cited by: 6
Author(s): Rong Li, Xing-Feng Pang, Zhi‐Guang Huang, Lihua Yang, Zhigang Peng, Jie Ma, Rong‐Quan He
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-019-5548-x

iGEAK: an interactive gene expression analysis kit for seamless workflow using the R/shiny platform
Cited by: 35
Author(s): Kwangmin Choi, Nancy Ratner
Software Mentions: 3
Published: over 7 years ago

10.1111/1462-2920.14788

Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a <i>Zygnema</i> green algal mat from Svalbard (High Arctic)
Cited by: 25
Author(s): Martin Rippin, Martina Pichrtová, Erwann Arc, Ilse Kranner, Burkhard Becker, Andreas Holzinger
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-87955-9

Induced pluripotent stem cells from subjects with Lesch-Nyhan disease
Cited by: 5
Author(s): Diane Sutcliffe, Ashok R. Dinasarapu, Jasper E. Visser, Joery den Hoed, Fatemeh Seifar, Piyush Joshi, Irène Ceballos-Picot, Tejas Sardar, Ellen J. Hess, Yan V. Sun, Zhexing Wen, Michael E. Zwick, Hyder A. Jinnah
Software Mentions: 3
Published: over 5 years ago

10.3390/genes12040545

A Complex Gene Network Mediated by Ethylene Signal Transduction TFs Defines the Flower Induction and Differentiation in Olea europaea L.
Cited by: 2
Author(s): Amelia Salimonti, Ivano Forgione, Tiziana Maria Sirangelo, Guglielmo Puccio, Antonio Mauceri, Francesco Mercati, Francesco Sunseri, Fabrizio Carbone
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms21030861

Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways
Cited by: 21
Author(s): Yingdan Yuan, Bo Zhang, Xinggang Tang, Jinchi Zhang, Jie Lin
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-016-2897-6

Detection of high variability in gene expression from single-cell RNA-seq profiling
Cited by: 35
Author(s): Hung I Harry Chen, Yufang Jin, Yufei Huang, Yidong Chen
Software Mentions: 3
Published: about 10 years ago

10.3389/fimmu.2020.01033

Adjuvanting Allergen Extracts for Sublingual Immunotherapy: Calcitriol Downregulates CXCL8 Production in Primary Sublingual Epithelial Cells
Cited by: 3
Author(s): Michael Pelst, Clara Hôbart, Charlotte Wallaeys, H. de Rooster, Yannick Gansemans, Filip Van Nieuwerburgh, Bert Devriendt, Eric Cox
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-021-87278-9

Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
Cited by: 8
Author(s): Lingshu Han, Yuena Sun, Yue Cao, Peng Gao, Zijiao Quan, Yaqing Chang, Jun Ding
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07959-7

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens
Cited by: 7
Author(s): Arnar K. S. Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lundén, Karin Troell, Staffan G. Svärd, Robert Söderlund
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-86795-x

Distinct transcriptomic response to Newcastle disease virus infection during heat stress in chicken tracheal epithelial tissue
Cited by: 2
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 3
Published: over 5 years ago

10.1111/acel.12795

Differential aging-related changes in neurophysiology and gene expression in IB4-positive and IB4-negative nociceptive neurons
Cited by: 5
Author(s): Malgorzata A. Mis, Mark F. Rogers, Aaron R. Jeffries, Anna Wilbrey, Lubin Chen, Yang Yang, Sulayman D. Dib‐Hajj, Stephen G. Waxman, Edward B. Stevens, Andrew D. Randall
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-015-1254-5

Global transcriptomic profiling demonstrates induction of oxidative stress and of compensatory cellular stress responses in brown trout exposed to glyphosate and Roundup
Cited by: 85
Author(s): Tamsyn M. Uren Webster, Eduarda M. Santos
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-016-2565-x

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome
Cited by: 14
Author(s): Aimee Benjamin, Benjamin B. Green, B.A. Crooker, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-017-4296-z

Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews
Cited by: 19
Author(s): Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun, Ryohei Terauchi
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-016-2572-y

Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies
Cited by: 33
Author(s): Bas van Schooten, Chris D. Jiggins, Adriana D. Briscoe, Riccardo Papa
Software Mentions: 3
Published: over 10 years ago

10.1186/s13195-019-0558-0

APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain
Cited by: 36
Author(s): Iliya Lefterov, Cody M. Wolfe, Nicholas F. Fitz, Kyong Nyon Nam, Florent Letronne, Richard J. Biedrzycki, Julia Kofler, Xianlin Han, Jianing Wang, Jonathan Schug, Radosveta Koldamova
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-43075-z

A universal transcriptomic signature of age reveals the temporal scaling of Caenorhabditis elegans aging trajectories
Cited by: 35
Author(s): Andrei E. Tarkhov, Ramani Alla, Srinivas Ayyadevara, Mikhail A. Pyatnitskiy, L. I. Men’shikov, Robert J. Shmookler Reis, П. О. Федичев
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-16-S12-S7

