bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/tp.2016.67

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report
Cited by: 26
Author(s): Michael S. Breen, Anne Uhlmann, Christiane M. Nday, Stephen J. Glatt, Mario Mitt, A. Metsalpu, Dan J. Stein, Nicola Illing
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1005184

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
Cited by: 111
Author(s): Li Zhao, Janneke Wit, Nicolas Svetec, David J. Begun
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.24570

EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Cited by: 36
Author(s): Shanshan Ai, Yong Peng, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence Prendiville, Wen Zheng, Yuli Liu, Stuart H. Orkin, Dazhi Wang, Jia Yu, William T. Pu, Aibin He
Software Mentions: 4
Published: over 7 years ago

10.1016/j.celrep.2021.108860

COX2 regulates senescence secretome composition and senescence surveillance through PGE2
Cited by: 30
Author(s): S. Goncalves, Kai Yin, Yoko Itō, Adelyne Chan, Ioana Olan, Sarah Gough, Liam Cassidy, Eva M. Serrao, Stephen Smith, Andrew Young, Masashi Narita, Matthew Hoare
Software Mentions: 4
Published: almost 4 years ago

10.3390/cancers12082210

Human FBXL8 Is a Novel E3 Ligase Which Promotes BRCA Metastasis by Stimulating Pro-Tumorigenic Cytokines and Inhibiting Tumor Suppressors
Cited by: 10
Author(s): Shu Chun Chang, Wei‐Hsiu Hsu, Emily Chia Yu Su, Chin Sheng Hung, Jeak Ling Ding
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.53237

Rapid sex-specific adaptation to high temperature in Drosophila
Cited by: 20
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schlötterer
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: almost 9 years ago

10.3390/plants8120531

Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development
Cited by: 9
Author(s): Giulio Testone, Elena Baldoni, Maria Adelaide Iannelli, Chiara Nicolodi, Elisabetta Di Giacomo, Fabrizio Pietrini, Giovanni Mele, Donato Giannino, Giovanna Frugis
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2015.00065

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data
Cited by: 48
Author(s): Sylvie Schulze, Sebastian Henkel, Dominik Driesch, Reinhard Guthke, JÃ¶rg Linde
Software Mentions: 4
Published: almost 10 years ago

10.15252/embj.2019103932

<scp>RNF</scp> 43 truncations trap <scp>CK</scp> 1 to drive niche‐independent self‐renewal in cancer
Cited by: 24
Author(s): Maureen Spit, Nicola Fenderico, Ingrid Jordens, Tomasz Radaszkiewicz, Rik G.H. Lindeboom, Jeroen M. Bugter, Alba Cristobal, Lars Ootes, Max van Osch, Eline Janssen, Kim E. Boonekamp, Kateřina Hanáková, David Potěšil, Zbyněk Zdráhal, Sylvia F. Boj, Jan Paul Medema, Vı́tězslav Bryja, Bon‐Kyoung Koo, Michiel Vermeulen, Madelon M. Maurice
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1006760

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
Cited by: 6
Author(s): Vikash Pandey, Vassily Hatzimanikatis
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0181192

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity
Cited by: 23
Author(s): Ulrika Lind, Michael Järvå, Magnus Alm Rosenblad, Piero Pingitore, Emil Karlsson, Anna-Lisa Wrange, Emelie Kamdal, Kristina Sundell, Carl André, Per R. Jonsson, Jonathan N. Havenhand, Leif A. Eriksson, Kristina Hedfalk, Anders Blomberg
Software Mentions: 4
Published: over 7 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: over 8 years ago

10.1186/s13227-019-0135-4

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
Cited by: 16
Author(s): Graham A. McCulloch, Andrew Oliphant, Peter K. Dearden, Andrew J. Veale, Charles W. Ellen, Jonathan M. Waters
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2016.01431

