Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: edgeR

https://packages.ecosyste.ms/registries/bioconductor.org/packages/edgeR

Empirical Analysis of Digital Gene Expression Data in R
3 versions
Latest release: about 1 year ago
166 dependent packages
2,704,225 downloads total

Papers Mentioning edgeR 6,568

10.1111/acel.13381
Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF‐16‐induced longevity
Cited by: 7
Author(s): Rebecca L. McIntyre, Simone Denis, Rashmi Kamble, Marte Molenaars, Michael Petr, Bauke V. Schomakers, Mizanur Rahman, Siddhartha Datta Gupta, Márton L. Tóth, Siva A. Vanapalli, Aldo Jongejan, Morten Scheibye‐Knudsen, Riekelt H. Houtkooper, Georges E. Janssens
Software Mentions: 6
Published: over 3 years ago
10.1016/j.celrep.2021.108739
Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer’s disease
Cited by: 40
Author(s): Hongtian Yang, Kristen D. Onos, Kwangbom Choi, Kelly J. Keezer, Daniel A. Skelly, Gregory W. Carter, Gareth R. Howell
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12864-020-6748-0
Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches
Cited by: 19
Author(s): Vladislav V. Babenko, Oleg V. Podgorny, Valentin A. Manuvera, Artem S. Kasianov, Alexander I. Manolov, Ekaterina N. Grafskaia, Dmitriy A. Shirokov, Alexey S. Kurdyumov, D. V. Vinogradov, Anastasia S. Nikitina, Sergey I. Kovalchuk, Nikolay Anikanov, Ivan Butenko, Olga Pobeguts, Daria Matyushkina, Daria V. Rakitina, Elena S. Kostryukova, Victor G. Zgoda, I. P. Baskova, В. М. Трухан, Mikhail S. Gelfand, Vadim M. Govorun, Helgi B. Schiöth, В. Н. Лазарев
Software Mentions: 6
Published: over 4 years ago
10.3389/fmicb.2021.723682
Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon)
Cited by: 13
Author(s): Ying Zhu, Yudong Li, Hai-Qiong Yang, Ke He, Keyi Tang
Software Mentions: 6
Published: over 3 years ago
10.3389/fmicb.2018.00294
Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities
Cited by: 108
Author(s): Annelein Meisner, Samuel Jacquiod, L. Basten Snoek, Freddy C. ten Hooven, Wim H. van der Putten
Software Mentions: 6
Published: almost 7 years ago
10.1186/s12915-018-0615-3
Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways
Cited by: 79
Author(s): Ziyun Wu, Megan M. Senchuk, Dylan J. Dues, Benjamin K. Johnson, Jason Cooper, Leira Lew, Emily Machiela, Claire E. Schaar, Heather DeJonge, T. Keith Blackwell, Jeremy M. Van Raamsdonk
Software Mentions: 6
Published: about 6 years ago
10.3389/fgene.2019.01111
Translated Long Non-Coding Ribonucleic Acid ZFAS1 Promotes Cancer Cell Migration by Elevating Reactive Oxygen Species Production in Hepatocellular Carcinoma
Cited by: 17
Author(s): Zhi-Wei Guo, Yijun Meng, Xiang-Ming Zhai, Chen Xie, Na Zhao, Min Li, Chen Zhou, Kun Li, Tiancai Liu, Xu Yang, Yangyang Wu
Software Mentions: 6
Published: about 5 years ago
10.3389/fimmu.2021.724015
Transcriptional, Epigenetic, and Functional Reprogramming of Monocytes From Non-Human Primates Following Chronic Alcohol Drinking
Cited by: 11
Author(s): Sloan A. Lewis, Suhas Sureshchandra, Brianna Doratt, Vanessa Jiménez, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 3 years ago
10.3389/fimmu.2020.00714
Characterization of the Impact of Daclizumab Beta on Circulating Natural Killer Cells by Mass Cytometry
Cited by: 7
Author(s): Thanmayi Ranganath, Laura J. Simpson, Anne-Maud Ferreira, Christof Seiler, Elena Vendrame, Nancy Q. Zhao, Jason D. Fontenot, Susan Holmes, Catherine A. Blish
Software Mentions: 6
Published: over 4 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 4 years ago
