pypi: Sickle | Projects | Ecosyste.ms: Papers

10.3390/v12111229

RNAseq of Deformed Wing Virus and Other Honey Bee-Associated Viruses in Eight Insect Taxa with or without Varroa Infestation
Cited by: 17
Author(s): Laura E. Brettell, Declan C. Schroeder, Stephen J. Martin
Software Mentions: 10
Published: about 4 years ago

10.1038/s41598-017-14576-6

Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Cited by: 37
Author(s): Meiser Anjuli, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
Software Mentions: 9
Published: about 7 years ago

10.3389/fmicb.2018.02452

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter
Cited by: 52
Author(s): Umer Zeeshan Ijaz, Lojika Sivaloganathan, Aaron McKenna, Anne Richmond, Carmel Kelly, Mark Linton, Alexandros Ch. Stratakos, Ursula Lavery, Abdi Elmi, Brendan W. Wren, Nick Dorrell, Nicolae Corcionivoschi, Ozan Gundogdu
Software Mentions: 9
Published: about 6 years ago

10.1186/s13059-016-1000-6

Blood lipids influence DNA methylation in circulating cells
Cited by: 149
Author(s): Koen F. Dekkers, Maarten van Iterson, Roderick C. Slieker, Matthijs Moed, Marc Jan Bonder, M.A. van Galen, Hailiang Mei, Daria V. Zhernakova, Leonard H van den Berg, Joris Deelen, Jenny van Dongen, Diana van Heemst, Albert Hofman, Jouke Jan Hottenga, Carla Kallen, Casper G. Schalkwijk, Coen D. A. Stehouwer, Ettje F. Tigchelaar, André G. Uitterlinden, Gonneke Willemsen, Alexandra Zhernakova, Lude Franke, Peter A.C. ’t Hoen, Ritsert C. Jansen, Joyce B. J. van Meurs, Dorret I. Boomsma, Cornelia M. van Duijn, Marleen M.J. van Greevenbroek, Jan H. Veldink, Cisca Wijmenga, Erik W. van Zwet, P. Eline Slagboom, J. Wouter Jukema, Bastiaan T. Heijmans
Software Mentions: 9
Published: over 8 years ago

10.1128/mSystems.00474-21

Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics
Cited by: 12
Author(s): Elizabeth A. McDaniel, Francisco Moya-Flores, Natalie K. Beach, Pamela Y. Camejo, Ben O. Oyserman, Matthew Kizaric, Eng Hoe Khor, Daniel R. Noguera, Katherine D. McMahon
Software Mentions: 9
Published: about 3 years ago

10.17179/excli2015-168

Data- and knowledge-based modeling of gene regulatory networks: an update.
Cited by: 24
Author(s): Jörg Linde, Sylvie Schulze, Sebastian Henkel, Reinhard Guthke
Software Mentions: 8
Published: almost 10 years ago

10.1038/s41598-018-34921-7

Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion
Cited by: 37
Author(s): Jo De Vrieze, Umer Zeeshan Ijaz, Aaron Marc Saunders, Susanne Theuerl
Software Mentions: 8
Published: about 6 years ago

