bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fimmu.2020.582358

Transcriptional Memory-Like Imprints and Enhanced Functional Activity in γδ T Cells Following Resolution of Malaria Infection
Cited by: 7
Author(s): Rasika Kumarasingha, Lisa J Ioannidis, Waruni Abeysekera, Stephanie I Studniberg, Dinidu S Wijesurendra, Ramin Mazhari, Daniel P. Poole, Ivo Müeller, Louis Schofield, Diana S. Hansen, Emily M. Eriksson
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2019.01960

Differential Impact of Co-expressed SP-A1/SP-A2 Protein on AM miRNome; Sex Differences
Cited by: 16
Author(s): Nithyananda Thorenoor, Yuka Imamura Kawasawa, Chintan K. Gandhi, Xuesheng Zhang, Joanna Floros
Software Mentions: 3
Published: about 7 years ago

10.1186/s12860-020-00331-9

Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages
Cited by: 18
Author(s): Sabin Bhandari, Ruomei Li, Jaione Simón-Santamaría, Peter McCourt, Steinar Johansen, Bård Smedsrød, Iñigo Martínez-Zubiaurre, Karen Kristine Sørensen
Software Mentions: 3
Published: almost 6 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

10.1186/s12870-016-0775-7

B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)
Cited by: 53
Author(s): Wei Huang, Yan Du, Xin Zhao, Weiwei Jin
Software Mentions: 3
Published: over 10 years ago

10.3389/fimmu.2021.678699

The Zinc Nutritional Immunity of Epinephelus coioides Contributes to the Importance of znuC During Pseudomonas plecoglossicida Infection
Cited by: 12
Author(s): Lixing Huang, Yanfei Zuo, Yingxue Qin, Lingmin Zhao, Mao Lin, Qingpi Yan
Software Mentions: 3
Published: over 5 years ago

10.1038/s41420-021-00588-9

Integrated analysis of high-throughput sequencing data reveals the key role of LINC00467 in the invasion and metastasis of testicular germ cell tumors
Cited by: 21
Author(s): Hao Bo, Fang Zhu, Zhizhong Liu, Qi Deng, Guangmin Liu, Ruixue Li, Wenbing Zhu, Yue‐Qiu Tan, Gang Liu, Jingyu Fan, Liqing Fan
Software Mentions: 3
Published: about 5 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/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

10.3389/fimmu.2021.656846

Expression of Senescence Marker TIGIT Identifies Polyfunctional Donor-Reactive CD4+ T Cells Preferentially Lost After Kidney Transplantation
Cited by: 12
Author(s): Amy C. J. van der List, Nicolle H.R. Litjens, Mariska Klepper, M. Betjes
Software Mentions: 3
Published: over 5 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

10.3389/fimmu.2018.00879

Cord Blood CD8+ T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner
Cited by: 11
Author(s): Yuxia Zhang, Jovana Maksimovic, Bing Huang, David P. De Souza, Gaetano Naselli, Huan Chen, Li Zhang, Kai Weng, Hanquan Liang, Yanhui Xu, John M. Wentworth, Nicholas D. Huntington, Alicia Oshlack, Sitang Gong, Axel Kallies, Peter Vuillermin, Min Yang, Leonard C. Harrison
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2407-14-880

Deep Sequencing the microRNA profile in rhabdomyosarcoma reveals down-regulation of miR-378 family members
Cited by: 55
Author(s): Francesca Megiorni, Samantha Cialfi, Heather P. McDowell, Armando Felsani, Simona Camero, Alessandro Guffanti, Barry Pizer, Aldo Clerico, Alessandra De Grazia, Antonio Pizzuti, Anna Moles, Carlo Dominici
Software Mentions: 3
Published: almost 12 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/s12885-018-4594-0

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples
Cited by: 13
Author(s): George Vasmatzis, Xue Wang, James B. Smadbeck, Stephen J. Murphy, Katherine B. Geiersbach, Sarah H. Johnson, Athanasios Gaitatzes, Yan W. Asmann, Farhad Kosari, Mitesh J. Borad, Daniel J. Serie, Sarah A. McLaughlin, Jennifer M. Kachergus, Brian M. Necela, E. Aubrey Thompson
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.26845

Unfolded protein response transducer IRE1-mediated signaling independent of XBP1 mRNA splicing is not required for growth and development of medaka fish
Cited by: 34
Author(s): Tokiro Ishikawa, Makoto Kashima, Atsushi J. Nagano, Tomoko Ishikawa-Fujiwara, Yasuhiro Kamei, Tomoki Todo, Kazutoshi Mori
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.43352

Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF
Cited by: 39
Author(s): Manju Sharma, Anuj Srivastava, Heather Fairfield, David E. Bergstrom, William F. Flynn, Robert E. Braun
Software Mentions: 3
Published: about 7 years ago

10.1038/celldisc.2016.10

Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing
Cited by: 161
Author(s): Wenqiang Liu, Xiaoyu Liu, Chenfei Wang, Yawei Gao, Rui Gao, Xiaochen Kou, Yanhong Zhao, Jingyi Li, You Wu, Wenchao Xiu, Su Wang, Jie Yin, Wei Liu, Tao Cai, Hong Wang, Yong Zhang, Shaorong Gao
Software Mentions: 3
Published: about 10 years ago

10.1038/celldisc.2016.41

NANOG reprograms prostate cancer cells to castration resistance via dynamically repressing and engaging the AR/FOXA1 signaling axis
Cited by: 40
Author(s): Collene Jeter, Bigang Liu, Yue Lu, Hsueh-Ping Chao, Dingxiao Zhang, Xin Liu, Xin Chen, Qiuhui Li, Kiera Rycaj, Tammy Calhoun-Davis, Li Yan, Qiang Hu, Jianmin Wang, Jianjun Shen, Song Liu, Dean G. Tang
Software Mentions: 3
Published: almost 10 years ago

10.18632/oncotarget.27112

Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells
Cited by: 2
Author(s): Piyush More, Ute Goedtel-Armbrust, Viral Shah, Marianne Mathaes, Thomas Kindler, Miguel A. Andrade‐Navarro, Leszek Wojnowski
Software Mentions: 3
Published: almost 7 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

10.1016/j.chom.2019.10.004

An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling
Cited by: 41
Author(s): Alessandro Pagliuso, Tristan Tham, Eric Allemand, Stevens Robertin, Bruno Dupuy, Quentin Bertrand, Christophe Bécavin, Mikael Koutero, Valérie Najburg, Marie–Anne Nahori, Frédéric Tangy, Fabrizia Stavru, Sergey Bessonov, Andréa Dessen, Christian Muchardt, Alice Lebreton, Anastassia V. Komarova, Pascale Cossart
Software Mentions: 3
Published: over 6 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

10.1186/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/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

10.1016/j.jcmgh.2021.05.020

Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation
Cited by: 11
Author(s): Gaurav V. Sarode, Kari Neier, Noreene M. Shibata, Yuanjun Shen, Dmitry A. Goncharov, Elena A. Goncharova, Tagreed A. Mazi, Nikhil Joshi, Matthew L. Settles, Janine M. LaSalle, Valentina Medici
Software Mentions: 3
Published: over 5 years ago

10.3389/fendo.2018.00245

Drosophila Insulin-Like Peptides DILP2 and DILP5 Differentially Stimulate Cell Signaling and Glycogen Phosphorylase to Regulate Longevity
Cited by: 65
Author(s): Stephanie Post, Galina Karashchuk, John D. Wade, Waseem Sajid, Pierre De Meyts, Marc Tatar
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.49882

Obesity-linked suppression of membrane-bound O-acyltransferase 7 (MBOAT7) drives non-alcoholic fatty liver disease
Cited by: 84
Author(s): Robert N Helsley, Venkateshwari Varadharajan, Amanda Brown, Anthony D. Gromovsky, Rebecca C. Schugar, Iyappan Ramachandiran, Kevin Fung, Mohammad Nasser Kabbany, Rakhee Banerjee, Chase Neumann, Chelsea Finney, Preeti Pathak, Danny Orabi, Lucas J Osborn, William Massey, Renliang Zhang, Anagha Kadam, Brian E. Sansbury, Calvin Pan, Jessica Sacks, Richard G. Lee, Rosanne M. Crooke, Mark Graham, Madeleine E. Lemieux, Valentin Gogonea, John P. Kirwan, Daniela S. Allende, Mete Civelek, Paul L. Fox, Lawrence L. Rudel, Aldons J. Lusis, Matthew Spite
Software Mentions: 3
Published: almost 7 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

