bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fpls.2018.00108

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Cited by: 61
Author(s): Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Élie Maza
Software Mentions: 8
Published: over 8 years ago

10.1038/srep44736

Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells
Cited by: 5
Author(s): Jian Yu, Constance Ciaudo
Software Mentions: 8
Published: over 9 years ago

10.3390/ijms22073296

Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases
Cited by: 5
Author(s): Markus Kwik, Stefan Hainzl, Jan Oppelt, Boris Tichý, Ulrich Koller, Emanuele Bernardinelli, Markus J. Steiner, Greta Zara, Charity Nofziger, Serge Weis, Markus Paulmichl, Silvia Dossena, Wolfgang Patsch, Selma M. Soyal
Software Mentions: 8
Published: over 5 years ago

10.3390/ijerph18115564

Identification of Hub Genes in Different Stages of Colorectal Cancer through an Integrated Bioinformatics Approach
Cited by: 2
Author(s): Abhijeet R. Patil, Ming-Ying Leung, Sourav Roy
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-021-93570-5

Three dimensional modeling of biologically relevant fluid shear stress in human renal tubule cells mimics in vivo transcriptional profiles
Cited by: 18
Author(s): Emily J. Ross, Emily R. Gordon, Hanna Sothers, Roshan Darji, Oakley Baron, Dustin W. Haithcock, Balabhaskar Prabhakarpandian, Kapil Pant, R Myers, Sara J. Cooper, Nancy J. Cox
Software Mentions: 8
Published: about 5 years ago

10.1186/s13059-020-02072-6

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Cited by: 7
Author(s): Guy Karlebach, Peter J. Hansen, Diogo Veiga, Robin Steinhaus, Daniel Daniš, Sheng Li, Olga Anczuków, Peter N. Robinson
Software Mentions: 8
Published: about 6 years ago

10.3389/fonc.2021.706915

A Novel Nine-lncRNA Risk Signature Correlates With Immunotherapy in Hepatocellular Carcinoma
Cited by: 8
Author(s): Ye Nie, Jianhui Li, Wenlong Wu, Dongnan Guo, Xinjun Lei, Tianchen Zhang, Yanfang Wang, Zhenzhen Mao, Xuan Zhang, Wenjie Song
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0187722

Plasma microRNA profiling: Exploring better biomarkers for lymphoma surveillance
Cited by: 47
Author(s): Drirh Khare, Neta Goldschmidt, Aya Bardugo, Devorah Gur‐Wahnon, Iddo Z. Ben‐Dov, Batia Avni
Software Mentions: 8
Published: almost 9 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0244122

Easyreporting simplifies the implementation of Reproducible Research layers in R software
Cited by: 0
Author(s): Dario Righelli, Claudia Angelini
Software Mentions: 8
Published: over 5 years ago

10.1038/s41597-020-00696-8

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
Cited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: almost 6 years ago

10.3389/fmicb.2019.02492

Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow?
Cited by: 17
Author(s): Benoît Bergk Pinto, Lorrie Maccario, Aurélien Dommergue, Timothy M. Vogel, Catherine Larose
Software Mentions: 8
Published: almost 7 years ago

10.1186/s40168-018-0468-6

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate
Cited by: 44
Author(s): Pål Trosvik, Eric J. de Muinck, Eli Knispel Rueness, Peter J. Fashing, Evan C. Beierschmitt, Kadie R. Callingham, Jacob B. Kraus, Thomas H. Trew, Amera Moges, Addisu Mekonnen, Vivek V. Venkataraman, Nga Nguyen
Software Mentions: 8
Published: over 8 years ago

10.1038/s41597-019-0183-6

CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder
Cited by: 127
Author(s): Gabriel E. Hoffman, Jaroslav Bendl, Georgios Voloudakis, Kelsey S. Montgomery, Laura Sloofman, Ying-Chih Wang, Hardik Shah, Mads E. Hauberg, Jessica Johnson, Kiran Girdhar, Lingyun Song, John F. Fullard, Robin Kramer, Chang-Gyu Hahn, Raquel E. Gur, Stefano Marenco, Barbara K. Lipska, David A. Lewis, Vahram Haroutunian, Scott E. Hemby, Patrick F. Sullivan, Schahram Akbarian, Andrew Chess, Joseph D. Buxbaum, Greg Crawford, Enrico Domenici, Bernie Devlin, Solveig K. Sieberts, Mette A. Peters, Panos Roussos
Software Mentions: 8
Published: almost 7 years ago

