bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giaa068

Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution
Cited by: 8
Author(s): Michael Kluge, Marie-Sophie Friedl, Amrei L Menzel, Caroline C. Friedel
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2020.585943

Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring
Cited by: 5
Author(s): Avishek Dutta, Ben Smith, Thomas Goldman, Leanne Walker, Matthew Streets, Bob Eden, Reinhard Dirmeier, Jeff S. Bowman
Software Mentions: 7
Published: almost 6 years ago

10.15252/msb.20198831

The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
Cited by: 40
Author(s): Marco Galardini, Bede P. Busby, Cristina Viéitez, Alistair S. Dunham, Athanasios Typas, Pedro Beltrão
Software Mentions: 7
Published: almost 7 years ago

10.1007/s00572-020-01001-6

Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome
Cited by: 6
Author(s): Christina Paparokidou, Jonathan R. Leake, David J. Beerling, Stephen A. Rolfe
Software Mentions: 7
Published: almost 6 years ago

10.1002/edm2.191

Sex and oestrogen receptor β have modest effects on gene expression in the mouse brain posterior cortex
Cited by: 1
Author(s): Jasmine A. Fels, Gabriella Casalena, Giovanni Manfredi
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41392-021-00703-3

Differential immune responses in pregnant patients recovered from COVID-19
Cited by: 21
Author(s): Ge Chen, Yiming Zhang, Yaoyao Zhang, Jihui Ai, Bin Yang, Mengge Cui, Qiande Liao, Hanxiao Chen, Hualin Bai, Dashing Shang, Jing Chen, Chaoyang Sun, Haiyi Liu, Fengyuan Liu, Biming Mao, Guoqiang Sun, Lu Chen, Jing-wen Lin, Kezhen Li
Software Mentions: 7
Published: about 5 years ago

10.1093/bib/bbt086

Comparison of software packages for detecting differential expression in RNA-seq studies
Cited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: almost 13 years ago

10.3389/fpls.2017.00413

Identification of Circular RNAs in Kiwifruit and Their Species-Specific Response to Bacterial Canker Pathogen Invasion
Cited by: 54
Author(s): Zupeng Wang, Yifei Liu, Dawei Li, Li Li, Qiong Zhang, Shuaibin Wang, Hongwen Huang
Software Mentions: 7
Published: over 9 years ago

10.3390/v13061059

Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses
Cited by: 5
Author(s): Roberto J. Cieza, Jonathan L. Golob, Justin A. Colacino, Christiane E. Wobus
Software Mentions: 7
Published: over 5 years ago

10.1186/s13007-021-00791-w

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture
Cited by: 3
Author(s): Amir Mahboubi, Nicolas Delhomme, Sara Lea Häggström, Johannes Hanson
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2021.693039

Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition
Cited by: 5
Author(s): Laura W. Dijkhuizen, Badraldin Ebrahim Sayed Tabatabaei, Paul Brouwer, Niels Rijken, Valerie A. Buijs, Erbil Güngör, Henriette Schluepmann
Software Mentions: 7
Published: about 5 years ago

10.3390/v13081614

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression
Cited by: 7
Author(s): Muhammad Hafiz Ismail, Katharine A. Michie, Yu Fen Goh, Parisa Noorian, Staffan Kjelleberg, Iain G. Duggin, Diane McDougald, Scott A. Rice
Software Mentions: 7
Published: about 5 years ago

10.3390/cells8080921

Genes Controlled by DNA Methylation Are Involved in Wilms Tumor Progression
Cited by: 12
Author(s): João Victor da Silva Guerra, Bruna Maria de Sá Pereira, Jéssica Gonçalves Vieira da Cruz, Nicole de Miranda Scherer, Carolina Furtado, Rafaela Montalvão de Azevedo, Paulo Sérgio Lopes de Oliveira, Paulo Faria, Mariana Boroni, Beatriz de Camargo, Mariana Maschietto
Software Mentions: 6
Published: about 7 years ago

