Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: multiqc
https://packages.ecosyste.ms/registries/pypi.org/packages/multiqc
Create aggregate bioinformatics analysis reports across many samples and tools
30 versions
Latest release: 11 months ago
2 dependent packages
16,118 downloads last month
Papers Mentioning multiqc 37
10.1038/s42003-021-02335-3
A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissuesCited by: 9
Author(s): José M. Ranz, Pablo M. González, Bryan D. Clifton, Nestor O. Nazario-Yepiz, Pablo Luis Hernández-Cervantes, María J. Palma-Martínez, Dulce I. Valdivia, Andrés Jiménez-Kaufman, Megan Lu, Therese A. Markow, Cei Abreu‐Goodger
Software Mentions: 13
Published: about 3 years ago
10.1016/j.xpro.2021.100397
Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during agingCited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: over 3 years ago
10.1186/s13059-021-02360-9
Role of epigenetics in unicellular to multicellular transition in DictyosteliumCited by: 8
Author(s): Simon Yuan Wang, Elizabeth A. Pollina, I‐Hao Wang, Lindsay K. Pino, Henry L. Bushnell, Ken Takashima, Colette Fritsche, George Sabin, Benjamin A. Garcia, Paul L. Greer, Eric Lieberman Greer
Software Mentions: 10
Published: over 3 years ago
10.1371/journal.ppat.1007945
Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotypeCited by: 28
Author(s): Bernd Hommel, Aude Sturny-Leclère, Stevenn Volant, Nathanaël Veluppillai, Magalie Duchateau, Chen-Hsin Albert Yu, Véronique Hourdel, Hugo Varet, Mariette Matondo, John R. Perfect, Arturo Casadevall, Françoise Dromer, Alexandre Alanio
Software Mentions: 10
Published: about 5 years ago
10.3390/cancers13061212
Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple MyelomaCited by: 3
Author(s): Ashwini Kumar, Sadiksha Adhikari, Matti Kankainen, Caroline A. Heckman
Software Mentions: 8
Published: over 3 years ago
10.3389/fcimb.2021.733619
Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory SignaturesCited by: 8
Author(s): Elizabeth H. Byrne, M Fărcăşanu, Seth M. Bloom, Nondumiso Xulu, Jiawu Xu, Barry L. Hykes, Nomfuneko A. Mafunda, Matthew R. Hayward, Mary Dong, Krista Dong, Thandeka Gumbi, Fransisca Xolisile Ceasar, Nasreen Ismail, Thumbi Ndung’u, Christina Gosmann, Musie Ghebremichael, Scott A. Handley, Caroline Mitchell, Alexandra Chloé Villani, Douglas S. Kwon
Software Mentions: 7
Published: about 3 years ago
10.1371/journal.pone.0218636
Characterizing the postmortem human bone microbiome from surface-decomposed remainsCited by: 23
Author(s): Alexandra L. Emmons, Amy Z. Mundorff, Sarah W. Keenan, Jonathan Davoren, Janna M. Andronowski, David Carter, Jennifer M. DeBruyn
Software Mentions: 7
Published: about 4 years ago
10.1002/1873-3468.13278
The gut microbiome participates in transgenerational inheritance of low‐temperature responses in <i>Drosophila melanogaster</i>Cited by: 23
Author(s): Aman Zare, Anna-Mia Johansson, Edvin Karlsson, Nicolas Delhomme, Per Stenberg
Software Mentions: 7
Published: almost 6 years ago
10.1186/s40168-020-00943-5
Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target speciesCited by: 26
Author(s): Antonio Suppa, Jouni Kvist, Xiaojing Li, Vignesh Dhandapani, Hanan Almulla, Antoine Y. Tian, Stephen Kissane, Jian Zhou, Alessio Perotti, Hayley Mangelson, Kyle W. Langford, Valeria Rossi, James B. Brown, Luisa Orsini
Software Mentions: 6
Published: almost 4 years ago
10.1093/gigascience/giy158
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomesCited by: 51
Author(s): Lisa K. Johnson, Harriet Alexander, C. Titus Brown
Software Mentions: 6
Published: almost 6 years ago
10.1111/mec.15047
Caste‐ and pesticide‐specific effects of neonicotinoid pesticide exposure on gene expression in bumblebeesCited by: 53
Author(s): Thomas J. Colgan, Isabel Fletcher, Andres N. Arce, Richard J. Gill, Ana Ramos Rodrigues, Eckart Stolle, Lars Chittka, Yannick Wurm
Software Mentions: 6
Published: over 5 years ago
10.1186/s40168-017-0279-1
A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platformCited by: 79
Author(s): Eric J. de Muinck, Pål Trosvik, Gregor D. Gilfillan, Johannes R. Hov, Arvind Sundaram
Software Mentions: 5
Published: about 7 years ago
10.1093/gbe/evab110
Transcriptomic Analysis of Skin Color in Anole LizardsCited by: 5
Author(s): Pietro Longo Hollanda de Mello, Paul M Hime, Richard E. Glor
Software Mentions: 5