10.1186/s13059-020-02038-8

Personalized and graph genomes reveal missing signal in epigenomic data
Cited by: 25
Author(s): Cristian Groza, Tony Kwan, Nicole Soranzo, Tomi Pastinen, Guillaume Bourque
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pcbi.1006378

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Cited by: 45
Author(s): Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom
Software Mentions: 8
Published: about 8 years ago

10.1155/2021/8859996

Potential Prognostic Biomarkers of Lung Adenocarcinoma Based on Bioinformatic Analysis
Cited by: 17
Author(s): Jili Hou, Yong Cheng
Software Mentions: 8
Published: over 5 years ago

10.1093/gbe/evab144

CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation
Cited by: 17
Author(s): Galen Martin, Danelle Seymour, Brandon S. Gaut
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0201830

Exposure to a firefighting overhaul environment without respiratory protection increases immune dysregulation and lung disease risk
Cited by: 14
Author(s): Stephen J. Gainey, Gavin P. Horn, Albert E. Towers, Maci L. Oelschlager, Vincent L. Tir, Jenny Drnevich, Kenneth W. Fent, Stephen Kerber, Denise L. Smith, Gregory G. Freund
Software Mentions: 7
Published: about 8 years ago

10.5808/GI.2019.17.1.e6

Statistical Analysis of Metagenomics Data
Cited by: 147
Author(s): M. Luz Calle
Software Mentions: 7
Published: over 7 years ago

10.7717/peerj.2888

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Cited by: 67
Author(s): Xun Zhu, Travers Ching, Xinghua Pan, Sherman M. Weissman, Lana X. Garmire
Software Mentions: 7
Published: over 9 years ago

10.3389/fpls.2021.684192

Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation From Its Location Outside the Nucleus
Cited by: 7
Author(s): Rachelle A. Lapham, Lan‐Ying Lee, Eder Xhako, Esteban Gañán Gómez, V. M. Nivya, Stanton B. Gelvin
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-021-02372-5

Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1
Cited by: 11
Author(s): Claudia Vivori, Panagiotis Papasaikas, Ralph Stadhouders, Bruno Di Stefano, Anna Ribó Rubio, Clara Berenguer Balaguer, Serena Francesca Generoso, Anna Mallol, José Luis Sardina, Bernhard Payer, Thomas Graf, Juan Valcárcel
Software Mentions: 7
Published: over 5 years ago

10.3389/fcell.2020.576996

Development and Validation of a Novel DNA Methylation-Driven Gene Based Molecular Classification and Predictive Model for Overall Survival and Immunotherapy Response in Patients With Glioblastoma: A Multiomic Analysis
Cited by: 9
Author(s): Zihao Wang, Lu Gao, Xiaopeng Guo, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-020-02087-z

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance
Cited by: 34
Author(s): Flora D’Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca Berrens, Junbin Qian, Paweł Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Jonathan De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N. Savvides, M. Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts
Software Mentions: 7
Published: about 6 years ago

10.3390/ijms221910451

Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance
Cited by: 1
Author(s): Stephanie Schaarschmidt, Ulrike Glaubitz, Alexander Erban, Joachim Kopka, Ellen Zuther
Software Mentions: 7
Published: almost 5 years ago

10.1534/g3.114.011759

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: about 12 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: over 10 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 5 years ago

10.1186/s12864-018-4896-2

Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands
Cited by: 8
Author(s): Panagiotis Moulos, Αλέξανδρος Αλεξανδράτος, Ioannis Nellas, Skarlatos G. Dedos
Software Mentions: 7
Published: about 8 years ago

10.7554/eLife.59610

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Cited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: about 6 years ago

10.3389/fpls.2020.619404

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I
Cited by: 18
Author(s): Abdellah Barakate, Jamie Orr, Miriam Schreiber, Isabelle Colas, Dominika Lewandowska, Nicola McCallum, Malcolm Macaulay, Jenny Morris, Mikel Arrieta, Pete E. Hedley, Luke Ramsay, Robbie Waugh
Software Mentions: 7
Published: over 5 years ago

10.1093/bioinformatics/btu638

HTSeq—a Python framework to work with high-throughput sequencing data
Cited by: 14,991
Author(s): Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Software Mentions: 7
Published: almost 12 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: almost 10 years ago

10.3390/microorganisms8101505

Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents
Cited by: 3
Author(s): Antônio Victor Campos Coelho, Romero Marinho de Moura, Sérgio Crovella
Software Mentions: 7
Published: almost 6 years ago