10.3390/biomedicines9060629

Activin-A Induces Early Differential Gene Expression Exclusively in Periodontal Ligament Fibroblasts from Fibrodysplasia Ossificans Progressiva Patients
Cited by: 8
Author(s): Ton Schoenmaker, Michal Mokrý, Dimitra Micha, Coen Netelenbos, Nathalie Bravenboer, Marjolijn Gilijamse, Elisabeth M. W. Eekhoff, Teun J. de Vries
Software Mentions: 3
Published: about 5 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: over 10 years ago

10.1186/s12870-021-03009-2

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)
Cited by: 8
Author(s): Guozhong Zhu, Shuang Hou, Xiaohui Song, Xing Wang, Wei Wang, Quanjia Chen, Wangzhen Guo
Software Mentions: 3
Published: about 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

10.3389/fcimb.2020.00082

Francisella novicida Two-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production
Cited by: 6
Author(s): Scott N. Dean, Morgan E. Milton, John Cavanagh, Monique L. van Hoek
Software Mentions: 3
Published: over 6 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

10.1038/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

10.3389/fcimb.2019.00254

Probiotic Supplementation During Human Pregnancy Affects the Gut Microbiota and Immune Status
Cited by: 19
Author(s): Yuyi Chen, Zhe Li, Kian Deng Tye, Huijuan Luo, Xiaomei Tang, Yu-Chieh Liao, Dongju Wang, Juan Zhou, Ping Yang, Yimi Li, Yingbing Su, Xiaomin Xiao
Software Mentions: 3
Published: about 7 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

10.1016/j.celrep.2015.12.012

NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR
Cited by: 27
Author(s): Kobe Yuen, Baoshan Xu, Ian D. Krantz, Jennifer L. Gerton
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-020-02506-0

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods
Cited by: 25
Author(s): Néstor Kippes, Carl VanGessel, James Hamilton, Ani Akpinar, Hikmet Budak, Jorge Dubcovsky, Stephen Pearce
Software Mentions: 3
Published: about 6 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

10.7554/eLife.47990

Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity
Cited by: 40
Author(s): Kasparas Petkevicius, Samuel Virtue, Guillaume Bidault, Benjamin Jenkins, Cankut Çubuk, Cecilia Morgantini, Myriam Aouadi, Joaquín Dopazo, Mireille J. Serlie, Albert Koulman, António Vidal-Puig
Software Mentions: 3
Published: about 7 years ago

10.1016/j.celrep.2019.04.113

Molecular Logic of Spinocerebellar Tract Neuron Diversity and Connectivity
Cited by: 33
Author(s): Min Won Baek, Vilas Menon, Thomas M. Jessell, Adam W. Hantman, Jeremy S. Dasen
Software Mentions: 3
Published: over 7 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: almost 7 years ago

10.7554/eLife.59659

Def6 regulates endogenous type-I interferon responses in osteoblasts and suppresses osteogenesis
Cited by: 9
Author(s): Zhonghao Deng, Courtney Ng, Kenzo Inoue, Ziyu Chen, Yuhan Xia, Xiaoyu Hu, Matthew B. Greenblatt, Alessandra B. Pernis, Baohong Zhao
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.102393

Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma
Cited by: 12
Author(s): Mingdong Li, Shengrong Long, Jinqu Hu, Zan Wang, Chao Geng, Shaowu Ou
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.celrep.2020.108453

The Microfluidic Environment Reveals a Hidden Role of Self-Organizing Extracellular Matrix in Hepatic Commitment and Organoid Formation of hiPSCs
Cited by: 23
Author(s): Federica Michielin, Giovanni Giuseppe Giobbe, Camilla Luni, Qianjiang Hu, Ida Maroni, Michael Orford, Anna Manfredi, Lucio Di Filippo, Anna L. David, Davide Cacchiarelli, Paolo De Coppi, Simon Eaton, Nicola Elvassore
Software Mentions: 3
Published: over 5 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/s12864-017-3743-1

Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python
Cited by: 30
Author(s): Audra L. Andrew, Blair W. Perry, Daren C. Card, Drew R. Schield, Robert P. Ruggiero, Suzanne E. McGaugh, Amit Choudhary, Stephen M. Secor, Todd A. Castoe
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.17002

A functional genomics screen in planarians reveals regulators of whole-brain regeneration
Cited by: 52
Author(s): Rachel H. Roberts-Galbraith, John L. Brubacher, Phillip A. Newmark
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12885-021-08229-1

