bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0186382

Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions
Cited by: 14
Author(s): Boon Huat Cheah, Sudhir Jadhao, Madavan Vasudevan, R Wickneswari V Ratnam, Kalaivani K. Nadarajah
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.mec.2021.e00184

Transport engineering for improving the production and secretion of valuable alkaloids in Escherichia coli
Cited by: 8
Author(s): Yasuyuki Yamada, Miya Urui, Hidehiro Oki, Kai Inoue, Haruyuki Matsui, Yoshito Ikeda, Akira Nakagawa, Fumihiko Sato, Hiromichi Minami, Nobukazu Shitan
Software Mentions: 1
Published: over 4 years ago

10.1038/s41419-021-03510-4

Suppression of steroid 5α-reductase type I promotes cellular apoptosis and autophagy via PI3K/Akt/mTOR pathway in multiple myeloma
Cited by: 12
Author(s): Renjie Dou, Jinjun Qian, Wei Wu, Yanxin Zhang, Ye Yuan, Mengjie Guo, Rongfang Wei, Shu Yang, Artur Jurczyszyn, Siegfried Janz, Meral Beksaç, Chunyan Gu, Ye Yang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-72448-y

Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion
Cited by: 6
Author(s): Katsuya Sakai, Takumi Nishiuchi, Shoichiro Tange, Yoshinori Suzuki, Seiji Yano, Minoru Terashima, Takeshi Suzuki, Kunio Matsumoto
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0200826

BRD4 amplification facilitates an oncogenic gene expression program in high-grade serous ovarian cancer and confers sensitivity to BET inhibitors
Cited by: 43
Author(s): Garrett W. Rhyasen, Yi Yao, Jingwen Zhang, Austin Dulak, Lillian Castriotta, Kelly Jacques, Wei Zhao, Farzin Gharahdaghi, Maureen M. Hattersley, Paul Lyne, Edwin Clark, Michael Zinda, Stephen E. Fawell, Gordon B. Mills, Huawei Chen
Software Mentions: 1
Published: about 8 years ago

10.1155/2020/1384907

Proteome and Transcriptome Analysis of the Antioxidant Mechanism in Chicken Regulated by Eucalyptus Leaf Polyphenols Extract
Cited by: 2
Author(s): Wei Li, Zeqi He, Xiaoying Zhang, Yunjiao Chen, Jianjun Zuo, Yong Cao
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0194765

IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs
Cited by: 17
Author(s): Louise Brogaard, Lars Erik Larsen, Peter M. H. Heegaard, Christian Anthon, Jan Gorodkin, Ralf Dürrwald, Kerstin Skovgaard
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0159372

Antennal and Abdominal Transcriptomes Reveal Chemosensory Genes in the Asian Citrus Psyllid, Diaphorina citri
Cited by: 39
Author(s): Zhongzhen Wu, Zuyong He, Shuying Bin, Lei Chen, Qunxin Han, Jintian Lin
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0200558

FAK auto-phosphorylation site tyrosine 397 is required for development but dispensable for normal skin homeostasis
Cited by: 8
Author(s): Joel B. Heim, Cera A. McDonald, Saranya P. Wyles, Sindhuja Sominidi‐Damodaran, Edwin J. Squirewell, Ming Li, Catherine Motsonelidze, Ralph T. Böttcher, Jan van Deursen, Alexander Meves
Software Mentions: 1
Published: about 8 years ago

10.3390/nu12123762

Sasa quelpaertensis Leaf Extract Ameliorates Dyslipidemia, Insulin Resistance, and Hepatic Lipid Accumulation in High-Fructose-Diet-Fed Rats
Cited by: 2
Author(s): Jeong Yong Park, Mi Jang, Jung Min Oh, Hee-Chul Ko, Sung‐Pyo Hur, Jae-Won Kim, Songyee Baek, Se-Jae Kim
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0187351

Kojic acid-mediated damage responses induce mycelial regeneration in the basidiomycete Hypsizygus marmoreus
Cited by: 10
Author(s): Jinjing Zhang, Hui Chen, Mingjie Chen, Hong Wang, Qian Wang, Xiaoxia Song, Haibo Hao, Zhen Feng
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41419-018-0705-8

Jnk2 deficiency increases the rate of glaucomatous neurodegeneration in ocular hypertensive DBA/2J mice
Cited by: 16
Author(s): Jeffrey M Harder, Pete A. Williams, Ileana Soto, Nicole E. Foxworth, Kimberly A. Fernandes, Nelson F. Freeburg, Richard T. Libby, Simon W. M. John
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-74049-1