10.3389/fmed.2021.681388
A Five-Gene-Based Prognostic Signature for Hepatocellular Carcinoma
Cited by: 7
Author(s): Dean Tian, Yang Yu, Li Zhang, Jiufeng Sun, Wentao Jiang
Software Mentions: 6
Published: over 3 years ago
10.1186/s12859-019-3121-x
A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons
Cited by: 2
Author(s): Stanislav Listopad, Trina M. Norden-Krichmar
Software Mentions: 6
Published: about 5 years ago
10.3389/fgene.2019.01152
RNA-Seq Perspectives to Improve Clinical Diagnosis
Cited by: 65
Author(s): Guillermo Marco-Puche, Sergio Lois, Javier Benítez, Juan Carlos Triviño
Software Mentions: 6
Published: about 5 years ago
10.3389/fmed.2021.587496
Potential Prognostic Immune Biomarkers of Overall Survival in Ovarian Cancer Through Comprehensive Bioinformatics Analysis: A Novel Artificial Intelligence Survival Prediction System
Cited by: 4
Author(s): Tingshan He, Liwen Huang, Jing Li, Peng Wang, Zhiqiao Zhang
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-020-06831-4
Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure
Cited by: 13
Author(s): Shubha Suresh, Teresa J. Crease, Melania E. Cristescu, Frédéric J. J. Chain
Software Mentions: 6
Published: over 4 years ago
10.3389/fendo.2021.626359
Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes
Cited by: 25
Author(s): Laila Silamiķele, Ivars Silamiķelis, Monta Ustinova, Zane Kalniņa, Ilze Elbere, Ramona Petrovska, Ineta Kalniņa, Jānis Kloviņš
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12859-020-03715-y
MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments
Cited by: 8
Author(s): Brian Vestal, Camille M. Moore, Elizabeth Wynn, Laura Saba, Tasha E. Fingerlin, Katerina Kechris
Software Mentions: 6
Published: over 4 years ago
10.3389/fcimb.2019.00392
Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution
Cited by: 13
Author(s): Regan J. Hayward, J. Wallis Marsh, Michael S. Humphrys, Wilhelmina M. Huston, Garry Myers
Software Mentions: 6
Published: about 5 years ago
10.3390/microorganisms9051104
Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea
Cited by: 6
Author(s): Ping Sun, Silu Zhang, Ying Wang, Bangqin Huang
Software Mentions: 6
Published: over 3 years ago
10.3389/fncel.2019.00510
Brainstem-Evoked Transcription of Defensive Genes After Spinal Cord Injury
Cited by: 2
Author(s): Walter J. Jermakowicz, Melissa M. Carballosa-Gautam, Alberto Vitores, Ian D. Hentall
Software Mentions: 6
Published: about 5 years ago
10.1523/JNEUROSCI.1675-19.2019
Midkine-a Is Required for Cell Cycle Progression of Müller Glia during Neuronal Regeneration in the Vertebrate Retina
Cited by: 28
Author(s): Mikiko Nagashima, Travis S. D’Cruz, Antoinette Eyram Danku, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Software Mentions: 6
Published: almost 5 years ago
10.3389/fmicb.2019.00745
Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model
Cited by: 22
Author(s): Zachary M. Burcham, Jennifer L. Pechal, Carl J. Schmidt, Jeffrey L. Bose, Jason W. Rosch, M. Eric Benbow, Heather R. Jordan
Software Mentions: 6
Published: over 5 years ago
10.3390/microorganisms7120595
Dynamic Succession of Microbiota during Ensiling of Whole Plant Corn Following Inoculation with Lactobacillus buchneri and Lactobacillus hilgardii Alone or in Combination
Cited by: 40
Author(s): Pascal Drouin, Julien Tremblay, Frédérique Chaucheyras‐Durand
Software Mentions: 6
Published: about 5 years ago
10.1016/j.isci.2021.102690
Functional and genomic adaptations of blood monocytes to pregravid obesity during pregnancy
