cran: eulerr | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1009317

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
Cited by: 11
Author(s): Ilario De Toma, Cesar Sierra, Mara Dierssen
Software Mentions: 14
Published: almost 3 years ago

10.1371/journal.ppat.1008653

Genome-wide transcriptomics identifies an early preclinical signature of prion infection
Cited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: about 4 years ago

10.7554/eLife.61980

Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues
Cited by: 43
Author(s): Andrew W. DeVilbiss, Zhiyu Zhao, Misty S. Martin-Sandoval, Jessalyn M. Ubellacker, Alpaslan Tasdogan, Michalis Agathocleous, Thomas P. Mathews, Sean J. Morrison
Software Mentions: 13
Published: over 3 years ago

10.3389/fgene.2021.706907

ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram
Cited by: 97
Author(s): Chunhui Gao, Guangchuang Yu, Peng Cai
Software Mentions: 12
Published: about 3 years ago

10.1038/s42003-019-0646-5

Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis
Cited by: 59
Author(s): Bart Rymen, Ayako Kawamura, Alice Lambolez, Soichi Inagaki, Arika Takebayashi, Akira Iwase, Yuki Sakamoto, Kaori Sako, David S. Favero, Momoko Ikeuchi, Takamasa Suzuki, Masanori Seki, Tetsuji Kakutani, François Roudier, Keiko Sugimoto
Software Mentions: 10
Published: almost 5 years ago

10.3389/fmicb.2021.706214

Dietary Exposure of Pacific Oyster (Crassostrea gigas) Larvae to Compromised Microalgae Results in Impaired Fitness and Microbiome Shift
Cited by: 5
Author(s): Julien Vignier, Olivier Laroche, Anne Rolton, Pandora Wadsworth, K. Kumanan, Branwen Trochel, Xavier Pochon, Nathan King
Software Mentions: 10
Published: about 3 years ago

10.1038/s41598-020-57760-x

Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems
Cited by: 8
Author(s): Ricardo Schöps, Kezia Goldmann, Lotte Korell, Helge Bruelheide, Tesfaye Wubet, François Buscot
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pgen.1009259

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration
Cited by: 9
Author(s): Passley Hargrove-Grimes, Anupam Mondal, Jessica Gumerson, Jacob Nellissery, Angel Aponte, Linn Gieser, Haohua Qian, Robert N Fariss, Juan S. Bonifacino, Tiansen Li, Anand Swaroop
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.54074

A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord
Cited by: 89
Author(s): Annette D. Allen, Megan C Neville, Sebastian Birtles, Vincent Croset, Christoph Daniel Treiber, Scott Waddell, Stephen F. Goodwin
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-021-81773-9

Verifying explainability of a deep learning tissue classifier trained on RNA-seq data
Cited by: 26
Author(s): Melvyn Yap, Rebecca L. Johnston, Helena Foley, Samual MacDonald, Olga Kondrashova, Khoa Tran, Kátia Nones, Lambros T. Koufariotis, Cameron Bean, John V. Pearson, Maciej Trzaskowski, Nicola Waddell
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-59516-z

Variability in estimated gene expression among commonly used RNA-seq pipelines
Cited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: over 4 years ago

10.1038/s41421-021-00279-w

Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication
Cited by: 7
Author(s): Wen Juan Tu, Robert McCuaig, Michelle Melino, Daniel J. Rawle, Thuy T. Le, Kexin Yan, Andreas Suhrbier, Rebecca L. Johnston, Lambros T. Koufariotis, Nicola Waddell, E.M. Cross, S. Tsimbalyuk, Amanda L. Bain, Elizabeth Ahern, Natasha Collinson, Simon Phipps, Jade K. Forwood, Nabila Seddiki, Sudha Rao
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0253847

TeamTree analysis: A new approach to evaluate scientific production
Cited by: 2
Author(s): Frank W. Pfrieger
Software Mentions: 8
Published: about 3 years ago

10.7554/eLife.65228

Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice
Cited by: 8
Author(s): Diptendu Mukherjee, Ben J. Gonzales, Reut Ashwal-Fluss, Hagit Turm, Maya Groysman, Ami Citri
Software Mentions: 8
Published: over 3 years ago

