bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12859-017-1808-4

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Cited by: 36
Author(s): Lian Liu, Shao Wu Zhang, Yufei Huang, Jia Meng
Software Mentions: 6
Published: almost 9 years ago

10.1186/s13059-019-1874-1

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Cited by: 2,100
Author(s): Christoph Hafemeister, Rahul Satija
Software Mentions: 6
Published: over 6 years ago

10.18632/aging.203448

Effects of Siberian fir terpenes extract Abisil on antioxidant activity, autophagy, transcriptome and proteome of human fibroblasts
Cited by: 1
Author(s): Anastasiya V. Lipatova, George S. Krasnov, Pavel Vorobyov, Pavel Melnikov, Olga N. Alekseeva, Yulia S. Vershinina, Alexander G. Brzhozovskiy, Daria Goliusova, Faniya Maganova, Natalia F. Zakirova, Anna V. Kudryavtseva, Alexey Moskalev
Software Mentions: 6
Published: almost 5 years ago

10.3390/v10090512

Robust Innate Immunity of Young Rabbits Mediates Resistance to Rabbit Hemorrhagic Disease Caused by Lagovirus Europaeus GI.1 But Not GI.2
Cited by: 28
Author(s): Matthew J. Neave, Robyn N. Hall, Nina Huang, Kenneth A. McColl, Peter J. Kerr, Marion Hoehn, Jennifer Taylor, Tanja Strive
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0175657

Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts
Cited by: 28
Author(s): Wolfgang Kaisers, Petra Boukamp, Hans Jürgen Stark, Holger Schwender, Julia Tigges, Jean Krutmann, Heiner Schaal
Software Mentions: 6
Published: over 9 years ago

10.1155/2020/8833438

Systematic Investigation of mRNA N6-Methyladenosine Machinery in Primary Prostate Cancer
Cited by: 7
Author(s): Mei Jiang, Yu‐Chuan Lu, Dongxia Duan, Hongxiang Wang, Gaoya Man, Ching Kang, Kesaier Abulimiti, Yao Li
Software Mentions: 6
Published: almost 6 years ago

10.1242/dev.195883

The BMP antagonist gremlin 1 contributes to the development of cortical excitatory neurons, motor balance and fear responses
Cited by: 4
Author(s): Mari Ichinose, Nobumi Suzuki, Tongtong Wang, Hiroki Kobayashi, Laura Vrbanac, Joseph Kim Fai Ng, Josephine Wright, Tamsin R.M. Lannagan, Krystyna A. Gieniec, Martin Lewis, Ryosuke Ando, Atsushi Enomoto, Simon Koblar, Paul Q. Thomas, Daniel L. Worthley, Susan L. Woods
Software Mentions: 6
Published: about 5 years ago

10.1093/database/bay014

TransAtlasDB: an integrated database connecting expression data, metadata and variants
Cited by: 2
Author(s): Modupeore O. Adetunji, Susan J. Lamont, Carl J. Schmidt
Software Mentions: 6
Published: over 8 years ago

10.1007/s10616-020-00384-w

Genome-wide expression profiling reveals increased stability and mitochondrial energy metabolism of the human liver cell line HepaRG-CAR
Cited by: 1
Author(s): Aziza A. A. Adam, Aldo Jongejan, Perry D. Moerland, Vincent A. van der Mark, Ronald P.J. Oude Elferink, R. A. F. M. Chamuleau, Ruurdtje Hoekstra
Software Mentions: 6
Published: over 6 years ago

10.1155/2015/178572

A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing Data
Cited by: 7
Author(s): Sheng Yang, Li Guo, Fang Shao, Yang Zhao, Feng Chen
Software Mentions: 6
Published: over 11 years ago

10.1038/s42003-021-02595-z

Single-cell profiling defines the prognostic benefit of CD39high tissue resident memory CD8+ T cells in luminal-like breast cancer
Cited by: 9
Author(s): Agnese Losurdo, Caterina Scirgolea, Giorgia Alvisi, Jolanda Brummelman, Valentina Errico, Luca Di Tommaso, Karolina Pilipow, Federico Colombo, Bethania Fernandes, Clelia Peano, Alberto Testori, Corrado Tinterri, Massimo Roncalli, Armando Santoro, Emilia Maria Cristina Mazza, Enrico Lugli
Software Mentions: 6
Published: almost 5 years ago