Identification of NTRK3 as a potential prognostic biomarker associated with tumor mutation burden and immune infiltration in bladder cancer
Cited by: 13
Author(s): Zhao Zhang, Yizhi Yu, Pengfei Zhang, Guofeng Ma, Mingxin Zhang, Ye Liang, Wei Jiao, Haitao Niu
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.26300

Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
Cited by: 52
Author(s): Oliver Mrowczynski, A. Madhankumar, Jeffrey M. Sundstrom, Yuanjun Zhao, Yuka Imamura Kawasawa, Becky Slagle‐Webb, Christine Mau, Russell Payne, Elias Rizk, Brad E. Zacharia, James R. Connor
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-018-4651-8

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry
Cited by: 11
Author(s): Yang Jin, Rolf Erik Olsen, Mari‐Ann Östensen, Gareth Benjamin Gillard, Sven Arild Korsvoll, Nina Santi, Arne B. Gjuvsland, Jon Olav Vik, Jacob Torgersen, Simen Rød Sandve, Yngvar Ôlsen
Software Mentions: 3
Published: over 8 years ago

10.1016/j.celrep.2015.11.040

Context-Specific Effects of TGF-β/SMAD3 in Cancer Are Modulated by the Epigenome
Cited by: 37
Author(s): Ana Tufegdžić Vidaković, Oscar M. Rueda, Stephin J. Vervoort, Ankita Batra, Mae A. Goldgraben, Santiago Uribe-Lewis, Wendy Greenwood, Paul J. Coffer, Alejandra Bruna, Carlos Caldas
Software Mentions: 3
Published: over 10 years ago

10.3389/fcell.2021.671211

Identification of ZNF26 as a Prognostic Biomarker in Colorectal Cancer by an Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Jiaqi Liu, Yimin Li, Yaqi Gan, Qing Xiao, Ruotong Tian, Guang Shu, Gang Yin
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2021.615098

Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation
Cited by: 2
Author(s): Chih-Yi Yang, Rita Jui-Hsien Lu, Ming-Kang Lee, Felix Shih-Hsian Hsiao, Ya-Ping Yen, Chi‐Feng Cheng, Pu-Sheng Hsu, Yi-Tzang Tsai, Shih‐Kuo Chen, I-Hsuan Liu, Pao‐Yang Chen, Shau-Ping Lin
Software Mentions: 3
Published: over 5 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

10.7554/eLife.08298

Starvation promotes concerted modulation of appetitive olfactory behavior via parallel neuromodulatory circuits
Cited by: 142
Author(s): Kang I. Ko, Cory M. Root, Scott A. Lindsay, Orel A. Zaninovich, Andrew K. Shepherd, Steven A. Wasserman, Susy M. Kim, Jing W. Wang
Software Mentions: 3
Published: about 11 years ago

10.1089/cell.2018.0008

Porcine Fetal-Derived Fibroblasts Alter Gene Expression and Mitochondria to Compensate for Hypoxic Stress During Culture
Cited by: 4
Author(s): Bethany R. Mordhorst, Shaun Murphy, Martin Schauflinger, Shirley Rojas-Salazar, Tieming Ji, Susanta K. Behura, Kevin D. Wells, Jonathan A. Green, Randall S. Prather
Software Mentions: 3
Published: about 8 years ago

10.1038/s41422-018-0103-x

Expansion and differentiation of human hepatocyte-derived liver progenitor-like cells and their use for the study of hepatotropic pathogens
Cited by: 105
Author(s): Gongbo Fu, Weijian Huang, Min Zeng, Zhou Xu, Hongping Wu, Changcheng Liu, Han Wu, Jun Weng, Hong‐Dan Zhang, Yongchao Cai, Charles Ashton, Min Ding, Dan Tang, Baohua Zhang, Yi Gao, Weifeng Yu, Bo Zhai, Zhiying He, Hongyang Wang, He‐Xin Yan
Software Mentions: 3
Published: almost 8 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

10.1038/cr.2017.124

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
Cited by: 152
Author(s): Changsong Zou, A Chen, Li Xiao, H.-A. Müller, Peter Ache, Georg Haberer, M Zhang, Jia Wei, Ping Deng, Ru Huang, Daniel Lang, Li Feng, Dong Zhan, Xiaoyong Wu, H Zhang, Jennifer Böhm, Ruirui Liu, Lana Shabala, Rainer Hedrich, J-K Zhu
Software Mentions: 3
Published: almost 9 years ago