10.3390/plants9121801

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil
Cited by: 10
Author(s): Andrey A. Belimov, А. И. Шапошников, D. S. Syrova, Arina Kichko, Polina Guro, O. S. Yuzikhin, T. S. Azarova, Anna L Sazanova, E. A. Sekste, Vladimir A Litvinskiy, Vladimir V. Nosikov, А. А. Завалин, E. E. Andronov, Vera I. Safronova
Software Mentions: 6
Published: over 5 years ago

10.1093/biostatistics/kxw055

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
Cited by: 112
Author(s): Aaron T. L. Lun, John C. Marioni
Software Mentions: 6
Published: over 9 years ago

10.1038/s41598-021-94442-8

Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
Cited by: 1
Author(s): Sebastian Friedrich, Hannah Müller, Caroline Riesterer, Hannah Schüller, Katja Friedrich, Carlotta Leonie Wörner, Tilman Busch, Amandine Viau, E. Wolfgang Kuehn, Michael Köttgen, Alexis Hofherr
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0184890

Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology
Cited by: 92
Author(s): Sarah E. Macdonald, Matthew J. Nolan, Kimberley Harman, Kay Boulton, David Hume, Fiona M. Tomley, Richard A. Stabler, Damer P. Blake
Software Mentions: 6
Published: almost 9 years ago

10.1038/s41598-021-92405-7

Microplastics accumulate fungal pathogens in terrestrial ecosystems
Cited by: 73
Author(s): Gerasimos Gkoutselis, Stephan Rohrbach, Janno Harjes, Martin Obst, Andreas Brachmann, Marcus A. Horn, Gerhard Rambold
Software Mentions: 6
Published: about 5 years ago

10.3390/v13020244

HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles
Cited by: 5
Author(s): Antônio Victor Campos Coelho, Rossella Gratton, João Paulo Britto de Melo, José Leandro Andrade‐Santos, Rafael Lima Guimarães, Sérgio Crovella, Paola Maura Tricarico, Lucas André Cavalcanti Brandão
Software Mentions: 6
Published: over 5 years ago

10.15252/msb.20199195

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

10.1371/journal.pntd.0009633

Identification of potential biomarkers in dengue via integrated bioinformatic analysis
Cited by: 5
Author(s): Lisha Xie, Xin Yin, Jie Bi, Hongyu Luo, Xun‐Jie Cao, Yu-Wen Ma, Ye-Ling Liu, Jianwen Su, Geng-Ling Lin, Xu‐Guang Guo
Software Mentions: 6
Published: about 5 years ago

10.15252/embr.202051289

LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis
Cited by: 16
Author(s): Andrea Bast‐Habersbrunner, Christoph Kiefer, Peter Weber, Tobias Fromme, Anna Schießl, Petra Schwalie, Bart Deplancke, Yongguo Li, Martin Klingenspor
Software Mentions: 6
Published: over 5 years ago

10.3390/cancers12123551

High-Plex and High-Throughput Digital Spatial Profiling of Non-Small-Cell Lung Cancer (NSCLC)
Cited by: 27
Author(s): James Monkman, Touraj Taheri, Majid Ebrahimi Warkiani, Connor O’Leary, Rahul Ladwa, Derek J. Richard, K.J. O’Byrne, Arutha Kulasinghe
Software Mentions: 6
Published: almost 6 years ago

10.15252/emmm.201708587

Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activator
Cited by: 54
Author(s): Snehajyoti Chatterjee, Raphaelle Cassel, Anne Schneider‐Anthony, Karine Mérienne, Brigitte Cosquer, Laura Tzeplaeff, Sarmistha Sinha, Manoj Kumar, Piyush Chaturbedy, M. Eswaramoorthy, Stéphanie Le Gras, Céline Keime, Olivier Bousiges, P. Dutar, Petnoï Petsophonsakul, Claire Rampon, Jean‐Christophe Cassel, Luc Buée, David Blum, Tapas K. Kundu, Anne‐Laurence Boutillier
Software Mentions: 6
Published: almost 8 years ago

10.3389/fimmu.2021.676173

Interleukin-17A Causes Osteoarthritis-Like Transcriptional Changes in Human Osteoarthritis-Derived Chondrocytes and Synovial Fibroblasts In Vitro
Cited by: 20
Author(s): Jolet Y Mimpen, Mathew Baldwin, Adam P. Cribbs, Martin Philpott, Andrew Carr, Stephanie G. Dakin, Sarah Snelling
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-021-00951-6

Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus
Cited by: 10
Author(s): Nandan P. Deshpande, Stephen M. Riordan, Claire J. Gorman, Shaun Nielsen, Tonia Russell, Carolina Correa-Ospina, Samitha Fernando, Shafagh A. Waters, Natalia Castaño‐Rodríguez, Si Ming Man, Nicodemus Tedla, Marc R. Wilkins, Nadeem O. Kaakoush
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.59388

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals
Cited by: 10
Author(s): Eric M. Sanford, Benjamin Emert, Allison Coté, Arjun Raj
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13073-018-0586-6

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
Cited by: 96
Author(s): Vanessa L. Hale, Patricio Jeraldo, Jun Chen, Michael B. Mundy, Jingwen Yao, Sambhawa Priya, Gary Keeney, Kelly Lyke, Jason M. Ridlon, Bryan A. White, Amy J. French, Stephen N. Thibodeau, Christian Diener, Osbaldo Reséndis-Antonio, Jaime Gransee, Tumpa Dutta, Xuan Mai Petterson, Jaeyun Sung, Ran Blekhman, Lisa A. Boardman, David W. Larson, Heidi Nelson, Nicholas Chia
Software Mentions: 6
Published: almost 8 years ago

10.1016/j.celrep.2019.06.039

Acute Iron Deprivation Reprograms Human Macrophage Metabolism and Reduces Inflammation In Vivo
Cited by: 67
Author(s): Marie Pereira, Tai‐Di Chen, Norzawani Buang, Antoni Olona, Jeong‐Hun Ko, Maria Prendecki, Ana S.H. Costa, Efterpi Nikitopoulou, Laura Tronci, Charles D. Pusey, H. Terence Cook, Stephen P. McAdoo, Christian Frezza, Jacques Behmoaras
Software Mentions: 6
Published: about 7 years ago

10.1186/s13073-016-0302-3

An adaptive association test for microbiome data
Cited by: 63
Author(s): Chong Wu, Jun Chen, Junghi Kim, Wei Pan
Software Mentions: 6
Published: over 10 years ago

10.1002/ece3.4724

Highly flexible infection programs in a specialized wheat pathogen
Cited by: 72
Author(s): Janine Haueisen, Mareike Möller, Christoph Eschenbrenner, Jonathan Grandaubert, Heike Seybold, Holger Adamiak, Eva H. Stukenbrock
Software Mentions: 6
Published: over 7 years ago

10.1126/sciadv.abe8978

Astrocytes and neurons share region-specific transcriptional signatures that confer regional identity to neuronal reprogramming
Cited by: 56
Author(s): Álvaro Herrero-Navarro, Lorenzo Puche-Aroca, Verónica Moreno‐Juan, Alejandro Sempere-Ferràndez, Ana Espinosa, Rafael Susín, Laia Torres-Masjoan, Eduardo Leyva-Díaz, Marisa Karow, María Figueres-Oñate, Laura López‐Mascaraque, José P. López‐Atalaya, Benedikt Berninger, Guillermina López‐Bendito
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2020.00954

Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite
Cited by: 22
Author(s): Fátima Jorge, Nolwenn M. Dheilly, Robert Poulin
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2018.00224

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
Cited by: 146
Author(s): Enkelejda Miho, Alexander Yermanos, Cédric R. Weber, Christoph T. Berger, Sai T. Reddy, Victor Greiff
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1009474

Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps
Cited by: 6
Author(s): Floria M. K. Uy, Christopher M. Jernigan, Natalie C. Zaba, Eshan Mehrotra, Sara Miller, Michael J. Sheehan
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-021-89531-7

Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics
Cited by: 2
Author(s): Stevan D. Stojanović, Maximilian Fuchs, Chunguang Liang, Kevin Schmidt, Xiaoyan Ke, Annette Just, Angelika Pfanne, Andreas Pich, G. Warnecke, Peter Braubach, Christina Petzold, Danny Jonigk, Jörg H W Distler, Jan Fiedler, Thomas Thum, Meik Kunz
Software Mentions: 6
Published: over 5 years ago