Quantitative Resistance to Verticillium Wilt in Medicago truncatula Involves Eradication of the Fungus from Roots and Is Associated with Transcriptional Responses Related to Innate Immunity
Cited by: 13
Author(s): Maoulida Toueni, Cécile Ben, Aurélie Le Ru, Laurent Gentzbittel, Martina Rickauer
Software Mentions: 4
Published: about 8 years ago

10.1038/s42003-021-02203-0

The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function
Cited by: 5
Author(s): Bergithe E. Oftedal, Stefano Maio, Adam E. Handel, White Mpj., Duncan Howie, Simon Davis, Nicolas Prevot, Ioanna A. Rota, Mary E. Deadman, Benedikt M. Kessler, Román Fischer, Nikolaus S. Trede, Erdinç Sezgin, Rick M. Maizels, G A Holländer
Software Mentions: 4
Published: over 3 years ago

10.3390/genes9010044

Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma
Cited by: 23
Author(s): Minjia Lu, Xingyu Xu, Baohang Xi, Qi Dai, Chenli Li, Li Su, Xiaobin Zhou, Min Tang, Yanwen Yao, Jialiang Yang
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0228722

Iron metabolic pathways in the processes of sponge plasticity
Cited by: 8
Author(s): Alexander D. Finoshin, Kim I. Adameyko, Kirill V. Mikhailov, О. И. Кравчук, Anton Georgiev, Н. Г. Горностаев, Igor A. Kosevich, Victor S. Mikhailov, Guzel Gazizova, Elena Shagimardanova, Oleg Gusev, Yu. V. Lyupina
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2017.01561

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
Cited by: 211
Author(s): Luisa W. Hugerth, Anders F. Andersson
Software Mentions: 4
Published: over 7 years ago

10.1111/eva.12463

Plasticity in gene transcription explains the differential performance of two invasive fish species
Cited by: 47
Author(s): Kyle Wellband, Daniel D. Heath
Software Mentions: 4
Published: over 7 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 years ago

10.3390/genes9040180

Non-Pleiotropic Coupling of Daily and Seasonal Temporal Isolation in the European Corn Borer
Cited by: 29
Author(s): Rebecca C. Levy, Genevieve M. Kozak, Erik B. Dopman
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-019-0391-9

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation
Cited by: 25
Author(s): Alborz Mazloomian, Shinsuke Araki, Momoko Ohori, Amal M. El-Naggar, Damian Yap, Ali Bashashati, Shigetomi Nakao, Poul H. Sorensen, Atsushi Nakanishi, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1004924

The Genetic Architecture of the Genome-Wide Transcriptional Response to ER Stress in the Mouse
Cited by: 29
Author(s): Clement Y. Chow, Xiaozhu Wang, David D. Riccardi, Mariana F. Wolfner, Andrew G. Clark
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pgen.1008537

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation
Cited by: 33
Author(s): Gregory R. Keele, Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, Paul Cotney, Gregory E. Crawford, William Valdar, Ivan Rusyn, Terrence S. Furey
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.597944

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing–Based Assessment of the Barossa Valley and Its Sub-Regions
Cited by: 8
Author(s): Jia Zhou, Timothy R. Cavagnaro, Roberta De Bei, Tiffanie M. Nelson, J. Stephen, Andrew Metcalfe, Matthew Gilliham, James Breen, Cassandra Collins, Carlos M. Rodríguez López
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms19010031

Transcriptome Analysis of Tomato Leaf Spot Pathogen Fusarium proliferatum: De novo Assembly, Expression Profiling, and Identification of Candidate Effectors
Cited by: 15
Author(s): Meiling Gao, Siyu Yao, Yang Liu, Haining Yu, Pao Xu, Wenhui Sun, Zhongji Pu, Hongman Hou, Yongming Bao
Software Mentions: 4
Published: almost 7 years ago

10.3390/genes9090431

Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots
Cited by: 16
Author(s): Gabriela Machaj, Hamed Bostan, Alicja Macko-Podgórni, Massimo Iorizzo, Dariusz Grzebelus
Software Mentions: 4
Published: over 6 years ago