De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites
Cited by: 8
Author(s): Nisha Dhiman, Anil Kumar, Dinesh Kumar, Amita Bhattacharya
Software Mentions: 1
Published: almost 6 years ago

10.1155/2020/8847226

A Prognostic 14-Gene Expression Signature for Lung Adenocarcinoma: A Study Based on TCGA Data Mining
Cited by: 4
Author(s): Jie Liu, Shiqiang Hou, Jinyi Wang, Zhengjun Chai, Xuan Hong, Tian Zhao, Zheng Sun, Liandi Bai, Hongyan Gao, Jing Gao, Guohan Chen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0130902

Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
Cited by: 23
Author(s): Yuanhao Zhang, Leahana Rowehl, Julia M. Krumsiek, Erika P. Orner, Nurmohammad Shaikh, Phillip I. Tarr, Erica Sodergren, George M. Weinstock, Edgar C. Boedeker, Xuejian Xiong, John Parkinson, Daniel N. Frank, Ellen Li, Grace Gathungu
Software Mentions: 1
Published: about 11 years ago

10.1155/2020/8591892

Fuzheng Huayu Recipe Prevented and Treated CCl4-Induced Mice Liver Fibrosis through Regulating Polarization and Chemotaxis of Intrahepatic Macrophages via CCL2 and CX3CL1
Cited by: 14
Author(s): Man Zhang, Hongliang Liu, Kai Huang, Yuan Peng, Tao Yue, Changqing Zhao, Xudong Hu, Chenghai Liu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0237744

Transcriptome analysis and comparison reveal divergence between the Mediterranean and the greenhouse whiteflies
Cited by: 1
Author(s): Yujun Wang, Hua-Ling Wang, Xiaowei Wang, Shu‐Sheng Liu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0100477

Transcriptomic Analysis of Prunus domestica Undergoing Hypersensitive Response to Plum Pox Virus Infection
Cited by: 35
Author(s): Bernardo Rodamilans, David San León, Louisa Mühlberger, Thierry Candresse, M. Neumüller, Juan Carlos Oliveros, Juan Antonio Garcı́a
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0165268

Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells
Cited by: 19
Author(s): Sarita Panula, Ahmed Reda, Jan-Bernd Stukenborg, Cyril Ramathal, Meena Sukhwani, Halima Albalushi, Daniel Edsgärd, Michiko Nakamura, Olle Söder, Kyle E. Orwig, Shinya Yamanaka, Renee A. Reijo Pera, Outi Hovatta
Software Mentions: 1
Published: almost 10 years ago

10.7554/eLife.64330

SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung
Cited by: 40
Author(s): Alan E. Mast, Alisa S. Wolberg, David Gailani, Michael R. Garvin, Christiane Alvarez, J Izaak Miller, Bruce J. Aronow, Daniel Jacobson
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0200210

Transcription factor induced conversion of human fibroblasts towards the hair cell lineage
Cited by: 23
Author(s): Maria B Duran Alonso, Iris Lopez Hernandez, Miguel A. de la Fuente, Javier García‐Sancho, Fernando Giráldez, Thomas Schimmang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0216294

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus
Cited by: 8
Author(s): Anna Abramova, Magnus Alm Rosenblad, Anders Blomberg, Tomas Larsson
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-74789-0

Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale
Cited by: 23
Author(s): Xinqiao Zhan, Jufeng Qi, Bin Zhou, Bizeng Mao
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13227-016-0044-8

HOX gene complement and expression in the planarian Schmidtea mediterranea
Cited by: 73
Author(s): Ko W. Currie, David D. R. Brown, Shujun Zhu, Changjiang Xu, Véronique Voisin, Gary D. Bader, Bret J. Pearson
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0178189

Systematic genomic and translational efficiency studies of uveal melanoma
Cited by: 27
Author(s): Chelsea Place Johnson, Ivana K. Kim, Bita Esmaeli, Ali Amin‐Mansour, Daniel J. Treacy, Scott L. Carter, Eran Hodis, Nikhil Wagle, Sara Seepo, Xiaoxing Yu, Anne Marie Lane, Evangelos S. Gragoudas, Francisca Vázquez, Elizabeth Nickerson, Kristian Cibulskis, Aaron McKenna, Stacey Gabriel, Gad Getz, Eliezer M. Van Allen, Peter A.C. ’t Hoen, Levi A. Garraway, Scott E. Woodman
Software Mentions: 1
Published: about 9 years ago