Published: over 3 years ago
10.3389/fmicb.2021.641756
Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant StreptomyceteCited by: 0
Author(s): Andrew Hesketh, Giselda Bucca, Colin P. Smith, Hee‐Jeon Hong
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2020.556418
Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.)Cited by: 14
Author(s): Yong Long, Xixi Li, Fengyang Li, Guodong Ge, Ran Liu, Guangliang Song, Qing Li, Zhengxue Qiao
Software Mentions: 4
Published: almost 4 years ago
10.1093/ve/vey027
Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strainsCited by: 24
Author(s): James R. Otieno, Everlyn Kamau, John W Oketch, Joyce M. Ngoi, Alex Gichuki, Špela Binter, Grieven P. Otieno, Mwanajuma Ngama, Charles N. Agoti, Patricia A. Cane, Paul Kellam, Matthew Cotten, Philippe Lemey, D. James Nokes
Software Mentions: 4
Published: about 6 years ago
10.3390/cancers12123738
Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia PatientsCited by: 9
Author(s): Ulf Schmitz, Jaynish S. Shah, Bijay Dhungel, Geoffray Monteuuis, Phuc-Loi Luu, Veronika Petrova, Cynthia Metierre, Shalima S. Nair, Charles G. Bailey, Verity A. Saunders, Ali G. Turhan, Deborah L. White, Susan Branford, Susan J. Clark, Timothy P. Hughes, Justin Wong, John E.J. Rasko
Software Mentions: 4
Published: almost 4 years ago
10.18632/oncotarget.26029
Identification of a novel gene fusion in ALT positive osteosarcomaCited by: 27
Author(s): Emily Mason-Osann, Anqi Dai, Jess Floro, Ying Jie Lock, Matthew Reiss, Himabindu Gali, Adeline Matschulat, Adam Labadorf, Rachel Litman Flynn
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pntd.0008059
Exposure of Anopheles mosquitoes to trypanosomes reduces reproductive fitness and enhances susceptibility to PlasmodiumCited by: 10
Author(s): Constentin Dieme, Natalia Marta Zmarlak, Emma Brito-Fravallo, Christelle Travaillé, Adrien Pain, Floriane Cherrier, Corinne Genève, Estefanía Calvo-Álvarez, Michelle M. Riehle, Kenneth D. Vernick, Brice Rotureau, Christian Mitri
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pntd.0009658
Describing the intestinal microbiota of Holstein Fasciola-positive and -negative cattle from a hyperendemic area of fascioliasis in central ColombiaCited by: 5
Author(s): Angie Ramírez, Giovanny Herrera, Marina Muñoz, Laura Vega, Lissa Cruz-Saavedra, Diego García-Corredor, Martín Orlando Pulido-Medellín, Diana María Bulla-Castañeda, Julio César Giraldo, María Consuelo Bernal, José Fernández-Manrique, Luis R. Vásquez-Arteaga, Juan David Ramírez
Software Mentions: 3
Published: about 3 years ago
10.3389/fbioe.2021.640419
Extracellular Vesicles Derived From Adult and Fetal Bone Marrow Mesenchymal Stromal Cells Differentially Promote ex vivo Expansion of Hematopoietic Stem and Progenitor CellsCited by: 8
Author(s): Corina Adriana Ghebes, Jess Morhayim, Marion Kleijer, Merve Koroglu, Stefan J. Erkeland, Remco M. Hoogenboezem, Eric Bindels, Floris P.J. van Alphen, Maartje van den Biggelaar, Martijn A. Nolte, Bram C. J. van der Eerden, Eric Braakman, Carlijn Voermans, Jeroen van de Peppel
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2021.658256
De novo Genome Assembly of the Raccoon Dog (Nyctereutes procyonoides)Cited by: 8
Author(s): Luis J. Chueca, Judith Kochmann, Tilman Schell, Carola Greve, Axel Janke, Markus Pfenninger, Sven Klimpel
Software Mentions: 3
Published: over 3 years ago
10.3389/fmicb.2021.662727
Side Effects of Pesticides and Metabolites in Groundwater: Impact on DenitrificationCited by: 22
Author(s): Caroline Michel, Nicole Baran, Laurent André, Mickaël Charron, Catherine Joulian
Software Mentions: 3
Published: over 3 years ago
10.1038/s41597-020-0519-2
Systems biology of acidophile biofilms for efficient metal extractionCited by: 7
Author(s): Antoine Buetti‐Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Sören Bellenberg, Olga Ilie, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Mark Dopson
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-018-24701-8
A compendium of long non-coding RNAs transcriptional fingerprint in multiple myelomaCited by: 33
Author(s): Domenica Ronchetti, Luca Agnelli, Alessandro Pietrelli, Katia Todoerti, Martina Manzoni, Elisa Taìana, Antonino Neri
Software Mentions: 3
Published: over 6 years ago
10.1186/s40425-019-0794-7
Longitudinal immune characterization of syngeneic tumor models to enable model selection for immune oncology drug discoveryCited by: 54