10.1038/s42003-021-02397-3

Three-dimensional CRISPR screening reveals epigenetic interaction with anti-angiogenic therapy
Cited by: 4
Author(s): Michael Y. He, Michael M. Halford, Ruofei Liu, James P Roy, Zoe L. Grant, Leigh Coultas, Niko Thio, Omer Gilan, Yih Chih Chan, Mark A. Dawson, Marc G. Achen, Steven A. Stacker
Software Mentions: 6
Published: about 5 years ago

10.1038/s42003-020-01616-7

Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons
Cited by: 24
Author(s): Dong Won Kim, Kai Li, Zoe Qianyi Wang, Yi Stephanie Zhang, Abhijith Bathini, Matthew Brown, Sonia Hao Lin, Parris Whitney Washington, Cuiyun Sun, Susan Lindtner, Bora Lee, Hong Wang, Tomomi Shimogori, John L.R. Rubenstein, Seth Blackshaw
Software Mentions: 6
Published: over 5 years ago

10.3390/cancers12113457

Exploring the Role of Osteosarcoma-Derived Extracellular Vesicles in Pre-Metastatic Niche Formation and Metastasis in the 143-B Xenograft Mouse Osteosarcoma Model
Cited by: 19
Author(s): Alekhya Mazumdar, Joaquín Urdínez, Aleksandar Boro, Matthias Arlt, Fabian E. Egli, Barbara Niederöst, Patrick K. Jaeger, Greta Moschini, Roman Muff, Bruno Fuchs, Jess G. Snedeker, Ana Gvozdenovic
Software Mentions: 6
Published: over 5 years ago

10.3390/cancers12061597

TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma
Cited by: 11
Author(s): Dagmara Rusinek, Aleksandra Pfeifer, Marta Cieślicka, M. Kowalska, Agnieszka Pawlaczek, Jolanta Krajewska, Sylwia Szpak‐Ulczok, Tomasz Tyszkiewicz, Monika Halczok, Agnieszka Czarniecka, Ewa Zembala‐Nożyńska, Mykola Chekan, Roman Lamch, Daria Handkiewicz-Junak, Aleksandra Ledwoń, Ewa Paliczka-Cieślik, Aleksandra Kropińska, Barbara Jarząb, Małgorzata Oczko-Wojciechowska
Software Mentions: 6
Published: about 6 years ago

10.1002/1878-0261.12965

The ZEB2‐dependent EMT transcriptional programme drives therapy resistance by activating nucleotide excision repair genes ERCC1 and ERCC4 in colorectal cancer
Cited by: 14
Author(s): Rahul Sreekumar, Hajir AlSaihati, Muhammad Emaduddin, Karwan A. Moutasim, Massimiliano Mellone, Ashish Patel, Seval Kılıç, Metin Çetįn, Sule Erdemir, Marta Salgado Navio, Maria A. Lopez, Nathan Curtis, Tamer Yağcı, John Primrose, Brendan D. Price, Geert Berx, Gareth J. Thomas, Eugene Tulchinsky, Alex H. Mirnezami, Emre Sayan
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-82989-5

CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities
Cited by: 5
Author(s): Evan Tarbell, Kaiyu Jiang, Teresa Hennon, Lucy C Holmes, Sonja D. Williams, Yao Fu, Patrick M. Gaffney, Tao Liu, James N. Jarvis
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-82156-w

Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy
Cited by: 23
Author(s): Wellison J. S. Diniz, Matthew S Crouse, Robert A. Cushman, Kyle J McLean, J. S. Caton, Carl R Dahlen, Lawrence P. Reynolds, Alison K Ward
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-81933-x

Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Cited by: 15
Author(s): Heleen H.T. Middelkamp, Anouk H.A. Verboven, Aisen Vivas, Chantal Schoenmaker, Teun Klein Gunnewiek, Robert Passier, Cornelis A. Albers, Peter-Bram A.C. ’t Hoen, Nael Nadif Kasri, Andries D. van der Meer
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-77055-5

Identification of transcription factor co-regulators that drive prostate cancer progression
Cited by: 11
Author(s): Manjunath Siddappa, Sajad A. Wani, Mark D. Long, Damien A. Leach, Ewy A. Mathé, Charlotte Bevan, Moray J. Campbell
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.19127

Regulation of X-linked gene expression during early mouse development by Rlim
Cited by: 36
Author(s): Feng Wang, Jongdae Shin, Jeremy Shea, Jun Yu, Ana Bošković, Meg Byron, Xiaochun Zhu, Alex K. Shalek, Aviv Regev, Jeanne B. Lawrence, Eduardo M. Torres, Lihua Julie Zhu, Oliver J. Rando, Ingolf Bach
Software Mentions: 6
Published: almost 10 years ago