10.1111/tpj.14184

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes
Cited by: 91
Author(s): Genevieve M. Hoopes, John Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart, C. Robin Buell
Software Mentions: 6
Published: over 7 years ago

10.3390/v11010053

Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus
Cited by: 13
Author(s): Florian Pfaff, Sara Hägglund, Martina Zoli, Sandra Blaise‐Boisseau, Eve Laloy, Susanne Koethe, Daniela Zühlke, Katharina Riedel, Stéphan Zientara, Labib Bakkali‐Kassimi, J. F. Valarcher, Dirk W. Höper, Martin Beer, Michael Eschbaumer
Software Mentions: 6
Published: over 7 years ago

10.1186/s13007-020-00611-7

DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models
Cited by: 22
Author(s): Ilana Lambert, Christine Paysant‐Le Roux, Stefano Colella, Marie-Laure Martin
Software Mentions: 6
Published: over 6 years ago

10.1016/j.celrep.2019.03.104

Notch Signaling Mediates Secondary Senescence
Cited by: 72
Author(s): Yee Voan Teo, Nattaphong Rattanavirotkul, Nelly Olova, Angela Salzano, Andrea Quintanilla, Núria Tarrats, Christos Kiourtis, Miryam Müller, Anthony Green, Peter D. Adams, Juan Carlos Acosta, Tom Bird, Kristina Kirschner, Nicola Neretti, Tamir Chandra
Software Mentions: 6
Published: over 7 years ago

10.3390/cancers12061507

Small Non-Coding RNA Profiling in Plasma Extracellular Vesicles of Bladder Cancer Patients by Next-Generation Sequencing: Expression Levels of miR-126-3p and piR-5936 Increase with Higher Histologic Grades
Cited by: 33
Author(s): Alexandru A Sabo, Giovanni Birolo, Alessio Naccarati, Mihnea P. Dragomir, Serena Aneli, Alessandra Allione, Marco Oderda, Marco Allasia, Paolo Gontero, Carlotta Sacerdote, Paolo Víneis, Giuseppe Matullo, Barbara Pardini
Software Mentions: 6
Published: over 6 years ago

10.1016/j.stem.2018.06.014

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells
Cited by: 137
Author(s): Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers
Software Mentions: 6
Published: about 8 years ago

10.3390/v12070695

Ross River Virus Provokes Differentially Expressed MicroRNA and RNA Interference Responses in Aedes aegypti Mosquitoes
Cited by: 10
Author(s): J. B. Sinclair, Sassan Asgari
Software Mentions: 6
Published: about 6 years ago

10.1080/19490976.2021.1902771

The intestinal microbiota and metabolites in patients with anorexia nervosa
Cited by: 44
Author(s): Petra Procházková, Radka Roubalová, Jiří Dvořák, Jakub Kreisinger, Martin Hill, Helena Tlaskalová‐Hogenová, Petra Tomášová, Helena Pelantová, M Cermáková, Marek Kuzma, Josef Bulant, Martin Bilej, Kvido Smitka, Alena Lambertová, Petra Holanová, Hana Papežová
Software Mentions: 6
Published: over 5 years ago

10.1016/j.stem.2019.07.009

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency
Cited by: 27
Author(s): Hannah Stuart, Giuliano Giuseppe Stirparo, Tim Lohoff, Lawrence E. Bates, Masaki Kinoshita, Chee Lim, Elsa Joana Sousa, Katsiaryna Maskalenka, Aliaksandra Radzisheuskaya, Andrew A. Malcolm, Mariana R. P. Alves, Rebecca L. Lloyd, Sonia Nestorowa, Peter Humphreys, William Mansfield, Wolf Reik, Paul Bertone, Jennifer Nichols, Berthold Göttgens, José C.R. Silva
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0218458

p73 regulates epidermal wound healing and induced keratinocyte programming
Cited by: 18
Author(s): J. Scott Beeler, Clayton B. Marshall, Paula I. González-Ericsson, Timothy M. Shaver, Gabriela L. Santos Guasch, Spencer Lea, Kimberly N. Johnson, Hailing Jin, Bryan J. Venters, Melinda E. Sanders, Jennifer A. Pietenpol
Software Mentions: 6
Published: about 7 years ago