Cited by: 12
Author(s): Suhas Sureshchandra, Nicole Marshall, Norma Mendoza, Allen Jankeel, Michael Z. Zulu, Ilhem Messaoudi
Software Mentions: 6
Published: over 3 years ago
10.1186/1471-2105-14-370
Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
Cited by: 36
Author(s): Hubert Rehrauer, Lennart Opitz, Ge Tan, Lina Sieverling, Ralph Schlapbach
Software Mentions: 6
Published: about 11 years ago
10.1186/1471-2105-15-S3-A7
Oqtans: a multifunctional workbench for RNA-seq data analysis
Cited by: 0
Author(s): Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Kaushik Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch
Software Mentions: 6
Published: almost 11 years ago
10.1186/s12864-019-6073-7
GENAVi: a shiny web application for gene expression normalization, analysis and visualization
Cited by: 36
Author(s): Alberto Luiz P Reyes, Tiago C. Silva, Simon Coetzee, Jasmine T Plummer, Brian D. Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther, Michelle R. Jones
Software Mentions: 6
Published: about 5 years ago
10.18632/aging.103350
A novel molecular-clinicopathologic nomogram to improve prognosis prediction of hepatocellular carcinoma
Cited by: 3
Author(s): Zhongjing Zhang, Wanqing Weng, Weiguo Huang, Boda Wu, Yi Zhou, Jie Zhang, Tuo Deng, Yan Wen, Jiecheng Zhang, Jian‐Yang Ao, Qiyu Zhang, Ke‐Qing Shi
Software Mentions: 6
Published: over 4 years ago
10.3390/ijms22179337
Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients
Cited by: 3
Author(s): Alicja Pacholewska, Christina Grimm, Carmen D. Herling, Matthias Lienhard, Anja Königs, Bernd Timmermann, Janine Altmüller, Oliver Mücke, Hans Christian Reinhardt, Christoph Plass, Ralf Herwig, Michael Hallek, Michal R. Schweiger
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-019-5686-1
aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data
Cited by: 4
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 6
Published: over 5 years ago
10.3389/fcell.2021.653305
Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development
Cited by: 9
Author(s): Xiangmei Zhang, Igor Mandric, Kevin Nguyen, Thao T. T. Nguyen, Matteo Pellegrini, James C. R. Grove, Steven Barnes, Xian-Jie Yang
Software Mentions: 6
Published: over 3 years ago
10.3390/ijms22147322
Effect of the Electromagnetic Field (EMF) Radiation on Transcriptomic Profile of Pig Myometrium during the Peri-Implantation Period—An In Vitro Study
Cited by: 6
Author(s): Ewa Monika Drzewiecka, Wiktoria Kozlowska, Łukasz Paukszto, Agata Żmijewska, Pawel Jozef Wydorski, J Jastrzebski, Anita Franczak
Software Mentions: 6
Published: over 3 years ago
10.3389/fmicb.2020.588778
Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription
Cited by: 21
Author(s): Benjamin Pontiller, Sandra Martínez‐García, Daniel Lundin, Jarone Pinhassi
Software Mentions: 6
Published: about 4 years ago
10.3389/fcell.2021.690167
Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs
Cited by: 0
Author(s): Miao Wang, Dong Chen, Huoqing Zheng, Luping Zhao, Xiao‐Feng Xue, Fengyun Yu, Yu Zhang, Chao Cheng, Qingsheng Niu, Shuai Wang, Yi Zhang, Liming Wu
Software Mentions: 6
Published: over 3 years ago
10.1016/j.celrep.2021.109362
Nutritional regulation of oligodendrocyte differentiation regulates perineuronal net remodeling in the median eminence
Cited by: 29
Author(s): Sara Kohnke, Sophie Buller, Danaé Nuzzaci, Katherine Ridley, Brian Lam, Helena Pivoňková, Marie A. Bentsen, Kimberly M. Alonge, Chao Zhao, John Tadross, Staffan Holmqvist, Takahiro Shimizu, Hannah A. Hathaway, Hui‐Liang Li, Wendy B. Macklin, Michael W. Schwartz, William D. Richardson, Giles S.H. Yeo, R. J. M. Franklin, Ragnhildur Thóra Káradóttir, David H. Rowitch, Clémence Blouet