Author(s): Molly A. Taylor, Adina Hughes, Josephine Walton, Anna M.L. Coenen-Stass, Łukasz Magiera, Lorraine Mooney, Sigourney Bell, Anna D. Staniszewska, Linda C. Sandin, Simon T. Barry, Amanda Watkins, Larissa S. Carnevalli, Elizabeth Hardaker
Software Mentions: 3
Published: almost 5 years ago
10.1016/j.molcel.2019.07.010
SLX4IP Antagonizes Promiscuous BLM Activity during ALT MaintenanceCited by: 60
Author(s): Stephanie Panier, Marija Marić, Graeme Hewitt, Emily Mason-Osann, Himabindu Gali, Anqi Dai, Adam Labadorf, Jean-Hugues Guervilly, Philip Ruis, Sandra Segura-Bayona, Ondrej Beláň, Paulina Marzec, Patrick Gaillard, Rachel Litman Flynn, Simon J. Boulton
Software Mentions: 2
Published: almost 5 years ago
10.1530/EJE-19-0771
High frequency of pathogenic ACAN variants including an intragenic deletion in selected individuals with short statureCited by: 20
Author(s): Lana Stavber, Tinka Hovnik, Primož Kotnik, Luca Lovrečić, Jernej Kovač, Tine Tesovnik, Sara Bertok, Klemen Dovč, Maruša Debeljak, Tadej Battelino, Magdalena Avbelj Stefanija
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.ppat.1008326
CRISPR/Cas with ribonucleoprotein complexes and transiently selected telomere vectors allows highly efficient marker-free and multiple genome editing in Botrytis cinereaCited by: 44
Author(s): Thomas Leisen, Fabian Bietz, J. Werner, Alex Wegner, Ulrich Schaffrath, David Scheuring, Felix Willmund, Andreas Mosbach, Gabriel Scalliet, Matthias Hahn
Software Mentions: 2
Published: about 4 years ago
10.3390/ijms21218381
Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicaeCited by: 16
Author(s): Qiaoxia Zhou, Leonardo Galindo‐González, Victor P. Manolii, Sheau‐Fang Hwang, Stephen E. Strelkov
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-019-41235-9
In situ 10-cell RNA sequencing in tissue and tumor biopsy samplesCited by: 24
Author(s): Shambhavi Singh, Lixin Wang, Dylan L. Schaff, Matthew D. Sutcliffe, Alexander F. Koeppel, Jung-Eun Kim, Suna Önengüt-Gümüşcü, Kwon-Sik Park, Hui Zong, Kevin A. Janes
Software Mentions: 2
Published: over 5 years ago
10.1126/science.abe6230
Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escapeCited by: 271
Author(s): Paul Koenig, Hrishikesh Das, Hejun Liu, Beate M. Kümmerer, Florian N. Gohr, Lea-Marie Jenster, Lisa Dominica Jacoba Schiffelers, Yonas Mehari Tesfamariam, Miki Uchima, Jennifer Deborah Wuerth, Karl Gatterdam, Natalia Ruétalo, Maria H Christensen, Caroline I. Fandrey, Sabine Normann, Jan M. P. Tödtmann, Steffen Pritzl, Leo Hanke, Jannik Boos, Meng Yuan, Xueyong Zhu, Jonathan L. Schmid-Burgk, Hiroki Kato, Michael Schindler, Ian A. Wilson, Matthias Geyer, Kerstin U. Ludwig, Bengt Hållberg, Nicholas C. Wu, Florian I. Schmidt
Software Mentions: 2
Published: over 3 years ago
10.1186/s13195-020-00627-0
Differential blood miRNA expression in brain amyloid imaging-defined Alzheimer’s disease and controlsCited by: 28
Author(s): Helen Zong Ying Wu, Anbupalam Thalamuthu, Lesley Cheng, Christopher Fowler, Colin L. Masters, Perminder S. Sachdev, Karen A. Mather
Software Mentions: 2
Published: over 4 years ago
10.7554/eLife.52676
Identification of a molecular basis for the juvenile sleep stateCited by: 14
Author(s): Leela Chakravarti Dilley, Milán Szuperák, Naihua N. Gong, Charlette E. Williams, Ricardo Linares-Saldana, David S. Garbe, Mubarak Hussain Syed, Rajan Jain, Matthew S. Kayser
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2020.00773
NtrBC Regulates Invasiveness and Virulence of Pseudomonas aeruginosa During High-Density InfectionCited by: 18
Author(s): Morgan A. Alford, Arjun Baghela, Amy Yeung, Daniel Pletzer, Robert E. W. Hancock
Software Mentions: 2
Published: over 4 years ago
10.1186/s40168-020-00796-y
Can rumen bacteria communicate to each other?Cited by: 33
Author(s): Miyoung Won, Linda Oyama, Stephen J. Courtney, Christopher J. Creevey, Sharon Huws
Software Mentions: 1
Published: over 4 years ago
10.18632/oncotarget.21774
Altered microRNA profiles during early colon adenoma progression in a porcine model of familial adenomatous polyposisCited by: 13
Author(s): Monika Stachowiak, Tatiana Flisikowska, Stefan Bauersachs, Carolin Perleberg, Hubert Pausch, M. Świtoński, Alexander Kind, Dieter Saur, Angelika Schnieke, Krzysztof Flisikowski
Software Mentions: 1
Published: almost 7 years ago