10.3389/fcell.2021.663032

Phenotypically Anchored mRNA and miRNA Expression Profiling in Zebrafish Reveals Flame Retardant Chemical Toxicity Networks
Cited by: 6
Author(s): Subham Dasgupta, Cheryl L. Dunham, Lisa Truong, Michael T. Simonich, Christopher Sullivan, Robyn L Tanguay
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.00520

Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy
Cited by: 11
Author(s): Phillip A. Richmond, Frans van der Kloet, Frédéric M. Vaz, David T.S. Lin, Anuli Uzozie, Emma Graham, Michael S. Kobor, Sara Mostafavi, Perry D. Moerland, Philipp F. Lange, Antoine H. C. van Kampen, Wyeth W. Wasserman, Marc Engelen, Stephan Kemp, Clara van Karnebeek
Software Mentions: 3
Published: about 6 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.1016/j.stem.2020.05.004

Human-iPSC-Derived Cardiac Stromal Cells Enhance Maturation in 3D Cardiac Microtissues and Reveal Non-cardiomyocyte Contributions to Heart Disease
Cited by: 302
Author(s): Elisa Giacomelli, Viviana Meraviglia, Giulia Campostrini, Amy Cochrane, Xu Cao, Ruben W.J. van Helden, Ana Krotenberg Garcia, Maria Mircea, Sarantos Kostidis, Richard P. Davis, Berend J. van Meer, Carolina R. Jost, Abraham J. Koster, Hailiang Mei, David G. Míguez, Aat A. Mulder, Mario Ledesma-Terrón, Giulio Pompilio, Luca Sala, Daniela Salvatori, Roderick C. Slieker, Elena Sommariva, Antoine A.F. de Vries, Martin Giera, Stefan Semrau, Leon G.J. Tertoolen, Valeria V. Orlova, Milena Bellin, Christine L. Mummery
Software Mentions: 3
Published: about 6 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

10.3389/fcell.2020.602493

The Identification of Plasma Exosomal miR-423-3p as a Potential Predictive Biomarker for Prostate Cancer Castration-Resistance Development by Plasma Exosomal miRNA Sequencing
Cited by: 29
Author(s): Tianyu Guo, Yang Wang, Jing Jia, Xueying Mao, Elżbieta Stankiewicz, Glenda Scandura, Edwina Burke, Lei Xu, Jacek Marzec, Caitlin R. Davies, Jiaying Lu, Prabhakar Rajan, Alistair Grey, K. H. Tipples, John Hines, Sakunthala C. Kudahetti, Tim Oliver, Thomas Powles, Constantine Alifrangis, Manish Kohli, Greg Shaw, Wen Wang, Na Feng, Jonathan Shamash, Daniel M. Berney, Liang Wang, Yong‐Jie Lu
Software Mentions: 3
Published: over 5 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

10.3389/fcell.2020.603815

Genome-Wide Integrated Analysis Revealed Functions of lncRNA–miRNA–mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala
Cited by: 14
Author(s): Yulong Chen, Shiming Wan, Qing Li, Xiaoru Dong, Jinghan Diao, Qing Liao, Guiying Wang, Zexia Gao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3396-5

DEIVA: a web application for interactive visual analysis of differential gene expression profiles
Cited by: 37
Author(s): Jayson Harshbarger, Anton Kratz, Piero Carninci
Software Mentions: 3
Published: over 9 years ago

10.3389/fcell.2020.583434

Human Fetal Scalp Dermal Papilla Enriched Genes and the Role of R-Spondin-1 in the Restoration of Hair Neogenesis in Adult Mouse Cells
Cited by: 9
Author(s): Elizabeth Weber, Yung-Chih Lai, Mingxing Lei, Ting‐Xin Jiang, Cheng‐Ming Chuong
Software Mentions: 3
Published: almost 6 years ago

10.3390/cells9122700

Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion
Cited by: 6
Author(s): Manuela Krüger, Oushadee A. J. Abeyawardana, Claudia Krüger, Miloslav Juříček, Helena Štorchová
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-021-03129-9

Tomato transcriptomic response to Tuta absoluta infestation
Cited by: 11
Author(s): Daniela D’Esposito, Daniele Manzo, Alessandro Ricciardi, Antonio P. Garonna, Antonino De Natale, Luigi Frusciante, Francesco Pennacchio, Maria Raffaella Ercolano
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12885-017-3860-x