Software Mentions: 6
Published: over 3 years ago
10.1186/s12863-021-00991-2
The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells
Cited by: 4
Author(s): Ritu Mann-Nüttel, Shafaqat Ali, Patrick Petzsch, Karl Köhrer, Judith Alferink, Stefanie Scheu
Software Mentions: 6
Published: about 3 years ago
10.3390/ijms22116034
mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex
Cited by: 9
Author(s): Martin Schüle, Tamer Butto, Sri Dewi, Laura Schlichtholz, Susanne Strand, Susanne Gerber, Kristina Endres, Susann Schweiger, Jennifer Winter
Software Mentions: 6
Published: over 3 years ago
10.1186/s40168-017-0389-9
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming
Cited by: 340
Author(s): Kyle Hartman, Marcel G. A. van der Heijden, Raphaël Wittwer, Samiran Banerjee, Jean Claude Walser, Klaus Schlaeppi
Software Mentions: 6
Published: almost 7 years ago
10.1186/s12862-017-1025-9
Epigenetic variation between urban and rural populations of Darwin’s finches
Cited by: 50
Author(s): Sabrina M. McNew, Daniel Beck, Ingrid Sadler‐Riggleman, Sarah A. Knutie, Jennifer A. H. Koop, Dale H. Clayton, Michael K. Skinner
Software Mentions: 6
Published: over 7 years ago
10.3390/ijms22116052
Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species
Cited by: 18
Author(s): Eugenia E. Montiel, Francisco Panzera, Teresa Palomeque, Pedro Lorite, Sebastián Pita
Software Mentions: 6
Published: over 3 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: about 8 years ago
10.3389/fendo.2021.568397
Development and Validation of an m6A RNA Methylation Regulators-Based Signature for Predicting the Prognosis of Adrenocortical Carcinoma
Cited by: 7
Author(s): Chengquan Shen, Jing Liu, Xiaokun Yang, Wei Jiao, Yonghua Wang
Software Mentions: 6
Published: almost 4 years ago
10.1002/pld3.279
Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis
Cited by: 12
Author(s): Will E. Hinckley, Judy A. Brusslan
Software Mentions: 6
Published: about 4 years ago
10.3390/ijms22136641
Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.)
Cited by: 5
Author(s): Chen Li, Meng Kou, Mohamed Hamed Arisha, Wei Tang, Meng Ma, Hui Yan, Xin Wang, Xiaoxiao Wang, Yungang Zhang, Yaju Liu, Runfei Gao, Qiang Li
Software Mentions: 6
Published: over 3 years ago
10.3389/fcell.2021.625212
Clinical Significance of a Novel Tumor Progression-Associated Immune Signature in Colorectal Adenocarcinoma
Cited by: 3
Author(s): Rui Mao, Fan Yang, Wei Zheng, Chang Xu, Qian Liu, Yanjun Liu, Tongtong Zhang
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12859-016-1195-2
A fuzzy method for RNA-Seq differential expression analysis in presence of multireads
Cited by: 16
Author(s): Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano, Mariano Francesco Caratozzolo, Sabino Liuni
Software Mentions: 6
Published: about 8 years ago
10.1186/s12864-018-4738-2
Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells
Cited by: 43
Author(s): Fernando H. Biase, Katelyn M. Kimble
Software Mentions: 6
Published: over 6 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: almost 4 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: over 4 years ago
10.1002/ctm2.234
Epigenetic consequences of hormonal interactions between opposite‐sex twin fetuses
Cited by: 4
Author(s): Siming Kong, Yong Peng, Wei Chen, Xinyi Ma, Wei Yuan, Yangyu Zhao, Rong Li, Jie Qiao, Liying Yan