10.1016/j.xcrm.2021.100267

Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma
Cited by: 2
Author(s): Hui Wen Lue, Daniel S. Derrick, Soumya Rao, Ahna Van Gaest, Larry C. Cheng, Jennifer Podolak, Samantha Lawson, Changhui Xue, Devin Garg, Ralph E. White, Christopher W. Ryan, Justin M. Drake, Anna Ritz, Laura M. Heiser, George V. Thomas
Software Mentions: 6
Published: over 5 years ago

10.3390/v12111303

Human Endogenous Retrovirus K Rec Forms a Regulatory Loop with MITF that Opposes the Progression of Melanoma to an Invasive Stage
Cited by: 16
Author(s): Manvendra Singh, Huiqiang Cai, Mario Bunse, Cédric Feschotte, Zsuzsanna Izsvák
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-021-02400-4

mbImpute: an accurate and robust imputation method for microbiome data
Cited by: 23
Author(s): Ruochen Jiang, Wei Vivian Li, Jingyi Jessica Li
Software Mentions: 6
Published: about 5 years ago

10.3390/brainsci9120381

A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder
Cited by: 6
Author(s): Laura B. Ferguson, Shruti Patil, Bailey A. Moskowitz, Igor Ponomarev, R. Adron Harris, R. Dayne Mayfield, Robert O. Messing
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pntd.0005246

The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni
Cited by: 39
Author(s): Kathrin K. Geyer, Umar Niazi, David Timothy Duval, Céline Cosseau, Chad Tomlinson, Iain W. Chalmers, Martin Swain, David Cutress, Utibe Bickham-Wright, Sabrina E. Munshi, Christoph Grunau, Timothy P. Yoshino, Karl F. Hoffmann
Software Mentions: 6
Published: over 9 years ago

10.1038/sdata.2017.51

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

10.1093/gbe/evaa088

Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels
Cited by: 9
Author(s): Rahulsimham Vegesna, Marta Tomaszkiewicz, Oliver A. Ryder, Rebeca Campos-Sánchez, Paul Medvedev, Michael DeGiorgio, Kateryna D. Makova
Software Mentions: 6
Published: over 6 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: almost 7 years ago

10.15252/emmm.202013412

The immune suppressive microenvironment affects efficacy of radio‐immunotherapy in brain metastasis
Cited by: 23
Author(s): Katja Niesel, Marcel H. Schulz, Julian Anthes, Tijna Alekseeva, Jadranka Macas, Anna Salamero-Boix, Aylin Möckl, T. Oberwahrenbrock, Marco Lolies, Stefan Stein, Karl H. Plate, Yvonne Reiss, Franz Rödel, Lisa Sevenich
Software Mentions: 6
Published: over 5 years ago

10.3389/fcimb.2017.00262

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition
Cited by: 32
Author(s): Emanuel Heitlinger, Susana Carolina Martins Ferreira, Dagmar Thierer, Heribert Hofer, Marion L. East
Software Mentions: 6
Published: over 9 years ago

10.1186/s13073-021-00931-w

Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma
Cited by: 25
Author(s): Clément Meiller, François Montagne, Théo Z. Hirsch, Stefano Caruso, Julien De Wolf, Quentin Bayard, Jean-Baptiste Assié, Léa Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cécile Badoual, Sarah Humez, Françoise Galateau-Sallé, Marie‐Christine Copin, Éric Letouzé, Arnaud Scherpereel, Jessica Zucman–Rossi, Françoise Le Pimpec‐Barthes, Marie-Claude Jaurand, Didier Jean
Software Mentions: 6
Published: about 5 years ago

10.1002/pld3.242

Lipophilic signals lead to organ‐specific gene expression changes in Arabidopsis seedlings
Cited by: 4
Author(s): Ashley E. Cannon, Chengshi Yan, David J. Burks, Xiaolan Rao, Rajeev K. Azad, Kent D. Chapman
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0143563

RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression
Cited by: 135
Author(s): Adam Labadorf, Andrew G. Hoss, Valentina N. Lagomarsino, Jeanne C. Latourelle, Tiffany C. Hadzi, Joli Bregu, Marcy E. MacDonald, James F. Gusella, Jiang‐Fan Chen, Schahram Akbarian, Zhiping Weng, Richard H. Myers
Software Mentions: 6
Published: almost 11 years ago

10.1186/s13071-021-04717-2

Transcriptomic profiling of three-dimensional cholangiocyte spheroids long term exposed to repetitive Clonorchis sinensis excretory-secretory products
Cited by: 4
Author(s): Jung Woong Kim, Junyeong Yi, Jin‐Hong Park, Ji Hoon Jeong, Jin-Ho Kim, Jihee Won, Seok Chung, Tong Soo Kim, Jhang Ho Pak
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.55249

Generation of inner ear hair cells by direct lineage conversion of primary somatic cells
Cited by: 49
Author(s): Louise Menendez, Talon Trecek, Suhasni Gopalakrishnan, Litao Tao, Alexander L. Markowitz, Haoze V Yu, Xizi Wang, Juan Llamas, Chi‐Chou Huang, James Lee, Radha Kalluri, Justin K. Ichida, Neil Segil
Software Mentions: 6
Published: about 6 years ago

10.1098/rstb.2019.0242

Phylogenetic conservation of soil bacterial responses to simulated global changes
Cited by: 41
Author(s): Kazuo Isobe, Nicholas J. Bouskill, Eoin L. Brodie, Erika A. Sudderth, Jennifer B. H. Martiny
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.50069

Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta
Cited by: 49
Author(s): Emelyne Teo, Sudharshan Ravi, Diogo Barardo, Hyung-Seok Kim, Sheng Fong, Amaury Cazenave-Gassiot, Tsze Yin Tan, Jianhong Ching, Jean‐Paul Kovalik, Markus R. Wenk, Rudiyanto Gunawan, Philip K. Moore, Barry Halliwell, Nicholas S. Tolwinski, Jan Gruber
Software Mentions: 6
Published: almost 7 years ago

10.3390/biom10071041

Untargeted LC-MS Metabolomics Differentiates Between Virulent and Avirulent Clinical Strains of Pseudomonas aeruginosa
Cited by: 18
Author(s): Tobias Depke, Janne G. Thöming, Adrian Kordes, Susanne Häußler, Mark Brönstrup
Software Mentions: 6
Published: about 6 years ago

10.1002/ece3.3597

Gut microbiota composition is associated with environmental landscape in honey bees
Cited by: 94
Author(s): Julia C. Jones, Carmelo Fruciano, Falk Hildebrand, Hasan Al Toufalilia, Nicholas J. Balfour, Peer Bork, Philipp Engel, Francis L. W. Ratnieks, William O. Hughes
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0195534

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis
Cited by: 34
Author(s): Daniel Hagenfeld, Raphael Koch, Sebastian Jünemann, Karola Prior, Inga Harks, Peter Eickholz, Thomas Hoffmann, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Benjamin Ehmke, Dag Harmsen
Software Mentions: 6
Published: over 8 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: almost 6 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: over 5 years ago

10.15252/embr.201846401

Inherent <scp>DNA</scp> ‐binding specificities of the <scp>HIF</scp> ‐1α and <scp>HIF</scp> ‐2α transcription factors in chromatin
Cited by: 128
Author(s): James Smythies, Min Sun, Norma Masson, Rafik Salama, Peter Simpson, Elizabeth R. Murray, Viviana K. Neumann, Matthew E. Cockman, Hani Choudhry, Peter J. Ratcliffe, David R. Mole
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0189616

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments
Cited by: 37
Author(s): Nicholas D. Youngblut, Samuel E. Barnett, Daniel H. Buckley
Software Mentions: 6
Published: over 8 years ago

10.1186/s13072-019-0297-2

MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells
Cited by: 9
Author(s): Temesgen Fufa, Laura L. Baxter, Julia C. Wedel, Derek Gildea, Stacie K. Loftus, William J. Pavan
Software Mentions: 6
Published: about 7 years ago