10.3390/genes9120574

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
Cited by: 25
Author(s): Kadri Rekker, Signe Altmäe, Marina Suhorutshenko, Maire Peters, Juan F. Martínez-Blanch, Francisco M. Codoñer, Felipe Vilella, Carlos Simón, Andres Salumets, Agne Velthut-Meikas
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms18030627

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens
Cited by: 14
Author(s): Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert T. Greenlee, Deborah Multerer, Stacey Honda, Yihe G. Daida, Heather Spencer Feigelson, Andrew G. Glass, Fergus J. Couch, Thomas E. Rohan, Iddo Z. Ben‐Dov
Software Mentions: 4
Published: almost 8 years ago

10.1038/s12276-020-00538-y

Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer
Cited by: 39
Author(s): Hye Hyeon Eum, Minsuk Kwon, Daeun Ryu, Areum Jo, Wingyan Chung, Nayoung Kim, Yourae Hong, Dae‐Soon Son, Seung Tae Kim, Jeeyun Lee, Hae‐Ock Lee, Woong-Yang Park
Software Mentions: 4
Published: about 4 years ago

10.3390/genes9120579

Integrated Proteomic and Transcriptomic Analysis of Differential Expression of Chicken Lung Tissue in Response to NDV Infection during Heat Stress
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms22073674

Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?
Cited by: 3
Author(s): Cleonardo Augusto Silva, André M. Ribeiro-dos-Santos, Wanderson Gonçalves e Gonçalves, Pablo Diego do Carmo Pinto, Rafael Pompeu Pantoja, Tatiana Vinasco-Sandoval, André M. Ribeiro-dos-Santos, Mara H. Hutz, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo, Sidney Emanuel Batista dos Santos
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1006302

Activated entomopathogenic nematode infective juveniles release lethal venom proteins
Cited by: 87
Author(s): Dihong Lu, Marissa Macchietto, Dennis Chang, Mirayana M. Barros, J. G. Baldwin, A Mortazavi, Adler R. Dillman
Software Mentions: 4
Published: over 7 years ago

10.1098/rsob.200253

The role of antioxidants in restoring MAPK 14 and a DNA damage marker level following autophagy suppression
Cited by: 3
Author(s): Abdalla Elbialy
Software Mentions: 4
Published: about 4 years ago

10.3389/fpls.2018.00204

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses
Cited by: 55
Author(s): Elide Formentin, Cristina Sudiro, Giorgio Perin, Samantha Riccadonna, Elisabetta Barizza, Elena Baldoni, Enrico Lavezzo, Piergiorgio Stevanato, Gian Attilio Sacchi, Paolo Fontana, Stefano Toppo, Tomas Morosinotto, Michela Zottini, Fiorella Lo Schiavo
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms21249560

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses
Cited by: 2
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 4
Published: about 4 years ago

10.3390/genes10020089

A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment
Cited by: 12
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Neda Barghi, François Mallard, Kerstin Otte, Christian Schlötterer
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pbio.2003862

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice
Cited by: 290
Author(s): Joseph Edwards, Christian Santos‐Medellín, Zachary Liechty, Bao‐Anh Thi Nguyen, Eugene Lurie, Shane Eason, Gregory C. Phillips, Venkatesan Sundaresan
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0192383

Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen
Cited by: 40
Author(s): Claire Brice, Francisco A. Cubillos, Sylvie Dequin, Carole Camarasa, Claudio Martı́nez
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: about 10 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.47013

An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans
Cited by: 27
Author(s): Murilo Delgobo, Daniel A G B Mendes, Edgar Kozlova, Edroaldo Lummertz da Rocha, Gabriela F. Rodrigues-Luiz, Lucas Mascarin, Greicy Brisa Malaquias Dias, Daniel de Oliveira Patricio, Tim Dierckx, Maíra A. Bicca, G Bretton, Yonne Karoline Tenório de Menezes, Márick R Starick, Darcita Büerger Rovaris, Joanita Del Moral, Daniel Santos Mansur, Johan Van Weyenbergh, André Báfica
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00410

Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria
Cited by: 9
Author(s): Otmane Lamrabet, Astrid Melotti, Frédéric Burdet, Nabil Hanna, Jackie Perrin, Jahn Nitschke, Marco Pagni, Hubert Hilbi, Thierry Soldati, Pierre Cosson
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2019.00712

Prognostic lncRNAs, miRNAs, and mRNAs Form a Competing Endogenous RNA Network in Colon Cancer
Cited by: 33
Author(s): Qianrong Huang, Xin-Bin Pan
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.00588-21

An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Cited by: 6
Author(s): Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T. Belisle, A Mortazavi, Alan G. Barbour
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers13030559

Type 2 Innate Lymphoid Cells Protect against Colorectal Cancer Progression and Predict Improved Patient Survival
Cited by: 29
Author(s): Qiutong Huang, Nicolas Jacquelot, Adele Preaudet, Soroor Hediyeh-Zadeh, Fernando Souza-Fonseca-Guimarães, Andrew N. J. McKenzie, Philip M. Hansbro, Melissa J. Davis, Lisa A. Mielke, Tracy L. Putoczki, Gabrielle T. Belz
Software Mentions: 4
Published: almost 4 years ago

10.12688/f1000research.16005.3

MSF: Modulated Sub-graph Finder
Cited by: 0
Author(s): Mariam R. Farman, Ivo L. Hofacker, Fabian Amman
Software Mentions: 4
Published: over 5 years ago

10.1242/dmm.042713

Leptin and fractalkine: Novel subcutaneous cytokines in burn injury
Cited by: 4
Author(s): Dominic Friston, Sini Junttila, Júlia Borges Paes Lemes, Helen Laycock, Jose Vicente Torres-Pérez, Elizabeth J. Want, Attila Gyenesei, I. Nagy
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.00133

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun
Cited by: 15
Author(s): Vandana R. Prabhu, . Wasimuddin, Ranganathan Kamalakkannan, Moolamkudy Suresh Arjun, Muniyandi Nagarajan
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijerph17207386

Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics
Cited by: 0
Author(s): Stephanie M. Bilinovich, Kristy Lewis, Barbara L. Thompson, Jeremy W. Prokop, Daniel B. Campbell
Software Mentions: 4
Published: about 4 years ago

10.1186/s13046-019-1254-4

Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma
Cited by: 74
Author(s): Hong‐Gang Xiong, Hao Li, Yao Xiao, Qi‐Chao Yang, Leilei Yang, Lei Chen, Lin‐Lin Bu, Wenfeng Zhang, Jiali Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2019.01975

Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
Cited by: 8
Author(s): Qinglong Wu, Hung Chu, Aparna Padmanabhan, Nagendra P. Shah
Software Mentions: 4
Published: over 5 years ago

10.1098/rsob.160224

Interplay between RNA interference and heat shock response systems in <i>Drosophila melanogaster</i>
Cited by: 9
Author(s): S. Yu. Funikov, Sergei Ryazansky, Alexander Kanapin, Maria D. Logacheva, Aleksey A. Penin, А. В. Снежкина, Victoria Shilova, Д. Г. Гарбуз, Michael B. Evgen’ev, Olga G. Zatsepina
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 3 years ago

10.1186/s12974-018-1170-0

Novel insights into neuroinflammation: bacterial lipopolysaccharide, tumor necrosis factor α, and Ureaplasma species differentially modulate atypical chemokine receptor 3 responses in human brain microvascular endothelial cells
Cited by: 15
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Mathias Buttmann, Kirsten Glaser
Software Mentions: 4
Published: over 6 years ago

10.3390/genes10060433

BarkBase: Epigenomic Annotation of Canine Genomes
Cited by: 26
Author(s): Kate Megquier, Diane P. Genereux, Jessica P. Hekman, Ross Swofford, Jason Turner-Maier, Jeremy Johnson, Jacob Alonso, Li Xue, Kathleen M. Morrill, Lynne J. Anguish, Michele Koltookian, Brittney Logan, Claire R. Sharp, Lluís Ferrer, Kerstin Lindblad‐Toh, Vicki N. Meyers-Wallen, Andrew M. Hoffman, Elinor K. Karlsson
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: almost 11 years ago