10.1155/2020/4623107

Global Transcriptional Profiling Reveals Novel Autocrine Functions of Interleukin 6 in Human Vascular Endothelial Cells
Cited by: 8
Author(s): Liza U. Ljungberg, Mulugeta M. Zegeye, Caroline Kardeby, Knut Fälker, Dirk Repsilber, Allan Sirsjö
Software Mentions: 1
Published: over 6 years ago

10.3390/bioengineering8070090

Reengineering Tumor Microenvironment with Sequential Interleukin Delivery
Cited by: 7
Author(s): Marxa L. Figueiredo, Rachel A. Letteri, Delphine Chan‐Seng, Shreya Kumar, Cosette M. Rivera-Cruz, Todd Emrick
Software Mentions: 1
Published: about 5 years ago

10.1186/s13227-016-0050-x

Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges
Cited by: 42
Author(s): Jesús F. Peña, Alexandre Alié, Daniel J. Richter, Lingyu Wang, Noriko Funayama, Scott Nichols
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-020-73164-3

Assessing the prognostic value of stemness-related genes in breast cancer patients
Cited by: 5
Author(s): Wenjie Wang, Han Wang, Meng-Sen Wang, Yongzhen Huang, Yuan Ma, Jie Qi, Jianping Shi, Wei Li
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-75537-0

Enhanced FGFR3 activity in postmitotic principal neurons during brain development results in cortical dysplasia and axonal tract abnormality
Cited by: 5
Author(s): Jui-Yen Huang, Bruna Baumgarten Krebs, Marisha Lynn Miskus, May Lin Russell, Eamonn Patrick Duffy, Jason Michael Graf, Hui-Chen Lu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pntd.0002402

Sex-Biased Expression of MicroRNAs in Schistosoma mansoni
Cited by: 59
Author(s): A. De Marco, Ana Kozomara, Jerome H. L. Hui, Aidan M. Emery, David Rollinson, Sam Griffiths-Jones, Matthew Ronshaugen
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0003975

Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax
Cited by: 31
Author(s): Andrew P. Jackson, Sophie Goyard, Dong Xia, Bernardo J. Foth, Mandy Sanders, Jonathan M. Wastling, Paola Minóprio, Matthew Berriman
Software Mentions: 1
Published: about 11 years ago

10.1289/ehp.1408188

Effects of the Endocrine-Disrupting Chemical DDT on Self-Renewal and Differentiation of Human Mesenchymal Stem Cells
Cited by: 53
Author(s): Amy L. Strong, Zhenzhen Shi, Michael J. Strong, David F. Miller, Douglas B. Rusch, Aaron Buechlein, Erik K. Flemington, John A. McLachlan, Kenneth P. Nephew, Matthew E. Burow, Bruce A. Bunnell
Software Mentions: 1
Published: over 11 years ago

10.1111/eva.13024

Age‐dependent expression of cancer‐related genes in a long‐lived seabird
Cited by: 4
Author(s): Richard Meitern, Jérôme Fort, Mathieu Giraudeau, Kalev Rattiste, Elin Sild, Tuul Sepp
Software Mentions: 1
Published: about 6 years ago

10.1007/s00408-019-00257-w

Growth Hormone-Releasing Hormone Receptor Antagonist Modulates Lung Inflammation and Fibrosis due to Bleomycin
Cited by: 29
Author(s): Chongxu Zhang, Renzhi Cai, Aaron Lazerson, Gaëtan J.-R. Delcroix, Medhi Wangpaichitr, Mehdi Mirsaeidi, Anthony J. Griswold, Andrew V. Schally, Robert M. Jackson
Software Mentions: 1
Published: about 7 years ago

10.1186/s12944-020-01222-w

Bioinformatics analysis of vascular RNA-seq data revealed hub genes and pathways in a novel Tibetan minipig atherosclerosis model induced by a high fat/cholesterol diet
Cited by: 22
Author(s): Yongming Pan, Yu Chen, Junjie Huang, Yili Rong, Jiaojiao Chen, Minli Chen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0009377