10.3389/fpls.2021.642828

Natural Genetic Diversity in Tomato Flavor Genes
Cited by: 12
Author(s): Lara Pereira, Manoj Sapkota, Michael Alonge, Yi Zheng, Youjun Zhang, Hamid Razifard, Nathan K Taitano, Michael C. Schatz, Alisdair R. Fernie, Ying Wang, Zhangjun Fei, Ana L. Caicedo, Denise M. Tieman, Esther van der Knaap
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2017.01926

A Pectin Methylesterase ZmPme3 Is Expressed in Gametophyte factor1-s (Ga1-s) Silks and Maps to that Locus in Maize (Zea mays L.)
Cited by: 28
Author(s): Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott
Software Mentions: 6
Published: almost 9 years ago

10.3389/fpls.2020.570436

Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses
Cited by: 1
Author(s): Chidi Afamefule, Christine A. Raines
Software Mentions: 6
Published: almost 6 years ago

10.1007/s12275-020-9536-2

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
Cited by: 7
Author(s): Donghui Choe, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 6
Published: over 6 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: almost 7 years ago

10.1111/1462-2920.14516

Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples
Cited by: 12
Author(s): Fabien Cholet, Umer Zeeshan Ijaz, Cindy J. Smith
Software Mentions: 6
Published: over 7 years ago

10.7554/eLife.66321

Channel nuclear pore complex subunits are required for transposon silencing in Drosophila
Cited by: 10
Author(s): Marzia Munafò, Victoria R Lawless, Alessandro Passera, Serena MacMillan, Susanne Bornelöv, Irmgard U. Haussmann, Matthias Soller, Gregory J. Hannon, Benjamin Czech
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2019.00974

Identifying the Growth Modulon of Corynebacterium glutamicum
Cited by: 8
Author(s): Thorsten Haas, Michaela Graf, Alexander Nieß, Tobias Busche, Jörn Kalinowski, Bastian Blombach, Ralf Takors
Software Mentions: 6
Published: over 7 years ago

10.3389/fpls.2019.00698

PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation
Cited by: 5
Author(s): Hongryul Ahn, Kyuri Jo, Dabin Jeong, Minwoo Pak, Jihye Hur, Wi Hoon Jung, Sun Kim
Software Mentions: 6
Published: over 7 years ago

10.7554/eLife.50103

Developmental variability channels mouse molar evolution
Cited by: 14
Author(s): Luke Hayden, Kateřina Lochovská, Marie Sémon, Sabrina Renaud, Marie Laure Delignette-Muller, Maurine Vilcot, Renata Peterková, Maria Hovořáková, Sophie Pantalacci
Software Mentions: 6
Published: over 6 years ago

10.1186/s13072-018-0250-9

Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection
Cited by: 29
Author(s): José Luis Ruiz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Jean-Bosco Ouédraogo, Victor G. Corcés, Elena Gómez-Díaz
Software Mentions: 6
Published: over 7 years ago

10.7554/eLife.57189

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma
Cited by: 11
Author(s): Connor Rogerson, Samuel Ogden, Edward Britton, Yeng Ang, Andrew D. Sharrocks
Software Mentions: 6
Published: about 6 years ago

10.1186/s13068-021-01948-4

Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids
Cited by: 6
Author(s): Jose J De Vega, Ned Peel, Sarah Purdy, Sarah Hawkins, Iain S. Donnison, Sarah Dyer, Kerrie Farrar
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0249832

Non-small cell lung cancer microbiota characterization: Prevalence of enteric and potentially pathogenic bacteria in cancer tissues
Cited by: 14
Author(s): Nathan Dumont-Leblond, Marc Veillette, Christine Racine, Philippe Joubert, Caroline Duchaine
Software Mentions: 6
Published: over 5 years ago

10.1093/gigascience/giaa152

Tool recommender system in Galaxy using deep learning
Cited by: 7
Author(s): Anup Kumar, Helena Rasche, Björn Grüning, Rolf Backofen
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0233372

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs
Cited by: 20
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 6
Published: over 6 years ago