Software Mentions: 6
Published: about 4 years ago
10.1038/s42003-020-01364-8
Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2eGFP mouse
Cited by: 22
Author(s): Tingzhen Mu, Liqin Xu, Yu Zhong, Xinyu Liu, Zhikun Zhao, Changyuan Huang, Xiaofeng Lan, Chengchen Lufei, Yi Zhou, Yixun Su, Luang Xu, Miaomiao Jiang, Hong Zhou, Xinxin Lin, Liang Wu, Siqi Peng, Shiping Liu, Susanne Brix, Michael Dean, N. Ray Dunn, Kenneth S. Zaret, Xin-Yuan Fu, Yong Hou
Software Mentions: 6
Published: about 4 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: over 3 years ago
10.1002/advs.201903200
Size‐Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe‐by‐Design
Cited by: 34
Author(s): Artur Filipe Rodrigues, Leon Newman, Dhifaf Jasim, Sourav P. Mukherjee, Jun Wang, Isabella Anna Vacchi, Cécilia Ménard‐Moyon, Alberto Bianco, Bengt Fadeel, Kostas Kostarelos, Cyrill Bussy
Software Mentions: 6
Published: over 4 years ago
10.1186/s13148-018-0593-x
Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: about 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: about 4 years ago
10.1186/s13148-015-0123-z
High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Cited by: 32
Author(s): Daniel Nätt, I. Johansson, Tomas Faresjö, Johnny Ludvigsson, Annika Thorsell
Software Mentions: 6
Published: over 9 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: about 4 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: about 4 years ago
10.1186/s12920-018-0413-3
Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature
Cited by: 20
Author(s): Dan Li, William Yang, Yifan Zhang, Jack Yang, Renchu Guan, Dong Xu, Mary Qu Yang
Software Mentions: 6
Published: about 6 years ago
10.1007/s00439-020-02228-1
A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies
Cited by: 5
Author(s): Liliya Nazlamova, N. Simon Thomas, Man‐Kim Cheung, Jelmer Legebeke, Jenny Lord, Reuben J. Pengelly, William Tapper, Gabrielle Wheway
Software Mentions: 6
Published: about 4 years ago
10.1161/CIRCULATIONAHA.120.046464
Hyperglycemia Induces Trained Immunity in Macrophages and Their Precursors and Promotes Atherosclerosis
Cited by: 75
Author(s): Laurienne Edgar, Naveed Akbar, Adam Braithwaite, Thomas Krausgruber, Héctor Gallart-Ayala, Jade Bailey, Alastair Corbin, Tariq E. Khoyratty, Joshua T Chai, Mohammad Alkhalil, André F. Rendeiro, Klemen Žiberna, Ritu Arya, Thomas J. Cahill, Christoph Bock, Jurga Laurencikiene, Mark J. Crabtree, Madeleine E. Lemieux, Niels P. Riksen, Mihai G. Netea, Craig E. Wheelock, Keith M. Channon, Mikael Rydén, Irina A. Udalova, Ricardo Carnicer, Robin P. Choudhury
Software Mentions: 6
Published: about 3 years ago
10.26508/lsa.202000976
Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Cited by: 5
Author(s): Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-021-07656-5
Species and population specific gene expression in blood transcriptomes of marine turtles
Cited by: 8
Author(s): Shreya M. Banerjee, Jamie Adkins Stoll, Camryn D. Allen, Jennifer M. Lynch, Heather Harris, Lauren Kenyon, Richard E. Connon, Eleanor J. Sterling, Eugênia Naro‐Maciel, Kathryn M. McFadden, Margaret M. Lamont, James Benge, Nadia B. Fernández, Jeffrey A. Seminoff, Scott R. Benson, Rebecca L. Lewison, Tomoharu Eguchi, Tammy M. Summers, Jessy R. Hapdei, Marc Rice, Summer L. Martin, T. Todd Jones, Peter H. Dutton, George H. Balazs, Lisa M. Komoroske
Software Mentions: 6
Published: over 3 years ago
10.1016/j.stem.2020.11.005
Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency
Cited by: 125