Combined gene deletion of dihydrofolate reductase-thymidylate synthase and pteridine reductase in Leishmania infantum
Cited by: 5
Author(s): Arijit Bhattacharya, Philippe Leprohon, Marc Ouellette
Software Mentions: 1
Published: over 5 years ago

10.1186/s13059-019-1830-0

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses
Cited by: 152
Author(s): Ciara H. O’Flanagan, Kieran R Campbell, Allen W. Zhang, Farhia Kabeer, Jamie Lim, Justina Biele, Peter Eirew, Daniel Lai, Andrew McPherson, Esther Kong, Cherie Bates, Kelly Borkowski, Matt Wiens, Brittany Hewitson, James Hopkins, Jenifer Pham, Nicholas Ceglia, Richard A. Moore, Andrew J. Mungall, Jessica N. McAlpine, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-020-76171-6

Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments
Cited by: 6
Author(s): Sera Jung, Jong Hee Lee
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pntd.0006186

Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti
Cited by: 10
Author(s): Matthew W. Eng, Anthony Clemons, Casey Hill, Roberta Engel, David W. Severson, Susanta K. Behura
Software Mentions: 1
Published: over 8 years ago

10.1080/21655979.2019.1710932

Genome-wide analysis of PYL-PP2C-SnRK2s family in Camellia sinensis
Cited by: 18
Author(s): Ping Xu, Xueying Zhang, Hui Su, Xiaofen Liu, Yuefei Wang, Gaojie Hong
Software Mentions: 1
Published: over 6 years ago

10.1186/s12940-017-0288-3

Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment
Cited by: 18
Author(s): Zhao‐Xi Wang, Birgit Claus Henn, Chaolong Wang, Yongyue Wei, Su Li, Ryan Sun, Han Chen, Peter J. Wagner, Quan Lu, Xihong Lin, Robert O. Wright, David C. Bellinger, Molly L. Kile, Maitreyi Mazumdar, Martha María Téllez‐Rojo, Lourdes Schnaas, David C. Christiani
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.07125

The acinar differentiation determinant PTF1A inhibits initiation of pancreatic ductal adenocarcinoma
Cited by: 117
Author(s): Nathan M. Krah, Jean–Paul De La O, Galvin H. Swift, Chinh Q. Hoang, Spencer G. Willet, Fong Chen Pan, Gabriela M Cash, Mary P. Bronner, Christopher V.E. Wright, Raymond J. MacDonald, L. Charles Murtaugh
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pntd.0004634

Analysis on Gene Expression Profile in Oncospheres and Early Stage Metacestodes from Echinococcus multilocularis
Cited by: 28
Author(s): Fuqiang Huang, Zhisheng Dang, Yutaka Suzuki, T Horiuchi, Kinpei Yagi, Hirokazu Kouguchi, Takao Irie, Kyeong-Soon Kim, Yuzaburo Oku
Software Mentions: 1
Published: over 10 years ago

10.1186/s12940-020-00666-y

Epigenome-wide association study for pesticide (Permethrin and DEET) induced DNA methylation epimutation biomarkers for specific transgenerational disease
Cited by: 12
Author(s): Jennifer L. M. Thorson, Daniel Beck, Millissia Ben Maamar, Eric Nilsson, Michael K. Skinner
Software Mentions: 1
Published: almost 6 years ago

10.7554/eLife.63502

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Cited by: 88
Author(s): Anastasia A. Minervina, Ekaterina A. Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Z. Mamedov, André Franke, Grigory A. Efimov, Dmitriy M. Chudakov, Thierry Mora, Aleksandra M. Walczak, Yuri B Lebedev, Mikhail V. Pogorelyy
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.59469

Adrenergic activation modulates the signal from the Reissner fiber to cerebrospinal fluid-contacting neurons during development
Cited by: 20
Author(s): Yasmine Cantaut-Belarif, Adeline Orts-Del’Immagine, Margot Penru, Guillaume Pézeron, Claire Wyart, Pierre-Luc Bardet
Software Mentions: 1
Published: almost 6 years ago

10.1093/molbev/msab123

Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw
Cited by: 16
Author(s): Christine Hirschberger, Victoria A. Sleight, Katharine E. Criswell, Stephen J. Clark, J. Andrew Gillis
Software Mentions: 1
Published: over 5 years ago

10.1093/molbev/msv112

Ecological and Genetic Barriers Differentiate Natural Populations ofSaccharomyces cerevisiae
Cited by: 27
Author(s): Katie J. Clowers, Justin Heilberger, Jeff S. Piotrowski, Jessica L. Will, Audrey P. Gasch
Software Mentions: 1
Published: over 11 years ago