10.1038/s42003-020-0969-2

Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development
Cited by: 11
Author(s): Maria Victoria Gómez Roldán, Farhaj Izhaq, Marion Verdenaud, John Saviour Yaw Eleblu, Aimen Haraghi, Vivien Sommard, Pierre Chambrier, David Latrasse, Teddy Jégu, Moussa Benhamed, Judit Szécsi, Mohammed Bendahmane, Adnane Boualem, Abdelhafid Bendahmane
Software Mentions: 7
Published: over 4 years ago

10.1186/s12870-021-03142-y

Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives
Cited by: 5
Author(s): Simon Kallow, Bart Panis, Dang Toan Vu, Tuong Dang Vu, J. Paofa, Arne Mertens, Rony Swennen, Steven Janssens
Software Mentions: 7
Published: about 3 years ago

10.1093/molbev/msaa122

The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi
Cited by: 29
Author(s): Emile Gluck‐Thaler, Sajeet Haridas, Manfred Binder, Igor V. Grigoriev, Pedro W. Crous, Joseph W. Spatafora, Kathryn E. Bushley, Jason C. Slot
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pntd.0009607

One hundred years of zoonoses research in the Horn of Africa: A scoping review
Cited by: 17
Author(s): Lisa Cavalerie, Maya Wardeh, Ophélie Lebrasseur, Mark Nanyingi, K. Marie McIntyre, Mirgissa Kaba, Daniel Asrat, Robert M. Christley, Gina Pinchbeck, Matthew Baylis, Siobhan M. Mor
Software Mentions: 7
Published: about 3 years ago

10.1111/acel.13344

Senescence‐associated β‐galactosidase reveals the abundance of senescent CD8+ T cells in aging humans
Cited by: 62
Author(s): Ricardo Iván Martínez-Zamudio, Hannah K Dewald, Themistoklis Vasilopoulos, Lisa Gittens-Williams, Patricia Fitzgerald-Bocarsly, Utz Herbig
Software Mentions: 7
Published: over 3 years ago

10.1186/s13059-021-02309-y

Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways
Cited by: 11
Author(s): Carrie Kovalak, Scott Donovan, Alicia A. Bicknell, Mihir Metkar, Melissa J. Moore
Software Mentions: 7
Published: over 3 years ago

10.3390/proteomes7040032

In Silico Identification of Antimicrobial Peptides in the Proteomes of Goat and Sheep Milk and Feta Cheese
Cited by: 11
Author(s): Marios Tomazou, Anastasis Oulas, Athanasios K. Anagnostopoulos, George Th. Tsangaris, George M. Spyrou
Software Mentions: 7
Published: almost 5 years ago

10.1126/sciadv.aaz5373

Freezing and water availability structure the evolutionary diversity of trees across the Americas
Cited by: 47
Author(s): Rocío Cortés, R. Toby Pennington, Tim R. Baker, Fernanda Coelho de Souza, Danilo M. Neves, Charles C. Davis, Juan J. Armestó, Ary Olivera-Filho, Kyle G. Dexter
Software Mentions: 7
Published: over 4 years ago

10.3390/jcm10051073

Clinical Management of Hypertension, Inflammation and Thrombosis in Hospitalized COVID-19 Patients: Impact on Survival and Concerns
Cited by: 6
Author(s): Patricia Martínez-Botía, Ángel Bernardo, Andrea Acebes-Huerta, A Caro, Blanca Larrea Leoz, Daniel Martínez‐Carballeira, Carmen Palomo-Antequera, Inmaculada Soto, Laura Gutiérrez
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2020.526545

Nutrients and Pharmaceuticals Structure Bacterial Core Communities in Urban and Montane Stream Biofilms
Cited by: 4
Author(s): Elizabeth M. Ogata, Michelle A. Baker, Emma J. Rosi, Trevor B. Smart, Donald Long, Zachary T. Aanderud
Software Mentions: 6
Published: almost 4 years ago