A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology
Cited by: 3
Author(s): Buğra Özer, Uğur Sezerman
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-017-4016-8

Characterization of mechanisms underlying degradation of sclerotia of Sclerotinia sclerotiorum by Aspergillus aculeatus Asp-4 using a combined qRT-PCR and proteomic approach
Cited by: 15
Author(s): Xiaojia Hu, Lü Qin, Daniel P. Roberts, Dilip K. Lakshman, Yiqin Gong, Jude E. Maul, Lin Xie, Chang Yeon Yu, Yinshui Li, Lei Hu, Liao Xiang-sheng, Lixin Xing
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13195-021-00810-x

Comorbidity between Alzheimer’s disease and major depression: a behavioural and transcriptomic characterization study in mice
Cited by: 15
Author(s): Ana Martín‐Sánchez, Janet Piñero, Lara Nonell, Magdalena Arnal, Elena M. Ribé, Alejo J. Nevado‐Holgado, Simon Lovestone, Ferrán Sanz, Laura I. Furlong, Olga Valverde
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-06870-x

Shedding light on cashmere goat hair follicle biology: from morphology analyses to transcriptomic landascape
Cited by: 8
Author(s): Cristina Nocelli, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Francesca Mercati, Irene Pazzaglia, Samanta Mecocci, Marco Antonini, Carlo Renieri
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-43354-9

Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major
Cited by: 20
Author(s): Alberto Rastrojo, Laura Corvo, Rodrigo Lombraña, José Carlos Solana, Begoña Aguado, José Marı́a Requena
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43135-4

The transgenerational effects of oocyte mitochondrial supplementation
Cited by: 11
Author(s): Justin C. St. John, Yogeshwar Makanji, Jacqueline L. Johnson, Te-Sha Tsai, Simone Lagondar, Fleur Rodda, Xin Sun, Mulyoto Pangestu, Penny Chen, Peter Temple-Smith
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42680-2

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts
Cited by: 31
Author(s): Yuanhang Liu, Pritha Chanana, Jaime Davila, Xiaonan Hou, Valentina Zanfagnin, Cordelia D. McGehee, Ellen L. Goode, Eric C. Polley, Paul Haluska, S. John Weroha, Chen Wang
Software Mentions: 3
Published: over 7 years ago

10.7150/thno.46642

Precise and efficient silencing of mutant Kras<sup>G12D</sup> by CRISPR-CasRx controls pancreatic cancer progression
Cited by: 26
Author(s): Wang Jiang, Hao Li, Xiyu Liu, Jianping Zhang, Wuhu Zhang, Tianjiao Li, Liang Liu, Xianjun Yu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-021-08539-4

A methylation-based nomogram for predicting survival in patients with lung adenocarcinoma
Cited by: 5
Author(s): Xuelong Wang, Bin Zhou, Yuxin Xia, Jianjun Zuo, Yanchao Liu, Xin Bi, Xiong Luo, Chengwei Zhang
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-15-905

Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio)
Cited by: 54
Author(s): Ryan Y. Wong, Melissa M McLeod, John Godwin
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-019-5795-x

Transcriptional analysis of renal dopamine-mediated Na+ homeostasis response to environmental salinity stress in Scatophagus argus
Cited by: 10
Author(s): Maoliang Su, Jia Zhou, Zhengyu Duan, Junbin Zhang
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: over 6 years ago

10.1186/s12864-017-4374-2

A survey on cellular RNA editing activity in response to Candida albicans infections
Cited by: 3
Author(s): Yao‐Wei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Zhong Wu, Xuan Li, Chen Chen, Pei Hao
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

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: over 8 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-019-5502-y

Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes
Cited by: 2
Author(s): Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang, Zheng Guo
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39608-1

Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech
Cited by: 16
Author(s): Akiko Satake, Kazutaka Kawatsu, Kenjiro Teshima, Daisuke Kabeya, Qingmin Han
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-337

Transcriptome differences between two sister desert poplar species under salt stress
Cited by: 36
Author(s): Jian Zhang, Jiexiong Feng, Jing Lü, Yongzhi Yang, Xu Zhang, Dongshi Wan, Jianquan Liu
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-019-40754-9

Genome analysis of Pseudomonas syringae pv. actinidiae biovar 6, which produces the phytotoxins, phaseolotoxin and coronatine
Cited by: 34
Author(s): Takashi Fujikawa, Hiroyuki Sawada
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-6570-8

MicroRNA expression profile analysis in sperm reveals hsa-mir-191 as an auspicious omen of in vitro fertilization
Cited by: 37
Author(s): Hua Xu, Xin Wang, Zhikai Wang, Jianhui Li, Zhiming Xu, Maohua Miao, Guowu Chen, Xiang-Dong Lei, Jun Wu, Huijuan Shi, Ke Wang, Tiancheng Zhang, Xiaoxi Sun
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4521-4

Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species
Cited by: 20
Author(s): Yan Zhong, Xiaohui Zhang, Zong‐Ming Cheng
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-40016-8

Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas
Cited by: 10
Author(s): Greta Alì, Rossella Bruno, Anello Marcello Poma, Ornella Affinito, Antonella Monticelli, Paolo Piaggi, Sara Ricciardi, Marco Lucchi, Franca Melfi, Antonio Chella, Sérgio Cocozza, Gabriella Fontanini
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/6827057

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database
Cited by: 11
Author(s): Wenqing Zhou, Yongkui Pang, Yunmin Yao, Huiying Qiao
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms21010364

Global Gene Expression Analysis Identifies Age-Related Differences in Knee Joint Transcriptome during the Development of Post-Traumatic Osteoarthritis in Mice
Cited by: 25
Author(s): Aimy Sebastian, Deepa K. Murugesh, Melanie E. Mendez, Nicholas R. Hum, Naiomy Deliz Rios‐Arce, Jillian L. McCool, Blaine A. Christiansen, Gabriela G. Loots
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2018.00368

Integrated Analysis of a Competing Endogenous RNA Network Revealing a Prognostic Signature for Cervical Cancer
Cited by: 11
Author(s): Leilei Xia, Han Wang, Shengyun Cai, Xiaoling Su, Jizi Shen, Meng Qi, Yu Chen, Li Li, Jiuqiong Yan, Caihong Zhang, Man Xu
Software Mentions: 3
Published: almost 8 years ago

10.18632/aging.101578

High expression of the breast cancer susceptibility gene BRCA1 in long-lived termite kings
Cited by: 9
Author(s): Eisuke Tasaki, Yuki Mitaka, Tomonari Nozaki, Keiko Kobayashi, Kenji Matsuura, Yoshihito Iuchi
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-015-1955-9

The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy
Cited by: 51
Author(s): Katayoon Kasaian, Sam M. Wiseman, Blair Walker, Jacqueline E. Schein, Yongjun Zhao, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven J.M. Jones
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-37669-2

Molecular evidence for distinct modes of nutrient acquisition between visceral and neurotropic schistosomes of birds
Cited by: 10
Author(s): Roman Leontovyč, Neil D. Young, Pasi K. Korhonen, Ross S. Hall, Jana Bulantová, Veronika Jeřábková, Martin Kašný, Robin B. Gasser, Petr Horák
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-019-5556-x

Linear models enable powerful differential activity analysis in massively parallel reporter assays
Cited by: 272
Author(s): Leslie Myint, Dimitrios Avramopoulos, Loyal A. Goff, Kasper D. Hansen
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0036234

Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]
Cited by: 140
Author(s): Tao Xiang, Yinghong Gu, Haiyan Wang, Wen Zheng, Xiao Li, Chuan-Wu Zhao, Yizheng Zhang
Software Mentions: 3
Published: over 14 years ago

10.3390/ani9060313

Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs
Cited by: 11
Author(s): Xin Liu, Jianfei Gong, Ligang Wang, Xinhua Hou, Hongmei Gao, Yan Hua, Fuping Zhao, Longchao Zhang, Lixian Wang
Software Mentions: 3
Published: about 7 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: almost 6 years ago

10.1186/s12864-020-07151-3

Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production
Cited by: 3
Author(s): Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Yangji Cidan, Xiaoying Chen, Hui Jiang, Jincheng Zhong, Qiumei Ji
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5574-8

YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei
Cited by: 28
Author(s): Eva Hitzenhammer, Christoph Büschl, Michael Sulyok, Rainer Schuhmacher, Bernhard Kluger, Elisabeth Wischnitzki, Monika Schmoll
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms20236090

Disclosure of the Molecular Mechanism of Wheat Leaf Spot Disease Caused by Bipolaris sorokiniana through Comparative Transcriptome and Metabolomics Analysis
Cited by: 21
Author(s): Wei Ye, Taomei Liu, Weiyang Zhang, Saini Li, Muzi Zhu, Haohua Li, Yali Kong, Luoshan Xu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-016-2720-4

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Cited by: 27
Author(s): Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong, Paul Stothard, Joan K. Lunney, Graham Plastow, John C. S. Harding
Software Mentions: 3
Published: over 10 years ago

10.3390/ani10111944

Overexpression of PLIN1 Promotes Lipid Metabolism in Bovine Adipocytes
Cited by: 12
Author(s): Shijun Li, Sayed Haidar Abbas Raza, Chunping Zhao, Gong Chen, Zan Liu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-6223-y

Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process
Cited by: 23
Author(s): Rannyele Passos Ribeiro, Guillermo Ponz‐Segrelles, Christoph Bleidorn, M. Teresa Aguado
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-36866-3

Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway
Cited by: 12
Author(s): Jana Asselman, Emmanuel Van Acker, Maarten De Rijcke, Laurentijn Tilleman, Filip Van Nieuwerburgh, Jan Mees, Karel A.C. De Schamphelaere, Colin R. Janssen
Software Mentions: 3
Published: over 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568