10.1093/molbev/msab153

A Bivalve Biomineralization Toolbox
Cited by: 21
Author(s): Tejaswi Yarra, Mark Blaxter, Melody S. Clark
Software Mentions: 1
Published: about 5 years ago

10.1093/molbev/msab099

Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias
Cited by: 13
Author(s): Janaína Lima de Oliveira, Atahualpa Castillo-Morales, Laurence D. Hurst, Araxi O. Urrutia, Christopher Thompson, Jason B. Wolf
Software Mentions: 1
Published: over 5 years ago

10.1038/cddis.2015.392

Hemoglobinuria-related acute kidney injury is driven by intrarenal oxidative reactions triggering a heme toxicity response
Cited by: 96
Author(s): Jeremy Deuel, Christian A. Schaer, Felicitas S Boretti, Lennart Opitz, Inés García-Rubio, Jin Hyen Baek, Donat R. Spahn, Paul W. Buehler, Dominik J. Schaer
Software Mentions: 1
Published: over 10 years ago

10.1038/s41419-020-03107-3

ClC-3/SGK1 regulatory axis enhances the olaparib-induced antitumor effect in human stomach adenocarcinoma
Cited by: 12
Author(s): Zhuoyu Gu, Liping Wang, Xiaohan Yao, Long Qian, Kaping Lee, Jieyao Li, Dongli Yue, Shuman Yang, Yanfen Liu, Na Li, Yixin Li
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-74594-9

Involvement of neutrophils in machineries underlying the rupture of intracranial aneurysms in rats
Cited by: 19
Author(s): Mika Kushamae, Haruka Miyata, Makoto Shirai, Kampei Shimizu, Mieko Oka, Hirokazu Koseki, Yu Abekura, Isao Ono, Kazuhiko Nozaki, Tohru Mizutani, Tomohiro Aoki
Software Mentions: 1
Published: over 5 years ago

10.1186/1756-0500-5-506

The bench scientist's guide to statistical analysis of RNA-Seq data
Cited by: 35
Author(s): Craig R. Yendrek, Elizabeth A. Ainsworth, Jyothi Thimmapuram
Software Mentions: 1
Published: almost 14 years ago

10.1186/s13229-017-0148-6

Effects of a social stimulus on gene expression in a mouse model of fragile X syndrome
Cited by: 6
Author(s): Tiffany D. Rogers, Allison M.J. Anacker, Travis M. Kerr, C. Gunnar Forsberg, Jing Wang, Bing Zhang, Jeremy Veenstra‐VanderWeele
Software Mentions: 1
Published: about 9 years ago

10.1038/sdata.2016.89

Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases
Cited by: 312
Author(s): Mariet Allen, Minerva M. Carrasquillo, Cory C. Funk, Benjamin D. Heavner, Fanggeng Zou, Curtis S. Younkin, Jeremy D. Burgess, High Seng Chai, Julia E. Crook, James A. Eddy, Hongdong Li, Ben Logsdon, Mette A. Peters, Kristen K. Dang, Xue Wang, Daniel J. Serie, Chen Wang, Thuy Nguyen, Sarah Lincoln, Kimberly G. Malphrus, Gina Bisceglio, Li Ma, Todd E. Golde, Lara M. Mangravite, Yan W. Asmann, Nathan D. Price, Ronald C. Petersen, Neill R. Graff‐Radford, Dennis W. Dickson, Steven G. Younkin, Nilüfer Ertekin-Taner
Software Mentions: 1
Published: almost 10 years ago

10.1155/2021/9917060

Increased EHHADH Expression Predicting Poor Survival of Osteosarcoma by Integrating Weighted Gene Coexpression Network Analysis and Experimental Validation
Cited by: 1
Author(s): Juncheng Cui, Guoliang Yi, Jinxin Li, Yangtao Li, Dongyang Qian
Software Mentions: 1
Published: over 5 years ago

10.1016/j.bbrep.2021.101061

Transcriptome dynamics during cholesterol-induced transdifferentiation of human coronary artery smooth muscle cells: A Gene Ontology-centric clustering approach
Cited by: 1
Author(s): Kentaro Inoue, Hiromitsu Araki, Fumihito Miura, Takashi Ito
Software Mentions: 1
Published: almost 5 years ago