10.1186/s13059-020-02114-z

Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference
Cited by: 22
Author(s): Paul J. Hop, René Luijk, Lucia Daxinger, Maarten van Iterson, Koen F. Dekkers, Rick Jansen, Bastiaan T. Heijmans, Peter A.C. ’t Hoen, Joyce van Meurs, Rick Jansen, Lude Franke, Dorret I. Boomsma, René Pool, Jenny van Dongen, Jouke Jan Hottenga, Marleen M.J. van Greevenbroek, Coen D.A. Stehouwer, Carla J.H. van der Kallen, Casper G. Schalkwijk, Cisca Wijmenga, Sasha Zhernakova, Ettje F. Tigchelaar, P. Eline Slagboom, Marian Beekman, Joris Deelen, Diana van Heemst, Jan H. Veldink, Leonard H. van den Berg, Cornelia M. van Duijn, Aaron Isaacs, André G. Uitterlinden, P. Mila Jhamai, Michaël Verbiest, H. Eka D. Suchiman, Marijn Verkerk, Ruud van der Breggen, Jeroen van Rooij, Nico Lakenberg, Hailiang Mei, Maarten van Iterson, Dasha V. Zhernakova, Peter van ’t Hof, Patrick Deelen, Peter A.C. ’t Hoen, Martijn Vermaat, René Luijk, Marc Jan Bonder, Freerk van Dijk, Wibowo Arindrarto, Szymon M. Kiełbasa, Erik W. van Zwet, Peter-Bram ’t Hoen, Joyce B. J. van Meurs, Peter A.C. ’t Hoen, M. Arfan Ikram, Marleen M.J. van Greevenbroek, Dorret I. Boomsma, P. Eline Slagboom, Jan H. Veldink, Erik W. van Zwet, Bastiaan T. Heijmans
Software Mentions: 8
Published: about 4 years ago

10.1186/s13104-016-2171-7

The effect of DNA extraction methodology on gut microbiota research applications
Cited by: 54
Author(s): Konstantinos Gerasimidis, Martin Bertz, Christopher Quince, K. T. Brunner, Alanna E. Bruce, Emilie Combet, Szymon T. Calus, Nicholas J. Loman, Umer Zeeshan Ijaz
Software Mentions: 8
Published: over 8 years ago

10.3389/fimmu.2021.651475

Novel Insights Into Rheumatoid Arthritis Through Characterization of Concordant Changes in DNA Methylation and Gene Expression in Synovial Biopsies of Patients With Differing Numbers of Swollen Joints
Cited by: 5
Author(s): Andrew Y. Li Yim, Enrico Ferrero, Klio Maratou, Huw D. Lewis, George C. Royal, David F. Tough, Chris Larminie, Marcel M.A.M. Mannens, Peter Henneman, Wouter J. de Jonge, Marleen G H van de Sande, Daniëlle M. Gerlag, Rab K. Prinjha, Paul P. Tak
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2019.00675

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study
Cited by: 29
Author(s): Jordan Espenshade, Sofie Thijs, S.W. Gawroński, Hannelore Bové, Nele Weyens, Jaco Vangronsveld
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2020.01234

Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports
Cited by: 14
Author(s): Elena Tamburini, Lapo Doni, Raffaela Lussu, Federico Meloni, Giovanna Salvatorica Cappai, Alessandra Carucci, Enrico Casalone, Giorgio Mastromei, Francesco Vitali
Software Mentions: 7
Published: over 4 years ago

10.1128/mSystems.01381-20

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments
Cited by: 24
Author(s): Zhifeng Zhang, Jie Pan, Yue-Ping Pan, Meng Li
Software Mentions: 7
Published: over 3 years ago

10.1111/ele.12878

Ecological selection of siderophore‐producing microbial taxa in response to heavy metal contamination
Cited by: 90
Author(s): Elze Hesse, Siobhán O’Brien, Nicolas Tromas, Florian Bayer, Adela M. Luján, Eleanor M. van Veen, Dave Hodgson, Angus Buckling
Software Mentions: 7
Published: about 7 years ago

10.3389/fmicb.2018.01620

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory
Cited by: 26
Author(s): Flora Jane Mary O'Brien, Marc G. Dumont, Jeremy S. Webb, Guy M. Poppy
Software Mentions: 7
Published: over 6 years ago

10.3390/microorganisms7090349

Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment
Cited by: 16
Author(s): Aïda Bani, Luigimaria Borruso, Kirsty J. Matthews Nicholass, Tommaso Bardelli, Andrea Polo, Silvia Pioli, María Gómez-Brandòn, Heribert Insam, Alex J. Dumbrell, Lorenzo Brusetti
Software Mentions: 7
Published: about 5 years ago