Author(s): Masaki Kinoshita, M. Barber, William Mansfield, Yingzhi Cui, Daniel Spindlow, Giuliano Giuseppe Stirparo, Sabine Dietmann, Jennifer Nichols, Austin Smith
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12864-019-6076-4
Transcriptome analysis of the effect of C-C chemokine receptor 5 deficiency on cell response to Toxoplasma gondii in brain cells
Cited by: 7
Author(s): Kaoru Kobayashi, Kousuke Umeda, Fumie Ihara, Sadao Tanaka, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
Software Mentions: 6
Published: over 5 years ago
10.1128/mBio.02683-20
The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral <i>UL4</i> / <i>UL5</i> Transcripts
Cited by: 23
Author(s): Ana Cristina Gonzalez-Perez, Markus Stempel, Emanuel Wyler, Christian Urban, Antonio Piras, Thomas Hennig, Sabina Ganskih, Yuanjie Wei, Albert Heim, Markus Landthaler, Andreas Pichlmair, Lars Dölken, Mathias Munschauer, Florian Erhard, Melanie M. Brinkmann
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.103626
A novel hypoxic tumor microenvironment signature for predicting the survival, progression, immune responsiveness and chemoresistance of glioblastoma: a multi-omic study
Cited by: 6
Author(s): Zihao Wang, Lu Gao, Xiaopeng Guo, Yaning Wang, Yu Wang, Wenbin Ma, Yi Guo, Bing Xing
Software Mentions: 6
Published: over 4 years ago
10.1128/mBio.01849-21
Hofbauer Cells Spread Listeria monocytogenes among Placental Cells and Undergo Pro-Inflammatory Reprogramming while Retaining Production of Tolerogenic Factors
Cited by: 7
Author(s): Siavash Azari, Lauren J. Johnson, Amy Webb, Sophia M Kozlowski, Xiaoli Zhang, Kara M. Rood, Amal O. Amer, Stéphanie Seveau
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-017-3630-9
Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients
Cited by: 42
Author(s): Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller‐Brüsselbach, Silke Reinartz, Rolf Müller
Software Mentions: 6
Published: over 7 years ago
10.1002/cam4.4115
Development and validation of a <i>PBRM1</i>‐associated immune prognostic model for clear cell renal cell carcinoma
Cited by: 5
Author(s): Jiayi Chen, Chunlin Yao, Nan Qiao, Yangyang Ge, Jianhua Li, Yun Lin, Shanglong Yao
Software Mentions: 6
Published: about 3 years ago
10.1002/cam4.4161
Integrated pan‐cancer of <i>AURKA</i> expression and drug sensitivity analysis reveals increased expression of <i>AURKA</i> is responsible for drug resistance
Cited by: 12
Author(s): Noushin Miralaei, Ahmad Majd, Kamran Ghaedi, Maryam Peymani, Masoomeh Safaei
Software Mentions: 6
Published: over 3 years ago
10.7150/thno.55946
Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome
Cited by: 28
Author(s): Xiaomin Hu, Hanyu Li, Xinyue Zhao, Ronggang Zhou, Honghong Liu, Yiting Sun, Yue Fan, Yanan Shi, Shushan Qiao, Shuang‐Jiang Liu, Hongwei Liu, Shuyang Zhang
Software Mentions: 6
Published: almost 4 years ago
10.1016/j.celrep.2020.108545
CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
Cited by: 23
Author(s): Jonathan Martínez-Fábregas, Luopin Wang, Elizabeth Pöhler, Adeline Cozzani, Stephan Wilmes, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 6
Published: about 4 years ago
10.1186/s12859-018-2437-2
Adaptively capturing the heterogeneity of expression for cancer biomarker identification
Cited by: 1
Author(s): Xueping Xie, Yufeng Xie, Yitong Liu, Hongqiang Wang
Software Mentions: 6
Published: about 6 years ago
10.1016/j.celrep.2019.11.026
Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Cited by: 53
Author(s): Edward Lau, Yu Han, Damon R. Williams, Cody T Thomas, Rajani Shrestha, Joseph C. Wu, Maggie Lam