10.1093/eep/dvaa022

Effect of concentration and duration of particulate matter exposure on the transcriptome and DNA methylome of bronchial epithelial cells
Cited by: 12
Author(s): Steven K. Huang, Priya Tripathi, Lada A. Koneva, Raymond G. Cavalcante, N. Craig, Anne M. Scruggs, Maureen A. Sartor, Furong Deng, Yahong Chen
Software Mentions: 1
Published: over 5 years ago

10.1155/2018/7538204

An Efficient Feature Selection Strategy Based on Multiple Support Vector Machine Technology with Gene Expression Data
Cited by: 25
Author(s): Ying Zhang, Qingchun Deng, Wenbin Liang, Xuan Zou
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-020-77177-w

Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L.
Cited by: 6
Author(s): Lu Guo, Zhihua Wu, Peng Yan, Xiuhua Shang, Yi Xie, R. J. Arnold
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms9071408

Identification of Resistance Determinants for a Promising Antileishmanial Oxaborole Series
Cited by: 8
Author(s): Magali Van den Kerkhof, Philippe Leprohon, Dorien Mabille, Sarah Hendrickx, L.B. Tulloch, Richard J. Wall, Susan Wyllie, Eric Chatelain, Charles E. Mowbray, Stéphanie Braillard, Marc Ouellette, Louis Maes, Guy Caljon
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-77598-7

Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding
Cited by: 7
Author(s): Selisha A. Sooklal, Phelelani T. Mpangase, Mihai-Silviu Tomescu, Shaun Aron, Scott Hazelhurst, Robert H. Archer, Karl Rumbold
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms8020278

Differential Potential of Phytophthora capsici Resistance Mechanisms to the Fungicide Metalaxyl in Peppers
Cited by: 12
Author(s): Weiyan Wang, Xiao Liu, Tao Han, Kunyuan Li, Yang Qu, Zhimou Gao
Software Mentions: 1
Published: over 6 years ago

10.1038/s41419-020-2331-5

The nuclear gene rpl18 regulates erythroid maturation via JAK2-STAT3 signaling in zebrafish model of Diamond–Blackfan anemia
Cited by: 9
Author(s): Cheng Chen, Mengjia Lu, Shuo Lin, Wenzhi Qin
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.63938

Volatile DMNT directly protects plants against Plutella xylostella by disrupting the peritrophic matrix barrier in insect midgut
Cited by: 21
Author(s): Chen Chen, Hongyi Chen, Shenghong Huang, Tao‐Shan Jiang, Chuanhong Wang, Zhen Tao, Chen He, Qingfeng Tang, Peijin Li
Software Mentions: 1
Published: over 5 years ago

10.1038/sdata.2019.24

Long noncoding RNA and mRNA expression profiles following igf3 knockdown in common carp, Cyprinus carpio
Cited by: 29
Author(s): Fei Song, Lanmei Wang, Wenbin Zhu, Zaijie Dong
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-77293-7

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato
Cited by: 13
Author(s): Koichi Suematsu, Masaru Tanaka, Rie Kurata, Kai Yu
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms8030314

Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates
Cited by: 4
Author(s): Qianqian Li, Rebecca E. Cooper, Carl‐Eric Wegner, Kirsten Küsel
Software Mentions: 1
Published: over 6 years ago

10.1093/emph/eow010

Human fibroblasts display a differential focal adhesion phenotype relative to chimpanzee
Cited by: 5
Author(s): Alexander S. Advani, Annie Y. Chen, Courtney C. Babbitt
Software Mentions: 1
Published: over 10 years ago

10.1155/2021/5585884

Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress
Cited by: 5
Author(s): Jine Fu, Lingyun Wan, Lina Song, Lili He, Ni Jiang, Hairong Long, Juan Huo, Xiaowen Ji, Ying Wei, Shugen Wei, Limei Pan
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-78976-x

Early pregnancy maternal progesterone administration alters pituitary and testis function and steroid profile in male fetuses
Cited by: 13
Author(s): Katarzyna Siemienowicz, Yili Wang, Magda Marečková, Junko Nio‐Kobayashi, Paul A. Fowler, Michael T. Rae, W. Colin Duncan
Software Mentions: 1
Published: over 5 years ago