10.3389/fpls.2021.675227

Homologs of Circadian Clock Proteins Impact the Metabolic Switch Between Light and Dark Growth in the Cyanobacterium Synechocystis sp. PCC 6803
Cited by: 4
Author(s): N. M. Scheurer, Yogeswari Rajarathinam, Stefan Timm, Christin Köbler, Joachim Kopka, Martin Hagemann, Annegret Wilde
Software Mentions: 6
Published: about 3 years ago

10.1186/s12859-021-04121-8

Euler diagrams drawn with ellipses area-proportionally (Edeap)
Cited by: 6
Author(s): Michael Wybrow, Peter Rodgers, Fadi K. Dib
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.01961

Sponges and Their Microbiomes Show Similar Community Metrics Across Impacted and Well-Preserved Reefs
Cited by: 19
Author(s): Marta Turon, Joan Cáliz, Xavier Triadó–Margarit, Emilio O. Casamayor, María Jesús Uriz
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.58533

A new role for histone demethylases in the maintenance of plant genome integrity
Cited by: 28
Author(s): Javier Antunez-Sanchez, Matthew Naish, Juan S. Ramirez-Prado, Sho Ohno, Ying Huang, Alexander Dawson, Korawit Opassathian, Deborah Manza‐Mianza, Federico Ariel, Cécile Raynaud, Anjar Tri Wibowo, Josquin Daron, Minako Ueda, David Latrasse, R. Keith Slotkin, Detlef Weigel, Moussa Benhamed, José Gutierrez-Marcos
Software Mentions: 5
Published: almost 4 years ago

10.7717/peerj.9644

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters
Cited by: 26
Author(s): Giulia M. Marchioro, Bettina Glasl, Aschwin H. Engelen, Ester Á. Serrão, David G. Bourne, Nicole S. Webster, Pedro R. Frade
Software Mentions: 5
Published: about 4 years ago

10.15252/msb.20209885

Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function
Cited by: 12
Author(s): Wim J. de Jonge, Mariël Brok, Philip Lijnzaad, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12263-021-00692-6

Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis
Cited by: 7
Author(s): Kaitlin Day, Aimee L. Dordevic, Helen Truby, Melissa C. Southey, Susan L. Coort, Chiara Murgia
Software Mentions: 5
Published: about 3 years ago

10.3389/fmicb.2019.00708

Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals
Cited by: 24
Author(s): Kate C. Mellor, Liljana Petrovska, Nicholas R. Thomson, Kate Harris, S. Reid, Alison E. Mather
Software Mentions: 4
Published: over 5 years ago

10.1186/s13058-020-01279-6

Investigation of the adolescent female breast transcriptome and the impact of obesity
Cited by: 8
Author(s): Adam Burkholder, Dennis Akrobetu, Arun R. Pandiri, Kiki Ton, Sue Kim, Brian I. Labow, Laura C. Nuzzi, Joseph M. Firriolo, Sallie S. Schneider, Suzanne E. Fenton, Natalie D Shaw
Software Mentions: 4
Published: over 4 years ago

10.3389/fncel.2019.00370

Interplay of LIS1 and MeCP2: Interactions and Implications With the Neurodevelopmental Disorders Lissencephaly and Rett Syndrome
Cited by: 10
Author(s): Liraz Keidar, Gabi Gerlitz, Aditya Kshirsagar, Michael Tsoory, Tsviya Olender, Xing Wang, Ying Yang, Yu‐Sheng Chen, Yun‐Gui Yang, Irina Voineagu, Orly Reiner
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1008582

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality
Cited by: 32
Author(s): Katherine Lagree, Carol A. Woolford, Manning Y. Huang, Gemma E. May, C. Joel McManus, Norma V. Solis, Scott G. Filler, Aaron P. Mitchell
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008603

Chromatin modifiers and recombination factors promote a telomere fold-back structure, that is lost during replicative senescence
Cited by: 5
Author(s): Tina Wagner, Lara Pérez-Martínez, René Schellhaas, Marta Barrientos-Moreno, Merve Öztürk, Félix Prado, Falk Butter, Brian Luke
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2021.640135