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: about 5 years ago

10.3390/microorganisms9061116

Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress
Cited by: 2
Author(s): Laurens Maertens, Pauline Cherry, Françoise Tilquin, Rob Van Houdt, Jean-Yves Matroule
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-021-93509-w

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation
Cited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2021.661361

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks
Cited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: over 5 years ago

10.1016/j.gpb.2018.07.007

Deciphering Brain Complexity Using Single-cell Sequencing
Cited by: 50
Author(s): Quanhua Mu, Yiyun Chen, Jiguang Wang
Software Mentions: 7
Published: about 7 years ago

10.1186/s13040-017-0150-8

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
Cited by: 15
Author(s): Bork A. Berghoff, Torgny Karlsson, Thomas Källman, E. Gerhart H. Wagner, Manfred Grabherr
Software Mentions: 7
Published: about 9 years ago

10.3389/fpls.2019.01313

A Bioinformatics Guide to Plant Microbiome Analysis
Cited by: 45
Author(s): Rares Calin Lucaciu, Claus Pelikan, Samuel M. Gerner, Christos Zioutis, Stephan Köstlbacher, Harald Marx, Craig W. Herbold, Hannes Schmidt, Thomas Rattei
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41437-019-0251-x

Genetic and genomic analysis of the seed-filling process in maize based on a logistic model
Cited by: 14
Author(s): Yin Su, Pengcheng Li, Yongsheng Xu, Jun Li, Tiantian Yang, Jie Wei, Shaohang Xu, Junjie Yu, Huiying Fang, Li Xue, Dejun Hao, Zefeng Yang, Chenwu Xu
Software Mentions: 7
Published: about 7 years ago

10.1186/s40168-021-01013-0

animalcules: interactive microbiome analytics and visualization in R
Cited by: 16
Author(s): Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti, W. Evan Johnson
Software Mentions: 7
Published: over 5 years ago

10.1242/dmm.049068

A mechanism linking perinatal 2,3,7,8 tetrachlorodibenzo-p-dioxin exposure to lower urinary tract dysfunction in adulthood
Cited by: 4
Author(s): Anne E. Turco, S. G. Oakes, Kimberly P. Keil Stietz, Cheryl L. Dunham, Diya B. Joseph, Thrishna S Chathurvedula, Nicholas M Girardi, Andrew J. Schneider, Joseph Gawdzik, Celeste M Sheftel, Peiqing Wang, Zunyi Wang, Dale E. Bjorling, William A. Ricke, Weiping Tang, Laura Hernández, Janet R. Keast, Adrian D. Bonev, Matthew D Grimes, Douglas W. Strand, Nathan R. Tykocki, Robyn L Tanguay, Richard E. Peterson, Chad M. Vezina
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-021-87234-7

Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model
Cited by: 9
Author(s): Sk Md Mosaddek Hossain, Aanzil Akram Halsana, Lutfunnesa Khatun, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 7
Published: over 5 years ago

10.1242/dmm.039297

Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development
Cited by: 10
Author(s): Christopher Nash, Nadia Boufaied, Dunarel Badescu, Yu Chang Wang, Miltiadis Paliouras, Mark Trifiro, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 7
Published: about 7 years ago

10.1371/journal.pone.0230945

Timescales of variation in diversity and production of bacterioplankton assemblages in the Lower Mississippi River
Cited by: 3
Author(s): Jason T. Payne, Colin R. Jackson, Justin Millar, Clifford A. Ochs
Software Mentions: 7
Published: over 6 years ago

10.1186/s40168-019-0677-7

Maize synthesized benzoxazinoids affect the host associated microbiome
Cited by: 160
Author(s): Enoch Narh Kudjordjie, Rumakanta Sapkota, Stine K. Steffensen, Inge S. Fomsgaard, Mogens Nicolaisen
Software Mentions: 7
Published: over 7 years ago

10.1186/s40168-017-0374-3

Dietary energy drives the dynamic response of bovine rumen viral communities
Cited by: 63
Author(s): Christopher L. Anderson, Matthew B. Sullivan, Samodha C. Fernando
Software Mentions: 7
Published: almost 9 years ago

10.1002/jev2.12127

Inflammasome‐induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses
Cited by: 26
Author(s): Christina F. Budden, Linden J. Gearing, Romina Kaiser, Lena Standke, Paul J. Hertzog, Eicke Latz
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2021.639631