10.1038/s41597-019-0193-4

The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways
Cited by: 77
Author(s): Scott A. Ochsner, David Abraham, Kirt Martin, Wei Ding, Apollo McOwiti, Wasula H. Kankanamge, Zichen Wang, Kaitlyn J. Andreano, Ross A. Hamilton, Yue Chen, Angelica Hamilton, Marin L. Gantner, Michael Dehart, Shijing Qu, Susan G. Hilsenbeck, Lauren B. Becnel, Dave Bridges, Avi Ma’ayan, Janice M. Huss, Fabio Stossi, Charles E. Foulds, Anastasia Kralli, Donald P. McDonnell, Neil J. McKenna
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms9081626

Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle
Cited by: 1
Author(s): Anu Yadav, Laurens Maertens, Tim Meese, Filip Van Nieuwerburgh, Mohamed Mysara, Natalie Leys, Ann Cuypers, Paul Janssen
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-78781-6

Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus
Cited by: 6
Author(s): Chiaki Hori, Naoki Takata, Pui Ying Lam, Yuki Tobimatsu, Soichiro Nagano, Jenny C. Mortimer, Dan Cullen
Software Mentions: 1
Published: over 5 years ago

10.3389/fmolb.2017.00057

Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14
Cited by: 34
Author(s): Georges St. Laurent, Bernd Seilheimer, Michael Tackett, Jianhua Zhou, Dmitry Shtokalo, Yuri Vyatkin, Maxim Ri, Ian Toma, Dan Jones, Timothy A. McCaffrey
Software Mentions: 1
Published: about 9 years ago

10.1186/s12870-019-2011-8

Transcriptome analysis and identification of genes associated with fruiting branch internode elongation in upland cotton
Cited by: 9
Author(s): Feiyan Ju, Shaodong Liu, Siping Zhang, Huijuan Ma, Jing Chen, Changwei Ge, Qian Shen, Xiaomeng Zhang, Xinhua Zhao, Yongjiang Zhang, Chaoyou Pang
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms9030652

In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat
Cited by: 11
Author(s): Shigeru Kawai, Joval N. Martinez, Mads Lichtenberg, Erik Trampe, Michael Kühl, Marcus Tank, Shin Haruta, Arisa Nishihara, Satoshi Hanada, Vera Thiel
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms7120634

Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
Cited by: 16
Author(s): Junliang Zhong, Xihong Zhao
Software Mentions: 1
Published: over 6 years ago

10.1038/s41597-020-00751-4

Daily transcriptomes of the copepod Calanus finmarchicus during the summer solstice at high Arctic latitudes
Cited by: 4
Author(s): Laura Payton, Céline Noirot, Claire Hoede, Lukas Hüppe, Kim S. Last, David Wilcockson, E. A. Ershova, Sophie Valière, Bettina Meyer
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms9051065

Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake
Cited by: 1
Author(s): Liuhong Shen, Lang Gao, Mengjiao Yang, Jian Zhang, Yulu Wang, Yongdong Feng, Liping Wang, Shiwei Wang
Software Mentions: 1
Published: over 5 years ago

10.1038/srep02101

Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu
Cited by: 104
Author(s): Kuihua Han, Zhifeng Li, Rui Peng, Liping Zhu, Tao Zhou, Luguang Wang, Shuguang Li, Xiaobo Zhang, Wei Hu, Zhihong Wu, Nan Qin, Yuezhong Li
Software Mentions: 1
Published: about 13 years ago

10.3389/fmolb.2021.682769

Novel Insights into the Potential Diagnostic Value of Circulating Exosomal IncRNA-Related Networks in Large Artery Atherosclerotic Stroke
Cited by: 4
Author(s): Shuai Zhang, Jing Wang, Mei Jie Qu, Kun Wang, Jun Ai, Pan Xu, Xiao Jun Zhu
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms9081560

Transcriptome Analysis of Durusdinium Associated with the Transition from Free-Living to Symbiotic
Cited by: 3
Author(s): Ikuko Yuyama, Naoto Ugawa, Takeji Hashimoto
Software Mentions: 1
Published: about 5 years ago

10.1186/s40164-021-00230-5

Blocking siglec-10hi tumor-associated macrophages improves anti-tumor immunity and enhances immunotherapy for hepatocellular carcinoma
Cited by: 26
Author(s): Nan Xiao, Xiao‐Dong Zhu, Kangshuai Li, Yifan Chen, Xuefeng Li, Bin Xu, Ming Lei, Jiejie Xu, Hui–Chuan Sun
Software Mentions: 1
Published: about 5 years ago