10.15252/msb.20199195

Improved detection of differentially represented DNA barcodes for high‐throughput clonal phenomics
Cited by: 12
Author(s): Yevhen Akimov, Daria Bulanova, Sanna Timonen, Krister Wennerberg, Tero Aittokallio
Software Mentions: 6
Published: over 6 years ago

10.15252/msb.20167435

Transcriptional regulatory networks underlying gene expression changes in Huntington's disease
Cited by: 51
Author(s): Seth A. Ament, Jocelynn Pearl, Jeffrey P. Cantle, Robert M. Bragg, Peter J. Skene, Sydney R. Coffey, Dani E Bergey, Vanessa C. Wheeler, Marcy E. MacDonald, Nitin S. Baliga, Jim Rosinski, Leroy Hood, Jeffrey B. Carroll, Nathan D. Price
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-020-75998-3

Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption
Cited by: 8
Author(s): S. Lee, Stephen J. Bush, Susan Thorne, Nicola Mawson, Colin Farquharson, Guraa Bergkvist
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-020-75505-8

Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart
Cited by: 12
Author(s): Vishantie Dostal, Silas D. Wood, Cody T Thomas, Yu Han, Edward Lau, Maggie P. Y. Lam
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-020-74567-y

Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
Cited by: 11
Author(s): Tong Li, Po-Yen Wu, John H. Phan, Hamid R Hassazadeh, Weida Tong, May D. Wang
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-020-70334-1

Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Müller Glial regenerative potential
Cited by: 20
Author(s): Leah S. VandenBosch, Stefanie G. Wohl, Matthew S. Wilken, Marcus Hooper, Connor Finkbeiner, Kristen E. Cox, Laura B. Chipman, Thomas A. Reh
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-020-68879-2

Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins
Cited by: 2
Author(s): S. Yu. Funikov, Alexander P. Rezvykh, Д. А. Куликова, E. S. Zelentsova, Lyudmila A. Protsenko, Lyubov N. Chuvakova, Venera Tyukmaeva, Irina R. Arkhipova, Michael B. Evgen’ev
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-020-63355-3

Limits in the detection of m6A changes using MeRIP/m6A-seq
Cited by: 120
Author(s): Alexa B. R. McIntyre, Nandan S. Gokhale, Leandro Cerchietti, Samie R. Jaffrey, Stacy M. Horner, Christopher E. Mason
Software Mentions: 6
Published: over 6 years ago

10.1038/srep09549

Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV
Cited by: 33
Author(s): Jia Li, Zhisheng Chen, Junlong Zhao, Liurong Fang, Rui Fang, Jiang Xiao, Xing Chen, Ao Zhou, Yingyin Zhang, Liming Ren, Xiaoxiang Hu, Yaofeng Zhao, Shujun Zhang, Ning Li
Software Mentions: 6
Published: over 11 years ago

10.1038/srep35671

RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathways
Cited by: 22
Author(s): Lulu Jiang, Charles Hindmarch, Mark F. Rogers, Colin Campbell, Christy Waterfall, Jane A. Coghill, Peter W. Mathieson, Gavin I. Welsh
Software Mentions: 6
Published: almost 10 years ago

10.1038/srep34220

Widespread DNA hypomethylation and differential gene expression in Turner syndrome
Cited by: 99
Author(s): Christian Trolle, Morten Muhlig Nielsen, Anne Skakkebæk, Philippe Lamy, Søren Vang, Jakob Hedegaard, Iver Nordentoft, Torben F. Ørntoft, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 6
Published: almost 10 years ago

10.1186/s13046-020-01739-z

LncRNA MYLK-AS1 facilitates tumor progression and angiogenesis by targeting miR-424-5p/E2F7 axis and activating VEGFR-2 signaling pathway in hepatocellular carcinoma
Cited by: 72
Author(s): Fei Teng, Juxiang Zhang, Qimeng Chang, Xubo Wu, Wei‐Guo Tang, Jianfa Wang, Jin-Feng Feng, Ziping Zhang, Zhiqiu Hu
Software Mentions: 6
Published: almost 6 years ago

10.1038/sdata.2017.51

Transcriptomic analysis of gene signatures associated with sickle pain
Cited by: 8
Author(s): Jinny Paul, Anupam Aich, Juan E. Abrahante, Ying Wang, Rebecca S. LaRue, Susan K. Rathe, Krystina R. Kalland, Aditya Mittal, Ritu Jha, Fei Peng, David A. Largaespada, Anindya Bagchi, Kalpna Gupta
Software Mentions: 6
Published: about 9 years ago