Gene expression, regulation of DEN and HBx induced HCC mice models and comparisons of tumor, para-tumor and normal tissues
Cited by: 18
Author(s): Qin Tang, Qi Wang, Qiong Zhang, Sheng‐Yan Lin, Yanhong Zhu, Xiangliang Yang, An‐Yuan Guo
Software Mentions: 3
Published: over 8 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/s41598-018-36866-3

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

10.1186/s12885-017-3711-9

Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Cited by: 22
Author(s): Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong’echa, Ann M. Moormann, Jeffrey A. Bailey
Software Mentions: 3
Published: almost 9 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

10.3389/fcell.2021.685494

Novel Functional Genes Involved in Transdifferentiation of Canine ADMSCs Into Insulin-Producing Cells, as Determined by Absolute Quantitative Transcriptome Sequencing Analysis
Cited by: 2
Author(s): Pengxiu Dai, Jiakai Li, Yijing Chen, Luwen Zhang, Xinke Zhang, Jinglu Wang, Guixiang Qi, Yihua Zhang
Software Mentions: 3
Published: about 5 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

10.3390/v13061140

Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp
Cited by: 8
Author(s): Rebecca S. Millard, Lisa K. Bickley, Kelly S. Bateman, Audrey Farbos, Diana Minardi, Karen Moore, Stuart Ross, Grant D. Stentiford, Charles R. Tyler, Ronny van Aerle, Eduarda M. Santos
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-36059-y

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: over 7 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

10.7554/eLife.26575

Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids
Cited by: 206
Author(s): Marko Nikolić, Oriol Caritg, Quitz Jeng, Jo-Anne Johnson, Dawei Sun, Kate J. Howell, Jane Brady, Usua Laresgoiti, George E. Allen, Richard J. Butler, Matthias Zilbauer, Adam Giangreco, Emma L. Rawlins
Software Mentions: 3
Published: about 9 years ago

10.3390/cells8090986

RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications
Cited by: 19
Author(s): Kai Sen Tan, Anand Kumar Andiappan, Bernett Lee, Yan Yan, Jing Liu, See Aik Tang, Josephine Lum, Ting He, Yew Kwang Ong, Mark Thong, Hui Fang Lim, Hyung-Jin Choi, Olaf Rötzschke, Vincent Chow, De Yun Wang
Software Mentions: 3
Published: about 7 years ago

10.3390/v13081603

Characterization of the SARS-CoV-2 Host Response in Primary Human Airway Epithelial Cells from Aged Individuals
Cited by: 9
Author(s): Subramaniyan Bharathiraja, Jason L. Larabee, Manish Bodas, Andrew R. Moore, Anthony W. G. Burgett, Dean A. Myers, Constantin Georgescu, Jonathan D. Wren, James F. Papin, Matthew S. Walters
Software Mentions: 3
Published: about 5 years ago

10.7150/thno.44456

Cartilage Oligomeric Matrix Protein promotes epithelial-mesenchymal transition by interacting with Transgelin in Colorectal Cancer
Cited by: 57
Author(s): Weilong Zhong, Huiqin Hou, Tianyu Li, Shuai Su, Xiaonan Xi, Yusheng Liao, Runxiang Xie, Ge Jin, Xiang Liu, Lanping Zhu, Hongxia Zhang, Xueli Song, Cheng Yang, Tao Sun, Hailong Cao, Bangmao Wang
Software Mentions: 3
Published: over 6 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/s12864-019-5556-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

10.1186/1471-2164-16-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

10.3390/cells10092376

Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli
Cited by: 4
Author(s): Kimberly Wellman, Rui Fu, Amber Baldwin, Juilee Rege, Elisabeth Murphy, William E. Rainey, Neelanjan Mukherjee
Software Mentions: 3
Published: almost 5 years ago

10.3390/cells10030635

Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Cited by: 12
Author(s): Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.00807

The Pathogenic Effects of Fusobacterium nucleatum on the Proliferation, Osteogenic Differentiation, and Transcriptome of Osteoblasts
Cited by: 8
Author(s): Hui Gao, Tianyong Sun, Fanghong Yang, Jiakan Yuan, Mei Yang, Wenyan Kang, Di Tang, Jun Zhang, Qiang Feng
Software Mentions: 3
Published: almost 6 years ago

10.3390/cells10092289

Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch
Cited by: 1
Author(s): Julien Alban Nguinkal, Marieke Verleih, Lidia de los Ríos-Pérez, Ronald M. Brunner, Arne Sahm, Saptarshi Bej, Alexander Rebl, Tom Goldammer
Software Mentions: 3
Published: almost 5 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

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568