10.3389/fpls.2021.727302

Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses
Cited by: 4
Author(s): Minsu Park, Wookap Choi, Sang Yoon Shin, Hongman Moon, Dowhan Lee, Yun Shil Gho, Ki Hong Jung, Jong Seong Jeon, Chanseok Shin
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2019.01605

De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature
Cited by: 26
Author(s): Rubén Vicente, Anthony Bolger, Rafael Martínez‐Carrasco, Pilar Pérez Pérez, Elena Gutiérrez, Björn Usadel, Rosa Morcuende
Software Mentions: 4
Published: about 5 years ago

10.1186/s12974-019-1413-8

More than just inflammation: Ureaplasma species induce apoptosis in human brain microvascular endothelial cells
Cited by: 18
Author(s): Christine Silwedel, Axel Haarmann, Markus Fehrholz, Heike Claus, Christian P. Speer, Kirsten Glaser
Software Mentions: 4
Published: almost 6 years ago

10.1002/pld3.241

Control of translation during the unfolded protein response in maize seedlings: Life without PERKs
Cited by: 9
Author(s): Pulkit Kanodia, Paramasivan Vijayapalani, Renu Srivastava, Ran Bi, Peng Liu, W. Allen Miller, Stephen H. Howell
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.53704

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Cited by: 41
Author(s): Anastasia A. Minervina, Mikhail V. Pogorelyy, Ekaterina A. Komech, В. К. Карнаухов, Petra Bächer, Elisa Rosati, André Franke, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M. Walczak
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0169648

The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and Is Counteracted by the HBV X Protein Shortly after Infection
Cited by: 107
Author(s): Congrong Niu, Christine M. Livingston, Li Li, Rudolf K. F. Beran, Stéphane Daffis, Dhivya Ramakrishnan, Dara Burdette, Leanne Peiser, Eduardo Salas, Hilario J. Ramos, Mei Yu, Guofeng Cheng, Michel Strubin, William E. Delaney, Simon P. Fletcher
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0131504

A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: over 9 years ago

10.1093/jxb/eraa036

The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions
Cited by: 14
Author(s): Matthew Haas, Axel Himmelbach, Martin Mascher
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0255915

Reciprocal interplay between asporin and decorin: Implications in gastric cancer prognosis
Cited by: 6
Author(s): Dipjit Basak, Zarqua Jamal, Arnab Ghosh, Pronoy Kanti Mondal, Priyanka Dey Talukdar, Semanti Ghosh, Biswadeep Ghosh Roy, Ranajoy Ghosh, Ajay Halder, Abhijit Chowdhury, Gopal Krishna Dhali, Brajadulal Chattopadhyay, Makhan Saha, Abhimanyu Basu, Sukanta Roy, Chitranjan Mukherjee, Nidhan K. Biswas, Urmi Chatterji, Shalini Datta
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers12051325

Tumor Cell Associated Hyaluronan-CD44 Signaling Promotes Pro-Tumor Inflammation in Breast Cancer
Cited by: 18
Author(s): Patrice M Witschen, Thomas S. Chaffee, Nicholas J. Brady, Danielle N. Huggins, Todd P. Knutson, Rebecca S. LaRue, Sarah A. Munro, Lyubov Tiegs, James B. McCarthy, Andrew C. Nelson, Kathryn L. Schwertfeger
Software Mentions: 4
Published: over 4 years ago

10.1523/JNEUROSCI.0860-21.2021

Spinal Cord Injury Induces Permanent Reprogramming of Microglia into a Disease-Associated State Which Contributes to Functional Recovery
Cited by: 21
Author(s): Ramil Hakim, Vasilios Zachariadis, Sreenivasa Raghavan Sankavaram, Jinming Han, Robert A. Harris, Lou Brundin, Martin Enge, Mikael Svensson
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2019.02195

Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces
Cited by: 5
Author(s): Yu-Wen Lai, Chi Nam Ignatius Pang, Leona T. Campbell, Wen Chen, Marc R. Wilkins, Dee Carter
Software Mentions: 4
Published: about 5 years ago

10.3390/cancers12092543

CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas
Cited by: 4
Author(s): Ju Won Ahn, Young Joon Park, Su Jung Kang, So Jung Hwang, Kyung Gi Cho, Jaejoon Lim, KyuBum Kwack
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2019.03044

Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti
Cited by: 34
Author(s): Víctor M. Flores‐Núñez, Citlali Fonseca-García, Damaris Desgarennes, Emiley A. Eloe‐Fadrosh, Tanja Woyke, Laila P. Partida‐Martínez
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0246367

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Cited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0204038

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period
Cited by: 3
Author(s): Ramona Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael Cheung, Joseph J. Smolich, Salvatore Pepe
Software Mentions: 4
Published: about 6 years ago

10.1093/jxb/erx224

Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype
Cited by: 38
Author(s): Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre‐François Bert, Mindy Muñoz, Serge Delrot, Christophe Klopp, Nathalie Ollat, Virginie Lauvergeat
Software Mentions: 4
Published: over 7 years ago

10.1093/jxb/erx247

Delaying chloroplast turnover increases water-deficit stress tolerance through the enhancement of nitrogen assimilation in rice
Cited by: 35
Author(s): Nir Sade, Kamolchanok Umnajkitikorn, María del Mar Rubio Wilhelmi, Matthew Wright, Songhu Wang, Eduardo Blumwald
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.13806

Bronchial airway gene expression signatures in mouse lung squamous cell carcinoma and their modulation by cancer chemopreventive agents
Cited by: 20
Author(s): Donghai Xiong, Jing Pan, Qi Zhang, Éva Szabó, Mark Steven Miller, Ronald A. Lubet, Ming You, Yian Wang
Software Mentions: 4
Published: about 8 years ago

10.1096/fj.201600675R

New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration
Cited by: 22
Author(s): Svitlana Pasteuning-Vuhman, Johanna W Boertje-van der Meulen, Maaike van Putten, Maurice Overzier, Peter ten Dijke, Szymon M. Kiełbasa, Wibowo Arindrarto, Ron Wolterbeek, Ksenia Lezhnina, Ivan V. Ozerov, Aleksandr M Aliper, Willem M.H. Hoogaars, Annemieke Aartsma‐Rus, Cindy J.M. Loomans
Software Mentions: 4
Published: about 8 years ago

10.7150/ijms.51297

Heat shock factor 5 correlated with immune infiltration serves as a prognostic biomarker in lung adenocarcinoma
Cited by: 5
Author(s): Aizemaiti Rusidanmu, Zhigang Wu, Jie Tang, Haimeng Yan, Xiaoshu Lv
Software Mentions: 4
Published: almost 4 years ago

10.1128/mBio.00617-20

EspFu-Mediated Actin Assembly Enhances Enteropathogenic <i>Escherichia coli</i> Adherence and Activates Host Cell Inflammatory Signaling Pathways
Cited by: 12
Author(s): Fernando Henrique Martins, Ashwani Kumar, Cecília M. Abe, Enéas Carvalho, Milton Yutaka Nishiyama-Jr, Chao Xing, Vanessa Sperandio, Waldir P. Elias
Software Mentions: 4
Published: over 4 years ago

10.1016/j.celrep.2016.06.096

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Cited by: 60
Author(s): Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaž Curk, Anne-Marie Alleaume, Matthias W. Hentze, Andreas E. Kulozik
Software Mentions: 4
Published: over 8 years ago

10.1111/rssc.12213

A Bayesian Model Selection Approach for Identifying Differentially Expressed Transcripts from RNA Sequencing Data
Cited by: 5
Author(s): Panagiotis Papastamoulis, Magnus Rattray
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0109262