10.1038/s41392-021-00745-7

Melatonin enhances radiofrequency-induced NK antitumor immunity, causing cancer metabolism reprogramming and inhibition of multiple pulmonary tumor development
Cited by: 19
Author(s): Ming Li, Bingjie Hao, Menghuan Zhang, Russel J. Reíter, Shumeng Lin, Tiansheng Zheng, Xiangyun Chen, Yanru Ren, Liduo Yue, Аbay Baigenzhin, Guojie Chen, Xiao Xu, Yufeng Shi, Lihong Fan
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0207002

Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer
Cited by: 24
Author(s): Mansi Shah, Todd Z. DeSantis, José‐Miguel Yamal, Tiffany L. Weir, Elizabeth P. Ryan, Julia Cope, Emily B. Hollister
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41598-021-98059-9

Sex-dependent gene co-expression in the human body
Cited by: 9
Author(s): Robin Hartman, Michal Mokrý, Gérard Pasterkamp, Hester M. den Ruijter
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2020.01528

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation
Cited by: 7
Author(s): Nicholas C. Dove, Timothy J. Rogers, Christy Leppanen, Daniel Simberloff, James A. Fordyce, Veronica A. Brown, Anthony V. LeBude, Thomas G. Ranney, Melissa Cregger
Software Mentions: 6
Published: about 6 years ago

10.15252/msb.202110253

Model‐guided development of an evolutionarily stable yeast chassis
Cited by: 5
Author(s): Filipa Pereira, Helena Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, D. Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R. Patil
Software Mentions: 6
Published: about 5 years ago

10.3389/fpls.2021.609684

Transcriptomics of Differential Ripening in ‘d’Anjou’ Pear (Pyrus communis L.)
Cited by: 5
Author(s): Loren Honaas, Heidi Hargarten, John A. Hadish, Stephen P. Ficklin, Sara Serra, Stefano Musacchi, Eric Wafula, James P. Mattheis, Claude W. dePamphilis, David R. Rudell
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-92042-0

Socioeconomic position links circulatory microbiota differences with biological age
Cited by: 12
Author(s): Hannah Craven, Dagmara McGuinness, Sarah Buchanan, Norman Galbraith, David McGuinness, Brian Jones, Emilie Combet, Denise Mafra, Peter Bergman, Anne Ellaway, Peter Stenvinkel, Umer Zeeshan Ijaz, Paul G. Shiels
Software Mentions: 6
Published: over 5 years ago

10.1080/19490976.2021.1874815

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer
Cited by: 33
Author(s): Kellyanne Duncan, Kelly Carey-Ewend, Shipra Vaishnava
Software Mentions: 6
Published: over 5 years ago

10.1101/2020.08.11.20171108

ACE2 expression in adipose tissue is associated with COVID-19 cardio-metabolic risk factors and cell type composition
Cited by: 8
Author(s): Julia S. El-Sayed Moustafa, Anne Jackson, Sarah M. Brotman, Li Guan, Sergio Villicaña, Amy L. Roberts, Antonino Zito, Lori L. Bonnycastle, Michael R. Erdos, Narisu Narisu, Heather M. Stringham, Ryan Welch, Tingfen Yan, Timo A. Lakka, Stephen C. J. Parker, Jaakko Tuomilehto, Francis S. Collins, Päivi Pajukanta, Michael Boehnke, Heikki A. Koistinen, Markku Laakso, Mario Falchi, Jordana T. Bell, Laura J. Scott, Karen L. Mohlke, Kerrin S. Small
Software Mentions: 6
Published: about 6 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: almost 5 years ago

10.3389/fgene.2020.00404

Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization
Cited by: 20
Author(s): Hrant Hovhannisyan, Ester Saus, Ewa Księżopolska, Alex J Hinks Roberts, Edward J. Louis, Toni Gabaldón
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1009801

Tramtrack acts during late pupal development to direct ant caste identity
Cited by: 6
Author(s): Karl M. Glastad, Linyang Ju, Shelley L. Berger
Software Mentions: 6
Published: almost 5 years ago

10.1128/mSystems.00712-21

Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge
Cited by: 4
Author(s): Maxwell B. W. Madill, Yaqian Luo, Pranav Sampara, Ryan M. Ziels
Software Mentions: 6
Published: about 5 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583