10.3390/v12111284

Gene Expression Signatures in AML-12 Hepatocyte Cells upon Dengue virus Infection and Acetaminophen Treatment
Cited by: 3
Author(s): Jorge G. Ferreira, Sandra Grossi Gava, Edmundo Clarindo Oliveira, Izabella Cristina Andrade Batista, Gabriel da Rocha Fernandes, Marina Moraes Mourão, Carlos Eduardo Calzavara-Silva
Software Mentions: 6
Published: almost 6 years ago

10.1038/sdata.2016.73

Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands
Cited by: 7
Author(s): Panagiotis Moulos, Martina Samiotaki, George Panayotou, Skarlatos G. Dedos
Software Mentions: 6
Published: almost 10 years ago

10.3390/nu12041042

Green Tea Polyphenol EGCG Attenuates MDSCs-mediated Immunosuppression through Canonical and Non-Canonical Pathways in a 4T1 Murine Breast Cancer Model
Cited by: 33
Author(s): Ping Xu, Feng Yan, Yuhai Zhao, Xiangbo Chen, Shili Sun, Yuefei Wang, Le Ying
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1009162

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation
Cited by: 18
Author(s): Laure Bridoux, Peyman Zarrineh, Joshua Mallen, Mike Phuycharoen, Víctor Latorre, Frank Ladam, Marta Losa, Syed Murtuza Baker, Charles G. Sagerström, Kimberly A. Mace, Magnus Rattray, Nicoletta Bobola
Software Mentions: 6
Published: over 5 years ago

10.1093/gigascience/giz037

GenPipes: an open-source framework for distributed and scalable genomic analyses
Cited by: 107
Author(s): Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Létourneau, Joël Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, François Lefebvre, Gary Leveque, Eloi Mercier, David Bujold, Pascale Marquis, Patrick Tran Van, David Anderson de Lima Morais, Julien Tremblay, Xiaojian Shao, Édouard Henrion, Emmanuel González, Pierre-Olivier Quirion, B. Caron, Guillaume Bourque
Software Mentions: 6
Published: about 7 years ago

10.1093/gigascience/giz022

Digital expression explorer 2: a repository of uniformly processed RNA sequencing data
Cited by: 41
Author(s): Mark Ziemann, Antony Kaspi, Assam El‐Osta
Software Mentions: 6
Published: over 7 years ago

10.5808/gi.20074

Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing
Cited by: 2
Author(s): Jiyeon Han, Yeonjoo Jung, Yukyung Jun, Sungsu Park, Sanghyuk Lee
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1008037

Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast
Cited by: 24
Author(s): Kevin S. Myers, Nicholas M. Riley, Matthew E. MacGilvray, Trey K. Sato, Mick McGee, Justin Heilberger, Joshua J. Coon, Audrey P. Gasch
Software Mentions: 6
Published: over 7 years ago

10.1002/JLB.5MA0120-209R

Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells
Cited by: 28
Author(s): Giuseppe Ercolano, Tania Wyss, Bérengère Salomé, Pedro Romero, Sara Trabanelli, Camilla Jandus
Software Mentions: 6
Published: over 6 years ago

10.1186/s13073-021-00939-2

Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes
Cited by: 17
Author(s): David Z. Pan, Min‐Hua Zong, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñóz-Hernández, Miguel Francisco Herrera-Hernández, Marı́a Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Kirsi H. Pietiläinen, Jussi Pihlajamäki, Markku Laakso, Kristina M. Garske, Päivi Pajukanta
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pgen.1006279

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity
Cited by: 43
Author(s): Barbara Mair, Tomasz Konopka, Claudia Kerzendorfer, Katia Sleiman, Šejla Šalic, Violeta Serra, Markus K. Muellner, Vassiliki Théodorou, Sebastian M. Nijman
Software Mentions: 6
Published: almost 10 years ago

10.1155/2021/9921466

A Novel Immune-Related lncRNA-Based Model for Survival Prediction in Clear Cell Renal Cell Carcinoma
Cited by: 9
Author(s): Zedan Zhang, Yanlin Tang, Yanjun Liu, Hongkai Zhuang, Enyu Lin, Lu Xie, Xiaoqiang Feng, Kaiwen Tian, Jiayi Zeng, Jiumin Liu, Yuming Yu
Software Mentions: 6
Published: about 5 years ago