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca
Cited by: 11
Author(s): Piotr M. Kopec, Katarzyna Mikołajczyk, E. Jajor, A. Perek, Joanna Nowakowska, Christian Obermeier, Harmeet Singh Chawla, M. Korbas, I. Bartkowiak-Broda, Wojciech M. Karłowski
Software Mentions: 7
Published: over 5 years ago

10.1016/j.isci.2021.102870

Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance
Cited by: 14
Author(s): Katharina Gapp, Guillermo E. Parada, Fridolin Groß, Alberto Corcoba, Jasmine Kaur, Evelyn Grau, Martin Hemberg, Johannes Bohacek, Eric A. Miska
Software Mentions: 7
Published: about 5 years ago

10.3390/ijms22094917

The Cellular Composition of Bovine Coccygeal Intervertebral Discs: A Comprehensive Single-Cell RNAseq Analysis
Cited by: 24
Author(s): Martina Caliò, Benjamin Gantenbein, Marcel Egli, Lucy Poveda, Fabian Ille
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-52584-w

Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data
Cited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: almost 7 years ago

10.1038/sdata.2018.21

Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich’s ataxia patients
Cited by: 22
Author(s): Marta Seco-Cervera, Daymé González-Rodríguez, José Santiago Ibáñez-Cabellos, Lorena Peiró-Chova, Federico V. Pallardó, José Luis García-Giménez
Software Mentions: 7
Published: over 8 years ago

10.1186/s13059-020-02082-4

Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells
Cited by: 22
Author(s): Juli Liu, Sheng Liu, Hongyu Gao, Lei Han, Xun Chu, Sheng Yi, Weinian Shou, Yue Wang, Yunlong Liu, Jun Wan, Lei Yang
Software Mentions: 7
Published: about 6 years ago

10.1038/s41598-019-46412-4

Host–symbiont combinations dictate the photo-physiological response of reef-building corals to thermal stress
Cited by: 62
Author(s): Kenneth D. Hoadley, Allison M. Lewis, Drew C. Wham, D. Tye Pettay, Chris Grasso, Robin T. Smith, Dustin W. Kemp, Todd C. LaJeunesse, Mark E. Warner
Software Mentions: 7
Published: about 7 years ago

10.15252/emmm.202013180

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1
Cited by: 21
Author(s): George Sflomos, Laura Battista, Patrick Aouad, Fabio De Martino, Valentina Scabia, Athina Stravodimou, Ayyakkannu Ayyanan, Assia Ifticene‐Treboux, Philipp Bücher, Maryse Fiche, Giovanna Ambrosini, Cathrin Brisken, Rls
Software Mentions: 7
Published: over 5 years ago

10.15252/emmm.201809910

Overcoming resistance to anabolic SARM therapy in experimental cancer cachexia with an HDAC inhibitor
Cited by: 16
Author(s): Sophia G. Liva, Yu Chou Tseng, Anees M. Dauki, Michael G. Sovic, Trang Vu, Sally E. Henderson, Yi Chiu Kuo, Jason Benedict, Xiaoli Zhang, Bryan Remaily, Samuel K. Kulp, Moray J. Campbell, Tanios Bekaii‐Saab, Mitch A. Phelps, Ching Shih Chen, Christopher C. Coss
Software Mentions: 7
Published: over 6 years ago

10.1099/mgen.0.000445

Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase
Cited by: 12
Author(s): Domenico Giosa, Maria Rosa Felice, Letterio Giuffrè, Riccardo Aiese Cigliano, Andreu Paytuví-Gallart, Carla Lo Passo, Cinzia Barresi, Enrico D’Alessandro, Huaiqiu Huang, Giuseppe Criseo, Héctor M. Mora-Montes, Sybren de Hoog, Orazio Romeo
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0147249

Cell and Microvesicle Urine microRNA Deep Sequencing Profiles from Healthy Individuals: Observations with Potential Impact on Biomarker Studies
Cited by: 43
Author(s): Iddo Z. Ben‐Dov, Veronica M. Whalen, Béatrice Goilav, Klaas E.A. Max, Thomas Tuschl
Software Mentions: 7
Published: over 10 years ago

10.15698/mic2021.07.754

Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast
Cited by: 14
Author(s): Catalina A. Romila, StJohn Townsend, Michał Malecki, Stephan Kamrad, María Rodríguez-López, Olivia Hillson, Cristina Cotobal, Markus Ralser, Jürg Bähler
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pcbi.1008354

Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
Cited by: 5
Author(s): Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Škrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12864-017-3580-2

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data
Cited by: 37
Author(s): Yevhen Vainshtein, Karsten Rippe, Vladimir B. Teif
Software Mentions: 7
Published: over 9 years ago

10.1038/srep30794

Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry
Cited by: 33
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 7
Published: about 10 years ago

10.1097/MD.0000000000024184

Screening the key genes of prognostic value in the microenvironment for head and neck squamous cell carcinoma
Cited by: 4
Author(s): Di Meng, Tongjun Liu, Feng Ma, Mingguo Wang
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.684002

Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity
Cited by: 5
Author(s): Junjie Liu, Wei Lv, Shuling Li, Jingwen Deng
Software Mentions: 7
Published: almost 5 years ago

10.1126/sciimmunol.abg0833

SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Cited by: 127
Author(s): Bingyu Yan, Tilo Freiwald, Daniel Chauss, Luopin Wang, Erin E. West, Carmen Mirabelli, Zhang Cj, Eva-Maria Nichols, Nazish T. Malik, Richard I. Gregory, Marcus Bantscheff, Sonja Ghidelli-Disse, Martin Kolev, Tristan Frum, Jason R. Spence, Jonathan Z. Sexton, Konstantinos D. Alysandratos, Darrell N. Kotton, Stefania Pittaluga, Jack Bibby, Nathalie Niyonzima, Matthew R. Olson, Shahram Kordasti, Didier Portilla, Christiane E. Wobus, Arian Laurence, Michail S Lionakis, Claudia Kemper, Behdad Afzali, Majid Kazemian
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0232646

Two-step mixed model approach to analyzing differential alternative RNA splicing
Cited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41597-020-00659-z

lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA
Cited by: 35
Author(s): Fayaz Seifuddin, Komudi Singh, Abhilash Suresh, Jennifer Judy, Yun Ching Chen, Vijender Chaitankar, Ilker Tunc, Xiangbo Ruan, Ping Li, Yi Chen, Haiming Cao, Richard S. Lee, Fernando S. Goes, Peter P. Zandi, M. Saleet Jafri, Mehdi Pirooznia
Software Mentions: 7
Published: almost 6 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: over 10 years ago

10.3389/fnins.2021.600462

Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson’s Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1
Cited by: 10
Author(s): Linjing Shen, Changliang Wang, Liang Chen, Garry Wong
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-021-02466-0

Acute depletion of CTCF rewires genome-wide chromatin accessibility
Cited by: 26
Author(s): Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu, Chunliang Li
Software Mentions: 7
Published: about 5 years ago

10.1002/glia.23767

Transcriptional profiling of microglia; current state of the art and future perspectives
Cited by: 72
Author(s): Emma Gerrits, Yang Heng, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0216793

Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes
Cited by: 4
Author(s): A. Borys, Michał Seweryn, Tomasz Gołąbek, Łukasz Bełch, Agnieszka Klimkowska, Justyna Totoń‐Żurańska, Julita Machlowska, Piotr Chłosta, Krzysztof Okoń, Paweł Wołkow
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pcbi.1006792

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
Cited by: 25
Author(s): Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma
Software Mentions: 7
Published: over 7 years ago

10.1186/s13293-020-00312-9

Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data
Cited by: 27
Author(s): Kimberly C. Olney, Sarah M. Brotman, Jocelyn P. Andrews, Valeria A. Valverde-Vesling, Melissa A. Wilson
Software Mentions: 7
Published: about 6 years ago

10.1038/s41597-019-0207-2

Compendiums of cancer transcriptomes for machine learning applications
Cited by: 13
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 7
Published: almost 7 years ago

10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: over 8 years ago

10.1038/s41598-017-18435-2

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys
Cited by: 32
Author(s): Pål Trosvik, Eli Knispel Rueness, Eric J. de Muinck, Amera Moges, Addisu Mekonnen
Software Mentions: 7
Published: over 8 years ago

10.1038/s41598-017-14366-0

Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor Cells
Cited by: 10
Author(s): Christina Sollinger, Jacquelyn Lillis, Jeffrey Malik, Michael Getman, Christoph Pröschel, Laurie A. Steiner
Software Mentions: 7
Published: almost 9 years ago

10.7717/peerj.10836

Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry
Cited by: 9
Author(s): Kerri L. Steenwerth, Ian Arthur Morelan, Ruby J. Stahel, Rosa Figueroa‐Balderas, Dario Cantu, Jungmin Lee, Ron C. Runnebaum, Amisha T. Poret-Peterson
Software Mentions: 7
Published: over 5 years ago