10.1093/eep/dvy026

Fatherhood alters gene expression within the MPOA
Cited by: 7
Author(s): Adele M. H. Seelke, Jessica Bond, Trent C Simmons, Nikhil Joshi, Matthew L. Settles, Danielle S. Stolzenberg, Mijke Rhemtulla, Karen L. Bales
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep11136

Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera
Cited by: 50
Author(s): Abdullah M. Khamis, Adam R. Hamilton, Yulia A. Medvedeva, Tanvir Alam, Intikhab Álam, Magbubah Essack, Boris Umylny, Boris R. Janković, Nicholas L. Naeger, Makoto Suzuki, Matthias Harbers, Gene E. Robinson, Vladimir B. Bajic
Software Mentions: 1
Published: about 11 years ago

10.1038/srep12165

Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection
Cited by: 26
Author(s): Hai Peng, Zheng Chen, Zhiwei Fang, Jian Zhou, Xia Zhang, Lifen Gao, Lihong Chen, Lili Li, Tiantian Li, Wenxue Zhai, Weixiong Zhang
Software Mentions: 1
Published: about 11 years ago

10.1038/srep12620

Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine
Cited by: 32
Author(s): Hua Bao, Arun Kommadath, Guanxiang Liang, Xinwei Sun, Adriano S. Arantes, Christopher K. Tuggle, Shawn M. D. Bearson, Graham Plastow, Paul Stothard, Le Luo Guan
Software Mentions: 1
Published: about 11 years ago

10.1038/srep12946

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)
Cited by: 62
Author(s): Quanyuan Wan, Jian Su
Software Mentions: 1
Published: about 11 years ago

10.1038/srep13413

Large-scale RNA-Seq Transcriptome Analysis of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types
Cited by: 102
Author(s): Peng Li, Xiu Wu Bian, Di Kang Li, Chuan Xu, Guang Ming Wang, Qing Xia, Qing Xiong
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-020-80837-6

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium
Cited by: 6
Author(s): Aboozar Soorni, Amir Mohammad Akrami, Reza Abolghasemi, Maryam Vahedi
Software Mentions: 1
Published: over 5 years ago

10.1038/srep13608

Evidence for the expression of abundant microRNAs in the locust genome
Cited by: 23
Author(s): Yanli Wang, Feng Jiang, Huimin Wang, Tianqi Song, Yuanyuan Wei, Meiling Yang, Jianzhen Zhang, Le Kang
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep13980

Hyperinsulinemia shifted energy supply from glucose to ketone bodies in early nonalcoholic steatohepatitis from high-fat high-sucrose diet induced Bama minipigs
Cited by: 28
Author(s): Shulin Yang, Ji‐Han Xia, Yuanyuan Zhang, Jian‐Gao Fan, Hua Wang, Jing Yuan, Zhan-zhao Zhao, Qin Pan, Yulian Mu, Leilei Xin, Yao-xing Chen, Kui Li
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-020-80280-7

Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae
Cited by: 15
Author(s): He Meng, Mingming Sun, Zipeng Jiang, Yutong Liu, Yu Sun, Dan Liŭ, Caihong Jiang, Min Ren, Guangdi Yuan, Wenlong Yu, Qi Sheng Feng, Aiguo Yang, Lei Cheng, Yuanying Wang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12964-020-00648-0

Alpha-1 antitrypsin deficient individuals have circulating extracellular vesicles with profibrogenic cargo
Cited by: 19
Author(s): Nazli Khodayari, Regina Oshins, L. Shannon Holliday, Virginia Clark, Qiang Xiao, George Marek, Borna Mehrad, Mark Brantly
Software Mentions: 1
Published: almost 6 years ago

10.1038/srep15407

Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis
Cited by: 12
Author(s): Bin Luo, Wei Gu, Jiayong Zhong, Ying Wang, Gong Zhang
Software Mentions: 1
Published: almost 11 years ago

10.1002/ece3.7581

Comparative transcriptomics of albino and warningly‐coloured caterpillars
Cited by: 4
Author(s): Juan A. Galarza
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms9081591

Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study
Cited by: 4
Author(s): Susanne Jacksch, Christoph König, Dominik Kaiser, Mirko Weide, Stefan Ratering, Sylvia Schnell, Markus Egert
Software Mentions: 1
Published: about 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568