10.7150/ijms.49126

Construction and validation of a three-microRNA signature as prognostic biomarker in patients with hepatocellular carcinoma
Cited by: 9
Author(s): Xi Zhang, Li Ma, Li Zhai, Dong Chen, Yong Li, Zhongjun Shang, Zongmei Zhang, Yu Gao, Wei Yang, Yixun Li, Yu‐Qing Pan
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2018.01212

A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant–Microbe Interactions
Cited by: 12
Author(s): Silvia Zanini, Ena Šečić, Lukas Jelonek, Karl-Heinz Kögel
Software Mentions: 6
Published: almost 8 years ago

10.3389/fphar.2021.728368

A Novel Integrated Metabolism-Immunity Gene Expression Model Predicts the Prognosis of Lung Adenocarcinoma Patients
Cited by: 3
Author(s): Songming Chen, Yumei Duan, Yanhao Wu, Desong Yang, Jian An
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pgen.1006840

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks
Cited by: 54
Author(s): Syed Bukhari, Michael C. Saul, Christopher H. Seward, Huimin Zhang, Miles K. Bensky, Noelle James, Sihai Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell
Software Mentions: 6
Published: about 9 years ago

10.1186/s10020-021-00322-2

High expression of LAMA3/AC245041.2 gene pair associated with KRAS mutation and poor survival in pancreatic adenocarcinoma: a comprehensive TCGA analysis
Cited by: 11
Author(s): Chengming Tian, Xiyao Li, Chunlin Ge
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.725181

Identification of N6-Methylandenosine-Related lncRNAs for Subtype Identification and Risk Stratification in Gastric Adenocarcinoma
Cited by: 9
Author(s): Yuancheng Huang, Zehong Yang, Chao-Yuan Huang, Xiaotao Jiang, Yanhua Yan, Kunhai Zhuang, Yi Wen, Fengbin Liu, Peiwu Li
Software Mentions: 6
Published: almost 5 years ago

10.3389/fonc.2021.642563

A Novel Five-Gene Signature for Prognosis Prediction in Hepatocellular Carcinoma
Cited by: 14
Author(s): Lisa Su, Genhao Zhang, Xiangdong Kong
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pgen.1009432

Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans
Cited by: 12
Author(s): Chenglin Li, Mintie Pu, Wenke Wang, Amaresh Chaturbedi, Felicity J Emerson, Siu Sylvia Lee
Software Mentions: 6
Published: almost 5 years ago

10.1080/20013078.2020.1785746

Influence of species and processing parameters on recovery and content of brain tissue‐derived extracellular vesicles
Cited by: 62
Author(s): Yiyao Huang, Lesley Cheng, Andrey Turchinovich, Vasiliki Mahairaki, Juan C. Troncoso, Olga Pletniková, Norman J. Haughey, Laura J. Vella, Andrew F. Hill, Lei Zheng, Kenneth W. Witwer
Software Mentions: 6
Published: about 6 years ago

10.3389/fimmu.2020.628804

Transcriptomic Analysis of Long-Term Protective Immunity Induced by Vaccination With Mycoplasma gallisepticum Strain ts-304
Cited by: 5
Author(s): Sathya N Kulappu Arachchige, Neil D. Young, Anna Kanci Condello, Oluwadamilola S Omotainse, Amir H. Noormohammadi, Nadeeka K. Wawegama, Glenn F. Browning
Software Mentions: 6
Published: over 5 years ago

10.3389/fimmu.2021.688493

Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes
Cited by: 4
Author(s): Martín A. Rivas, Ceyda Durmaz, Andreas Kloetgen, Cristopher R Chin, Zhengming Chen, Bhavneet Bhinder, Amnon Koren, Aaron D. Viny, Christopher D. Scharer, Jeremy M. Boss, Olivier Elemento, Christopher E. Mason, Ari Melnick
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pgen.1007633

Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion
Cited by: 45
Author(s): Yasmine J. Liu, Georges E. Janssens, Rebecca L. McIntyre, Marte Molenaars, Rashmi Kamble, Arwen W. Gao, Aldo Jongejan, Michel van Weeghel, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 6
Published: over 7 years ago

10.3389/fimmu.2021.726747

Identifying Immune Cell Infiltration and Effective Diagnostic Biomarkers in Rheumatoid Arthritis by Bioinformatics Analysis
Cited by: 45
Author(s): Sheng Zhou, Hongmei Lü, Min Xiong
Software Mentions: 6
Published: about 5 years ago