10.3389/fonc.2020.00061

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma
Cited by: 18
Author(s): Yu Liu, Li-Yu Wang, Hengchang Liu, Chunxiang Li, Jie He
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.49658

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Cited by: 278
Author(s): Matthew T Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 7
Published: over 6 years ago

10.1186/s12864-019-6162-7

Transcriptome analysis of the differential effect of the NADPH oxidase gene RbohB in Phaseolus vulgaris roots following Rhizobium tropici and Rhizophagus irregularis inoculation
Cited by: 11
Author(s): Citlali Fonseca-García, Alejandra E. Zayas, Jesús Montiel, Noreide Nava, Federico Sánchez, Carmen Quinto
Software Mentions: 7
Published: almost 7 years ago

10.1186/s13148-019-0651-z

Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression
Cited by: 18
Author(s): Shivani Kamdar, Ruth Isserlin, Theodorus van der Kwast, Alexandre R. Zlotta, Gary D. Bader, Neil Fleshner, Bharati Bapat
Software Mentions: 7
Published: over 7 years ago

10.3389/fonc.2020.01409

Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma
Cited by: 43
Author(s): Yin Wu, Xingjun Jiang, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Chaohong Zhan, Xianyong Fu, Zhaoping Wu, Youwei Guo, Zhipeng Jiang, Chao Ren, Guihua Tang
Software Mentions: 7
Published: about 6 years ago

10.3389/fonc.2021.734873

DNA Methylation Regulator-Meditated Modification Patterns Define the Distinct Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 3
Author(s): Dejian Yuan, Zehong Wei, Yicheng Wang, Cheng Fang, Yujie Zeng, Yang Li, Shangyu Zhang, Jianbo Li, Renkuan Tang
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.66788

An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma
Cited by: 11
Author(s): Rediet Zewdu, Elnaz Mirzaei Mehrabad, Kelley Ingram, Pengshu Fang, Katherine L Gillis, Soledad A. Camolotto, Grace Orstad, Alex Jones, Michelle C. Mendoza, Benjamin T. Spike, Eric L. Snyder
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.13503

A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types
Cited by: 50
Author(s): Yasuyuki Shima, Ken Sugino, Chris M. Hempel, Masami Shima, Praveen Taneja, James B. Bullis, Sonam Mehta, Carlos Lois, Sacha B. Nelson
Software Mentions: 7
Published: over 10 years ago

10.1038/s41598-020-73391-8

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
Cited by: 36
Author(s): Meaghan L. Pimsler, Kennan Oyen, James D. Herndon, Jason M. Jackson, James P. Strange, Michael E. Dillon, Jeffrey D. Lozier
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0219723

Sex-dependent and -independent transcriptional changes during haploid phase gametogenesis in the sugar kelp Saccharina latissima
Cited by: 10
Author(s): Gareth A. Pearson, Neusa Martins, Pedro M Madeira, Ester Á. Serrão, Inka Bartsch
Software Mentions: 7
Published: almost 7 years ago

10.7717/peerj.8206

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Cited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: over 6 years ago

10.3389/fgene.2019.00292

Identification of Long Non-coding and Messenger RNAs Differentially Expressed Between Primary and Metastatic Melanoma
Cited by: 16
Author(s): Lichang Sun, Zhiguang Guan, Shanshan Wei, Rui Tan, Pengfei Li, Yan Liu
Software Mentions: 7
Published: over 7 years ago

10.3389/fpls.2019.01581

Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
Cited by: 24
Author(s): Tomás Carrasco-Valenzuela, Claudia Muñoz-Espinoza, Aníbal Riveros, Romina Pedreschi, Pere Arús, Reinaldo Campos-Vargas, Claudio Meneses
Software Mentions: 7
Published: almost 7 years ago

10.3389/fgene.2021.722981

Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
Cited by: 6
Author(s): Jing Li, Urminder Singh, Zebulun Arendsee, Eve Syrkin Wurtele
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-017-10853-6

The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: about 9 years ago

10.1186/s12864-021-07441-4

A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks
Cited by: 2
Author(s): Pedro Gabriel Nachtigall, Luiz Augusto Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-019-6308-7

Human gene expression variability and its dependence on methylation and aging
Cited by: 23
Author(s): Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
Software Mentions: 7
Published: almost 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568