10.1186/s40168-020-00813-0

Disinfection exhibits systematic impacts on the drinking water microbiome
Cited by: 37
Author(s): Zihan Dai, Maria C. Sevillano-Rivera, Szymon T. Calus, Quyen Melina Bautista-de los Santos, A. Murat Eren, P.W.J.J. van der Wielen, Umer Zeeshan Ijaz, Ameet J. Pinto
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-020-79296-w

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon
Cited by: 6
Author(s): Andrea M. Makkay, Artemis S. Louyakis, Nikhil Ram-Mohan, Uri Gophna, J. Peter Gogarten, R. Thane Papke
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.58019

Isolation and transcriptomic analysis of Anopheles gambiae oenocytes enables the delineation of hydrocarbon biosynthesis
Cited by: 17
Author(s): Linda Grigoraki, Xavier Grau‐Bové, Henrietta Carrington Yates, Gareth Lycett, Hilary Ranson
Software Mentions: 7
Published: over 4 years ago

10.1111/pbi.12834

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)
Cited by: 21
Author(s): Amanda Burridge, Paul Wilkinson, Mark Winfield, Gary Barker, Alexandra M. Allen, Jane A. Coghill, Christy Waterfall, Keith J. Edwards
Software Mentions: 6
Published: about 7 years ago

10.1128/mSystems.00017-19

Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis
Cited by: 128
Author(s): Jiachao Zhang, Zhihong Sun, Shuaiming Jiang, Xiaoye Bai, Chenchen Ma, Qingyun Peng, Kaining Chen, Haibo Chang, Tuanyu Fang, Heping Zhang
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1008822

An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons
Cited by: 37
Author(s): Gareth D. Weedall, Jacob M. Riveron, Jack Hearn, Helen Irving, Colince Kamdem, Caroline Fouet, Bradley J. White, Charles S. Wondji
Software Mentions: 6
Published: over 4 years ago

10.1128/mSphere.00261-18

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization
Cited by: 72
Author(s): Matthew L. Jenior, Jhansi L. Leslie, Vincent B. Young, Patrick D. Schloss
Software Mentions: 6
Published: over 6 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: almost 6 years ago

10.3389/fmicb.2021.607601

Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community – Enabling Continuous Production of Microalgal Biomass
Cited by: 7
Author(s): Eva Sörenson, Eric Capo, Hanna Farnelid, Elin Lindehoff, Catherine Legrand
Software Mentions: 6
Published: almost 4 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 3 years ago

10.1002/evl3.148

Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild
Cited by: 28
Author(s): Sónia Pascoal, Judith Risse, Xiao Zhang, Mark Blaxter, Timothée Cézard, Richard Challis, Karim Gharbi, John Hunt, Sujai Kumar, Emma Langan, Xuan Li, Jack G. Rayner, Michael G. Ritchie, L. Basten Snoek, Urmi Trivedi, Nathan W. Bailey
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2020.588778

Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription
Cited by: 21
Author(s): Benjamin Pontiller, Sandra Martínez‐García, Daniel Lundin, Jarone Pinhassi
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-019-52549-z

Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing
Cited by: 29
Author(s): Marta Reyman, Marlies A. van Houten, Kayleigh Arp, Elisabeth A. M. Sanders, Debby Bogaert
Software Mentions: 6
Published: about 5 years ago

10.3390/microorganisms8070982

Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural Starter
Cited by: 10
Author(s): Lucas von Gastrow, Marie‐Noëlle Madec, Victoria Chuat, S. Lubac, Clémence Morinière, Sébastien Lê, Sylvain Santoni, Delphine Sicard, Florence Valence
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.ppat.1005815

Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design
Cited by: 97
Author(s): Joseph G. Jardine, Devin Sok, Jean-Philippe Julien, Bryan Briney, Achyut Sarkar, Chi Liang, Erin A. Scherer, Carole J. Henry Dunand, Yumiko Adachi, Devan Diwanji, Jessica Hsueh, Meaghan Jones, Oleksandr Kalyuzhniy, Michael Kubitz, Skye Spencer, Matthias Pauthner, Karen L. Saye-Francisco, Fabian Sesterhenn, Patrick C. Wilson, Denise Galloway, Robyn L. Stanfield, Ian A. Wilson, Dennis R. Burton, William R. Schief
Software Mentions: 6
Published: about 8 years ago

10.1186/s13059-021-02300-7

riboCIRC: a comprehensive database of translatable circRNAs
Cited by: 39
Author(s): Huihui Li, Mingzhe Xie, Yan Wang, Ludong Yang, Zhi Xie
Software Mentions: 6
Published: over 3 years ago

10.5808/gi.20074

Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing
Cited by: 2
Author(s): Jiyeon Han, Yeonjoo Jung, Yukyung Jun, Sungsu Park, Sanghyuk Lee
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-017-0314-2

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis
Cited by: 61
Author(s): Fiona Whelan, Michael G. Surette
Software Mentions: 6
Published: over 7 years ago

10.3390/microorganisms8091449

Population Dynamics between Erwinia amylovora, Pantoea agglomerans and Bacteriophages: Exploiting Synergy and Competition to Improve Phage Cocktail Efficacy
Cited by: 18
Author(s): Steven Gayder, Michael Parcey, Darlene Nesbitt, Alan J. Castle, A. M. Svircev
Software Mentions: 6
Published: about 4 years ago

10.1098/rspb.2019.0804

Anthropogenic remediation of heavy metals selects against natural microbial remediation
Cited by: 11
Author(s): Elze Hesse, Daniel Padfield, Florian Bayer, Eleanor M. van Veen, Christopher G. Bryan, Angus Buckling
Software Mentions: 6
Published: over 5 years ago

10.1186/s13072-020-00379-z

DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna
Cited by: 15
Author(s): Jack Hearn, Fiona A. Plenderleith, Tom J. Little
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.58931

Recurrent evolution of high virulence in isolated populations of a DNA virus
Cited by: 11
Author(s): Tom Hill, Robert L. Unckless
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0236429

pH effect on strain-specific transcriptomes of the take-all fungus
Cited by: 1
Author(s): Kévin Gazengel, Lionel Lebreton, Nicolas Lapalu, Joëlle Amselem, Anne‐Yvonne Guillerm‐Erckelboudt, Denis Tagu, Stéphanie Daval
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-021-89950-6

Metabarcoding Malaise traps and soil eDNA reveals seasonal and local arthropod diversity shifts
Cited by: 15
Author(s): Ameli Kirse, Sarah J. Bourlat, Kathrin Langen, Vera G. Fonseca
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2021.675260

Aluminum or Low pH – Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress
Cited by: 16
Author(s): Miriam Szurman-Zubrzycka, Karolina Chwiałkowska, Magdalena Niemira, Mirosław Kwaśniewski, M. Nawrot, Monika Gajecka, Paul B. Larsen, Iwona Szarejko
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-018-0449-9

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool
Cited by: 113
Author(s): Jo De Vrieze, Ameet J. Pinto, William T. Sloan, Umer Zeeshan Ijaz
Software Mentions: 6
Published: over 6 years ago

10.1099/mgen.0.000240

Genomic analysis of bacteria in the Acute Oak Decline pathobiome
Cited by: 29
Author(s): James Doonan, Sandra Denman, Justin A. Pachebat, James E. McDonald
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.6448

The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont
Cited by: 10
Author(s): Stefanos Siozios, Jack Pilgrim, Alistair C. Darby, Matthew Baylis, Gregory D. D. Hurst
Software Mentions: 5
Published: over 5 years ago

10.3390/plants10071465

Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max
Cited by: 11
Author(s): Ramon de Koning, Raphaël Kiekens, Mary Esther Muyoka Toili, Geert Angenon
Software Mentions: 5
Published: over 3 years ago