10.3389/fimmu.2021.729217

Timing of Transcriptomic Peripheral Blood Mononuclear Cell Responses of Sheep to Fasciola hepatica Infection Differs From Those of Cattle, Reflecting Different Disease Phenotypes
Cited by: 4
Author(s): Dagmara A. Niedziela, Amalia Naranjo‐Lucena, Verónica Molina-Hernández, John A. Browne, Á. Martínez-Moreno, J. Pérez, David E. MacHugh, Grace Mulcahy
Software Mentions: 6
Published: almost 5 years ago

10.3389/fimmu.2017.00246

Host Genetic Background Strongly Affects Pulmonary microRNA Expression before and during Influenza A Virus Infection
Cited by: 19
Author(s): Matthias Preuße, Klaus Schughart, Frank Peßler
Software Mentions: 6
Published: over 9 years ago

10.3389/fimmu.2021.651254

High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells
Cited by: 5
Author(s): Kensei Kishimoto, Catera L. Wilder, Justin Buchanan, Minh Anh Nguyen, Chidera Okeke, Alexander Hoffmann, Quen J. Cheng
Software Mentions: 6
Published: over 5 years ago

10.3389/fimmu.2020.00435

Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells
Cited by: 10
Author(s): Stephanie S Pavlovich, Tamarand L. Darling, Adam J. Hume, Robert A. Davey, Feng Feng, Elke Mühlberger, Thomas B. Kepler
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.668311

Construction of a circRNA-Related Prognostic Risk Score Model for Predicting the Immune Landscape of Lung Adenocarcinoma
Cited by: 0
Author(s): Huawei Li, Jun Wang, Linyou Zhang
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2020.00992

Identification of the Six-RNA-Binding Protein Signature for Prognosis Prediction in Bladder Cancer
Cited by: 13
Author(s): Yucai Wu, Yi Liu, Anbang He, Bao Guan, Shiming He, Cuijian Zhang, Zhengjun Kang, Yanqing Gong, Xuesong Li, Liqun Zhou
Software Mentions: 6
Published: almost 6 years ago

10.3389/fgene.2021.571231

Identification and Analysis of Potential Key Genes Associated With Hepatocellular Carcinoma Based on Integrated Bioinformatics Methods
Cited by: 21
Author(s): Zhuolin Li, Yao Lin, Bizhen Cheng, Qiaoxin Zhang, Yingmu Cai
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2021.664379

Putative Causal Variants Are Enriched in Annotated Functional Regions From Six Bovine Tissues
Cited by: 19
Author(s): Claire P. Prowse-Wilkins, Jianghui Wang, Ruidong Xiang, Josie B. Garner, Michael E. Goddard, Amanda J. Chamberlain
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2020.562445

A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice
Cited by: 4
Author(s): Seth Jarvis, Nicol Birsa, Maria Secrier, Pietro Fratta, Vincent Plagnol
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2020.00011

Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance
Cited by: 6
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 6
Published: over 6 years ago

10.1084/jem.20200829

The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell function
Cited by: 80
Author(s): Christopher Mapperley, Louie Van De Lagemaat, Hannah Lawson, Andrea Tavosanis, J Paris, Joana Campos, David Wotherspoon, Jozef Durko, Annika Sarapuu, Joong-Seon Choe, Ivayla Ivanova, Daniela Krause, Alex von Kriegsheim, Christian Much, Marcos Morgan, Richard I. Gregory, Adam J. Mead, Dónal O’Carroll, Kamil R. Kranc
Software Mentions: 6
Published: almost 6 years ago

10.1084/jem.20192386

Transcription cofactor GRIP1 differentially affects myeloid cell–driven neuroinflammation and response to IFN-β therapy
Cited by: 4
Author(s): Sanda Mimouna, David A. Rollins, Gayathri Shibu, Bowranigan Tharmalingam, Dinesh K Deochand, Xi Chen, David J. Oliver, Yurii Chinenov, Inez Rogatsky
Software Mentions: 6
Published: almost 6 years ago

10.15252/embj.2018100882

Life‐long impairment of glucose homeostasis upon prenatal exposure to psychostimulants
Cited by: 11
Author(s): Solomiia Korchynska, Maria Krassnitzer, Katarzyna Maleńczyk, Rashmi B. Prasad, Evgenii Tretiakov, Sabah Rehman, Valentina Cinquina, Victoria Gernedl, Matthias Farlik, Julian Petersen, S Hannes, Julia Schachenhofer, Sonali N. Reisinger, Alice Zambon, Olof Asplund, Isabella Artner, Erik Keimpema, Gert Lübec, Jan Mulder, Christoph Bock, Daniela D. Pollak, Roman A. Romanov, Christian Pifl, Leif Groop, Tomas Hökfelt, Tibor Harkany
Software Mentions: 6
Published: over 6 years ago