Histone Demethylases ELF6 and JMJ13 Antagonistically Regulate Self-Fertility in Arabidopsis
Cited by: 9
Author(s): Charlie Keyzor, Benoît Mermaz, Efstathios Trigazis, SoYoung Jo, Jié Song
Software Mentions: 3
Published: over 3 years ago

10.3390/genes9120599

What Is the Giant Wall Gecko Having for Dinner? Conservation Genetics for Guiding Reserve Management in Cabo Verde
Cited by: 19
Author(s): Catarina J. Pinho, Bárbara Santos, Vanessa A. Mata, Mariana Seguro, Maria M. Romeiras, Ricardo J. Lopes, Raquel Vasconcelos
Software Mentions: 3
Published: almost 6 years ago

10.3390/md19060286

An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces
Cited by: 2
Author(s): Ricardo Valencia, Valentina González, Agustina Undabarrena, Leonardo Zamora-Leiva, Juan A. Ugalde, Beatríz Cámara
Software Mentions: 3
Published: over 3 years ago

10.12688/wellcomeopenres.14867.2

Tissue and host species-specific transcriptional changes in models of experimental visceral leishmaniasis
Cited by: 17
Author(s): Helen Ashwin, Karlheinz Seifert, Sarah Forrester, Najmeeyah Brown, Sandy MacDonald, Sally James, Dimitrios Lagos, Jon Timmis, Jeremy C. Mottram, Simon L. Croft, Paul M. Kaye
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.694033

Lifespan-Associated Gene Expression Signatures of Recombinant BXD Mice Implicates Coro7 and Set in Longevity
Cited by: 7
Author(s): Davide Vitiello, Alexander Dakhovnik, Cyril Statzer, Collin Y. Ewald
Software Mentions: 2
Published: about 3 years ago

10.1186/s43008-020-00050-y

Polypore fungi as a flagship group to indicate changes in biodiversity – a test case from Estonia
Cited by: 13
Author(s): Kadri Runnel, Otto Miettinen, Asko Lõhmus
Software Mentions: 2
Published: over 3 years ago

10.3390/foods10010017

Development of Antioxidant and Antihypertensive Properties during Growth of Lactobacillus helveticus, Lactobacillus rhamnosus and Lactobacillus reuteri on Cow’s Milk: Fermentation and Peptidomics Study
Cited by: 21
Author(s): A.V. Begunova, Оlga S. Savinova, Olga A. Glazunova, Konstantin V. Moiseenko, I.V. Rozhkova, Т. В. Федорова
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.661524

Comparison of Current Methods for Signal Peptide Prediction in Phytoplasmas
Cited by: 11
Author(s): Christophe Garcion, Laure Béven, Xavier Foissac
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-63372-2

Extensive transcriptome changes during seasonal leaf senescence in field-grown black cottonwood (Populus trichocarpa Nisqually-1)
Cited by: 12
Author(s): Haiwei Lu, Michael I. Gordon, Vindhya Amarasinghe, Steven H. Strauss
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-019-5781-3

Development and evaluation of a milk protein transcript depletion method for differential transcriptome analysis in mammary gland tissue
Cited by: 4
Author(s): J. Brodhagen, Rosemarie Weikard, Ulrike Thom, A. Heimes, Juliane Günther, Frieder Hadlich, Holm Zerbe, Wolfgang Petzl, M. Meyerholz, Martina Hoedemaker, Hans‐Joachim Schuberth, Susanne Engelmann, Christa Kühn
Software Mentions: 1
Published: over 5 years ago

10.1194/jlr.D119000393

Shared reference materials harmonize lipidomics across MS-based detection platforms and laboratories
Cited by: 52
Author(s): Alexander Triebl, Bo Burla, Jayashree Selvalatchmanan, Jeongah Oh, Sock Hwee Tan, Mark Y. Chan, Natalie A. Mellet, Peter J. Meikle, Federico Torta, Markus R. Wenk
Software Mentions: 1
Published: over 4 years ago

Projects: cran: eulerr

Papers Mentioning eulerr 47