Software Mentions: 6
Published: about 5 years ago
10.7150/thno.56141
Distinct placental molecular processes associated with early-onset and late-onset preeclampsia
Cited by: 31
Author(s): Zhonglu Ren, Yunfei Gao, Yue Gao, Guanmei Liang, Qian Chen, Sijia Jiang, Xiaoxue Yang, Cui-Xia Fan, Haizhen Wang, Jing Wang, Yi‐Wu Shi, Chaoqun Xiao, Ming Zhong, Xinping Yang
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12864-019-6061-y
Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks
Cited by: 12
Author(s): Jim A. Mossman, Leann M. Biancani, David M. Rand
Software Mentions: 6
Published: over 5 years ago
10.1016/j.celrep.2019.06.046
Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry
Cited by: 68
Author(s): Pavel Bouchal, Olga T. Schubert, Jakub Faktor, Lenka Čápková, Hana Imrichová, Karolína Zoufalová, Vendula Páralová, Roman Hrstka, Yansheng Liu, H. Alexander Ebhardt, Eva Budínská, Rudolf Nenutil, Ruedi Aebersold
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-019-55441-y
Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Cited by: 50
Author(s): Konstantin Carlberg, Marina Korotkova, Ludvig Larsson, Anca I. Catrina, Patrik L. Ståhl, Vivianne Malmström
Software Mentions: 6
Published: about 5 years ago
10.1186/s12935-020-01423-4
Identification of a three-long noncoding RNA prognostic model involved competitive endogenous RNA in kidney renal clear cell carcinoma
Cited by: 21
Author(s): Di Zhang, Song Zeng, Xiaopeng Hu
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-019-47921-y
Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation
Cited by: 9
Author(s): Aline Daniela Lopes Júlio, Ubiana de Cássia Mourão Silva, Julliane Dutra Medeiros, Daniel Morais, Vera Lúcia dos Santos
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: over 4 years ago
10.1038/s41598-019-44902-z
Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome
Cited by: 12
Author(s): Jingya Wang, Sadiye Amcaoglu Rieder, Jincheng Wu, Susana Hayes, Rebecca Halpin, Melissa de los Reyes, Yashaswi Shrestha, Roland Kolbeck, Rajiv Raja
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-019-46932-z
DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Cited by: 73
Author(s): Christian T. Wohnhaas, Germán Leparc, Francesc Fernández-Albert, David Kind, Florian Gantner, Coralie Viollet, Tobias Hildebrandt, Patrick Baum
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-019-41315-w
Novel Data Transformations for RNA-seq Differential Expression Analysis
Cited by: 23
Author(s): Zeyu Zhang, Danyang Yu, Minseok Seo, Craig P. Hersh, Scott T. Weiss, Weiliang Qiu
Software Mentions: 6
Published: almost 6 years ago
10.1186/1471-2164-12-619
A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation
Cited by: 102
Author(s): Monica F. Poelchau, Julie A. Reynolds, David L. Denlinger, Christine G. Elsik, Peter Armbruster
Software Mentions: 6
Published: about 13 years ago
10.1038/s41598-019-44302-3
Dose-dependent effects of chronic alcohol drinking on peripheral immune responses
Cited by: 41
Author(s): Suhas Sureshchandra, Anthony M. Raus, Allen Jankeel, Brian Jin Kee Ligh, Nicole A.R. Walter, Natali Newman, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 5 years ago
10.1128/mSystems.00145-20
Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens
Cited by: 14
Author(s): Briallen Lobb, Rhiannon Hodgson, Michael D. J. Lynch, Michael J. Mansfield, Jiujun Cheng, Trevor C. Charles, Josh D. Neufeld, Paul M. Craig, Andrew C. Doxey