10.15252/embj.2020104569

Translation is required for miRNA‐dependent decay of endogenous transcripts
Cited by: 15
Author(s): Adriano Biasini, Baroj Abdulkarim, Stefano de Pretis, Jennifer Y. Tan, Rajika Arora, Harry Wischnewski, René Dreos, Mattia Pelizzola, Constance Ciaudo, Ana C. Marques
Software Mentions: 6
Published: over 5 years ago

10.15252/embj.2020107100

De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis
Cited by: 17
Author(s): Sara Zocher, Rupert W. Overall, Gabriel Berdugo-Vega, Nicole Rund, Anne Karasinsky, Vijay S. Adusumilli, Christina Steinhauer, Sina Scheibenstock, Kristian Händler, Joachim L. Schultze, Federico Calegari, Gerd Kempermann
Software Mentions: 6
Published: about 5 years ago

10.1242/dmm.047225

Hearing impairment due to Mir183/96/182 mutations suggests both loss-of-function and gain-of-function effects
Cited by: 10
Author(s): Morag A. Lewis, Francesca Di Domenico, Neil J. Ingham, Haydn M. Prosser, Karen P. Steel
Software Mentions: 6
Published: over 5 years ago

10.3390/v13040553

Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection of Aedes albopictus Mosquitoes
Cited by: 11
Author(s): Michele Marconcini, Elisa Pischedda, Vincent Houé, Umberto Palatini, Nabor Lozada-Chávez, Davide Sogliani, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2020.01088

MMP25 Regulates Immune Infiltration Level and Survival Outcome in Head and Neck Cancer Patients
Cited by: 8
Author(s): Yujie Liang, Chenyu Guan, Kan Li, Guanghui Zheng, Tao Wang, Sien Zhang, Guiqing Liao
Software Mentions: 5
Published: about 6 years ago

10.1155/2021/9998697

Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19
Cited by: 12
Author(s): Shaocong Mo, Leijie Dai, Yulin Wang, Biao Song, Zongcheng Yang, Wenchao Gu
Software Mentions: 5
Published: almost 5 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.27014

Regulation of life span by the gut microbiota in the short-lived African turquoise killifish
Cited by: 262
Author(s): Patrick M. Smith, David Willemsen, Miriam Popkes, Franziska Metge, Edson Gandiwa, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 5
Published: almost 9 years ago

10.1155/2018/7691794

Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse
Cited by: 6
Author(s): Minjung Kim, Yi Yin Yu, Ji-Hoi Moon, Insong Koh, Jae Hyung Lee
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0214833

Disparate effects of antibiotic-induced microbiome change and enhanced fitness in Daphnia magna
Cited by: 27
Author(s): Asa Motiei, Björn Brindefalk, Martin Ogonowski, Rehab El-Shehawy, Paulina Pastuszek, Karin Ek, Birgitta Liewenborg, Klas I. Udekwu, Elena Gorokhova
Software Mentions: 5
Published: over 6 years ago

10.1038/s41438-021-00606-y

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L
Cited by: 8
Author(s): Brennan Hyden, Craig H. Carlson, Fred E. Gouker, Jeremy Schmutz, Kerrie Barry, Anna Lipzen, Aarti Sharma, Laura Sandor, Gerald A. Tuskan, Guanying Feng, Matthew S. Olson, Stephen P. DiFazio, Lawrence B. Smart
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1007981

Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes
Cited by: 29
Author(s): Eva Gómez-Orte, Beatriz Sáenz-Narciso, Angelina Zheleva, Begoña Ezcurra, María de Toro, Rosa López, Irene Gastaca, Hilde Nilsen, María P. Sacristán, Ralf Schnabel, Juan Cabello
Software Mentions: 5
Published: over 7 years ago

10.1038/s41438-021-00529-8

Chromatin accessibility and translational landscapes of tea plants under chilling stress
Cited by: 21
Author(s): Pengjie Wang, Shan Jin, Xuejin Chen, Lihua Wu, Yuanrun Zheng, Chuan Yue, Yan Guo, Xingtan Zhang, Jing Yang, Naixing Ye
Software Mentions: 5
Published: over 5 years ago