De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes
Cited by: 48
Author(s): Jing Wu, Lanfen Wang, Long Li, Shumin Wang
Software Mentions: 4
Published: about 10 years ago

10.3389/fmolb.2021.608369

Identification of a DNA Repair Gene Signature and Establishment of a Prognostic Nomogram Predicting Biochemical-Recurrence-Free Survival of Prostate Cancer
Cited by: 9
Author(s): Gongwei Long, Wei Ouyang, Yucong Zhang, Guoliang Sun, Jiahua Gan, Zhiquan Hu, Heng Li
Software Mentions: 4
Published: almost 4 years ago

10.1002/ece3.6946

Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress
Cited by: 6
Author(s): Peng Shi, Jun Zhou, Huali Song, Yujuan Wu, Lan Lan, Xiangyou Tang, Zhengang Ma, Charles R. Vossbrinck, Bettina Vossbrinck, Zeyang Zhou, Jianlong Xu
Software Mentions: 4
Published: about 4 years ago

10.3390/genes10090719

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice
Cited by: 50
Author(s): Mei-Ling Zhu, Hongjun Xie, Xiangjin Wei, Komivi Dossa, Yaying Yu, Suozhen Hui, Guohua Tang, Xiaoshan Zeng, Ye Yu, Jianlong Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 11 years ago

10.1093/dnares/dsz002

A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants
Cited by: 32
Author(s): Asuka Arimoto, Koki Nishitsuji, Yoshimi Higa, Nana Arakaki, Kanako Hisata, Chuya Shinzato, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0186794

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health
Cited by: 16
Author(s): Vittoria Roncalli, Andrew E. Christie, Stephanie A. Sommer, Matthew Cieslak, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 4
Published: about 7 years ago

10.3389/fnmol.2018.00178

Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation
Cited by: 21
Author(s): Renjitha Gopurappilly, Bipan Kumar Deb, Pragnya Chakraborty, Gaiti Hasan
Software Mentions: 4
Published: over 6 years ago

10.3390/genes10100745

Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses
Cited by: 4
Author(s): Ann M. Kemper, Jenny Drnevich, Molly E. McCue, Annette M. McCoy
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2020.00681

Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 50
Author(s): Chia‐Ying Li, Jia-Hua Cai, Jeffrey J. P. Tsai, Charles C.N. Wang
Software Mentions: 4
Published: over 4 years ago

10.1002/2211-5463.13062

Chondroitin polymerizing factor promotes breast carcinoma cell proliferation, invasion and migration and affects expression of epithelial‐mesenchymal transition‐related markers
Cited by: 6
Author(s): Li Yang, Hui Gong, Lei Feng, Dan Mao, Yujie Xiao, Yunqi Wang, Huang Li-zhong
Software Mentions: 4
Published: almost 4 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: about 4 years ago

10.3389/fnmol.2018.00288

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis
Cited by: 84
Author(s): Maria Liguori, Nicoletta Nuzziello, Alessandro Introna, Arianna Consiglio, Flavio Licciulli, Eustachio D’Errico, Antonio Scarafino, Eugenio Distaso, Isabella Laura Simone
Software Mentions: 4
Published: over 6 years ago

10.3389/fphar.2021.678256

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells
Cited by: 5
Author(s): Yanwei Cheng, Xue Cao, Jiange Zhang, Dong Chen, Juan Zhu, Lijun Xu, Lijie Qin
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2020.613333

Construction of Bone Metastasis-Specific Regulation Network Based on Prognostic Stemness-Related Signatures in Breast Invasive Carcinoma
Cited by: 2
Author(s): Runzhi Huang, Zhenyu Li, Jiayao Zhang, Zhiwei Zeng, Jiaqi Zhang, Mingxiao Li, Siqao Wang, Shuyuan Xian, Yuna Xue, Xi Chen, Jie Li, Wing Yan Elizabeth Cheng, Bin Wang, Penghui Yan, Daoke Yang, Zongqiang Huang
Software Mentions: 4
Published: almost 4 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568