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-018-37397-7
Temporal dynamics in meta longitudinal RNA-Seq data
Cited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
Software Mentions: 6
Published: almost 6 years ago
10.1186/s12864-019-5797-8
Concurrent and long-term associations between the endometrial microbiota and endometrial transcriptome in postpartum dairy cows
Cited by: 13
Author(s): S.G. Moore, Aaron C. Ericsson, Susanta K. Behura, W. R. Lamberson, Timothy J. Evans, Matthew S. McCabe, S.E. Poock, M.C. Lucy
Software Mentions: 6
Published: over 5 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 7 years ago
10.1186/s12864-017-3683-9
Reduced changes in protein compared to mRNA levels across non-proliferating tissues
Cited by: 72
Author(s): Kobi Perl, Kathy Ushakov, Yair Pozniak, Ofer Yizhar-Barnea, Yoni Bhonker, Shaked Shivatzki, Tamar Geiger, Karen B. Avraham, Ron Shamir
Software Mentions: 6
Published: over 7 years ago
10.1371/journal.ppat.1008754
JNK pathway restricts DENV2, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands
Cited by: 37
Author(s): Avisha Chowdhury, Cassandra M. Modahl, Siok Thing Tan, Benjamin Wong Wei Xiang, Dorothée Missé, Thomas Vial, R. Manjunatha Kini, Julien Pompon
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.ppat.1009567
ATRX limits the accessibility of histone H3-occupied HSV genomes during lytic infection
Cited by: 7
Author(s): Joseph M Cabral, Camille H. Cushman, Catherine Sodroski, David M. Knipe
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0250655
The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments
Cited by: 16
Author(s): Diana Luise, Mathilde Le Sciellour, Arnaud Buchet, Rémi Resmond, Charlène Clement, Marie Rossignol, Déborah Jardet, Olivier Zemb, Catherine Belloc, Elodie Merlot
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.ppat.1009280
Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
Cited by: 29
Author(s): TuShun R. Powers, Amanda L. Haeberle, Alexander V. Predeus, Disa L. Hammarlöf, Jennifer A. Cundiff, Zeus Saldaña‐Ahuactzi, Karsten Hokamp, Jay C. D. Hinton, Leigh A. Knodler
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0106084
Patterns of MiRNA Expression in Arctic Charr Development
Cited by: 24
Author(s): Kalina H. Kapralova, Sigríður Rut Franzdóttir, Hákon Jónsson, Sigurður S. Snorrason, Zophonı́as O. Jónsson
Software Mentions: 6
Published: over 10 years ago
10.1111/jcmm.14991
Mutational landscape and genetic signatures of cell‐free DNA in tumour‐induced osteomalacia
Cited by: 2
Author(s): Nan Wu, Zhen Zhang, Xi Zhou, Hengqiang Zhao, Yue Ming, Xue Wu, Xian Zhang, Xinzhuang Yang, Meng Zhou, Hua Bao, Weisheng Chen, Yong Wu, Sen Liu, Huizi Wang, Yuchen Niu, Yalun Li, Yu Zheng, Yang Shao, Na Gao, Ying Yang, Ying Liu, Wenli Li, Jia Liu, Na Zhang, Yang Xu, Yuan Xu, Mei Li, Yingli Sun, Jianzhong Su, Jianguo Zhang, Weibo Xia, Guixing Qiu, Yong Liu, Jiaqi Liu, Zhihong Wu
Software Mentions: 6
Published: over 4 years ago
10.1242/jcs.259051
The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription
Cited by: 0
Author(s): David Z. Kochan, Julia S. P. Mawer, Jennifer Massen, Kiril Tishinov, Swati Parekh, Martin Graef, Anne Spang, Peter Tessarz
Software Mentions: 6
Published: over 3 years ago
10.1111/jcmm.14721
Integrated analysis of co‐expression and ceRNA network identifies five lncRNAs as prognostic markers for breast cancer
Cited by: 41
Author(s): Yan Yao, Tingting Zhang, Ling‐Yu Qi, Chao Zhou, Junyu Wei, Fubin Feng, Ruijuan Liu, Changgang Sun
Software Mentions: 6
Published: about 5 years ago