10.1038/sdata.2016.4

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Cited by: 10
Author(s): Anneleen Decock, Maté Ongenaert, Wim Van Criekinge, Franki Speleman, Jo Vandesompele
Software Mentions: 5
Published: over 10 years ago

10.1038/sdata.2016.51

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome
Cited by: 40
Author(s): Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser‐Klopp, J. J. Arranz
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0153925

Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)
Cited by: 66
Author(s): . Shumayla, Shailesh Sharma, Ajay Kumar Pandey, Kashmir Singh, Santosh Kumar Upadhyay
Software Mentions: 5
Published: over 10 years ago

10.1038/sdata.2018.136

A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: about 8 years ago

10.1038/sdata.2018.290

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance
Cited by: 5
Author(s): Hengyou Zhang, Christine Zuelsdorf, Darin S. Penneys, Shoujin Fan, Janice Kofsky, Bao‐Hua Song
Software Mentions: 5
Published: over 7 years ago

10.1038/s41597-020-0352-7

Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.
Cited by: 69
Author(s): Won-Hee Kang, Young Mi Sim, Namjin Koo, Jae Do Nam, Junesung Lee, Nayoung Kim, Hakgi Jang, Yongmin Kim, Seon-In Yeom
Software Mentions: 5
Published: over 6 years ago

10.3389/fonc.2020.01195

Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model
Cited by: 82
Author(s): Barbara Schrörs, Sebastian Boegel, Christian Albrecht, Thomas Bukur, Valesca Bukur, Christoph Holtsträter, Christoph Ritzel, Katja Manninen, Arbel D. Tadmor, Mathias Vormehr, Uğur Şahin, Martin Löwer
Software Mentions: 5
Published: about 6 years ago

10.1038/srep25668

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
Cited by: 76
Author(s): Konrad J. Dębski, Asla Pitkänen, Noora Puhakka, Anna Bot, Ishant Khurana, K N Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El‐Osta, Katarzyna Łukasiuk, Katja Kobow
Software Mentions: 5
Published: over 10 years ago

10.1093/hmg/ddab031

Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma
Cited by: 10
Author(s): Ruhina Shirin Laskar, Peng Li, Szilvia Ecsedi, Behnoush Abedi‐Ardekani, G. Durand, Nivonirina Robinot, Jean-Noël Hubert, Vladimír Janout, Давид Заридзе, Anush Mukeria, Dana Mateș, Ivana Holcátová, Lenka Foretová, Beata Świątkowska, Zoran Džamić, Saša Milosavljević, Robert Olaso, Anne Boland, Jean‐François Deleuze, David C. Muller, James McKay, Paul Brennan, Florence Le Calvez-Kelm, Ghislaine Scélo, Estelle Chanudet
Software Mentions: 5
Published: over 5 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pgen.1006222

KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans
Cited by: 68
Author(s): Agnieszka Gacek‐Matthews, Harald Berger, Takahiko Sasaki, Kathrin Wittstein, Clemens Gruber, Zachary A. Lewis, Joseph Strauss
Software Mentions: 5
Published: almost 10 years ago

10.1038/srep29647

Tracking Cancer Genetic Evolution using OncoTrack
Cited by: 4
Author(s): Asoke K. Talukder, Mahima Agarwal, Kenneth H. Buetow, Patrice Denèfle
Software Mentions: 5
Published: about 10 years ago

10.1074/mcp.TIR119.001646

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis
Cited by: 109
Author(s): Yong Zhu, Lukas M. Orre, Yan Zhou Tran, Georgios Mermelekas, Henrik J. Johansson, Alina Malyutina, Simon Anders, Janne Lehtiö
Software Mentions: 5
Published: about 6 years ago

10.1038/srep33813

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae)
Cited by: 20
Author(s): Charles J. Mason, Erin D. Scully, Scott M. Geib, Kelli Hoover
Software Mentions: 5
Published: almost 10 years ago

10.1016/j.molmet.2017.02.007

Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Cited by: 125
Author(s): Brian Y.H. Lam, Irène Cimino, Joseph Polex-Wolf, Sara Kohnke, Debra Rimmington, Valentine P. Iyemere, Nicholas Heeley, Chiara Cossetti, Reiner Schulte, Luís R. Saraiva, Darren W. Logan, Clémence Blouet, Stephen O’Rahilly, Anthony P. Coll, Giles S.H. Yeo
Software Mentions: 5
Published: over 9 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568