10.1186/gb-2013-14-6-r66

Separating homeologs by phasing in the tetraploid wheat transcriptome
Cited by: 129
Author(s): Ksenia V. Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Eduard Akhunov, Cristóbal Uauy, Jorge Dubcovsky
Software Mentions: 5
Published: over 11 years ago

10.1186/s40168-017-0304-4

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome
Cited by: 145
Author(s): Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
Software Mentions: 5
Published: over 7 years ago

10.3389/fpls.2019.00156

Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens
Cited by: 12
Author(s): Anne L. Sternberger, Megan J. Bowman, Colin Kruse, Kevin L. Childs, Harvey E. Ballard, Sarah E. Wyatt
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13075-015-0544-2

Transcriptome analysis of ageing in uninjured human Achilles tendon
Cited by: 61
Author(s): Mandy J. Peffers, Yongxiang Fang, Kathleen Cheung, Tim Koh Jia Wei, Peter Clegg, Helen L. Birch
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0139868

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Cited by: 31
Author(s): Mohan A. V. S. K. Katta, Aamir W. Khan, Dadakhalandar Doddamani, Mahendar Thudi, Rajeev K. Varshney
Software Mentions: 5
Published: about 9 years ago

10.7554/eLife.03703

Selection of chromosomal DNA libraries using a multiplex CRISPR system
Cited by: 298
Author(s): Owen Ryan, Jeffrey M. Skerker, Matthew J. Maurer, Xin Li, Jordan C. Tsai, Snigdha Poddar, Michael E. Lee, Will DeLoache, John E. Dueber, Adam P. Arkin, Jamie H. D. Cate
Software Mentions: 5
Published: over 10 years ago

10.1186/s40168-017-0322-2

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments
Cited by: 147
Author(s): Nina Dombrowski, Kiley W. Seitz, Andreas Teske, Brett J. Baker
Software Mentions: 5
Published: about 7 years ago

10.3389/fpls.2018.01256

Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicagotruncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms
Cited by: 14
Author(s): Kai Battenberg, Daniel Potter, Christine A. Tabuloc, Joanna C. Chiu, Alison M. Berry
Software Mentions: 5
Published: about 6 years ago

10.1099/mgen.0.000333

Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity
Cited by: 13
Author(s): Miguel Morard, Yaiza Benavent‐Gil, Guadalupe Ortiz-Tovar, Laura Pérez‐Través, Amparo Querol, Christina Toft, Eladio Barrio
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1008055

Loss of function mutations in essential genes cause embryonic lethality in pigs
Cited by: 38
Author(s): Martijn F.L. Derks, Arne B. Gjuvsland, Mirte Bosse, Marcos S. Lopes, Maren van Son, B. Harlizius, Beatrice Tan, Hanne Hamland, Eli Grindflek, Martien A. M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.01282

Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities
Cited by: 37
Author(s): Brandon Kieft, Li Zhou, Samuel Bryson, Byron C. Crump, Robert L. Hettich, Chongle Pan, Xavier Mayali, Robert F. Mueller
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pbio.2003962

Design of synthetic bacterial communities for predictable plant phenotypes
Cited by: 157
Author(s): Sur Herrera Paredes, Tianxiang Gao, Theresa F. Law, Omri M. Finkel, Tatiana S. Mucyn, Paulo José Pereira Lima Teixeira, Isaí Salas González, Meghan E. Feltcher, Matthew J. Powers, Elizabeth A. Shank, Corbin D. Jones, Vladimir Jojic, Jeffery L. Dangl, Gabriel Castrillo
Software Mentions: 5
Published: almost 7 years ago

10.3390/cancers12041039

Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma
Cited by: 32
Author(s): Sophie Thornton, Sarah E. Coupland, Lisa Olohan, Julie Sibbring, John Kenny, Christiane Hertz‐Fowler, Xuan Li, Sam Haldenby, Heinrich Heimann, Rumana Hussain, Natalie Kipling, Azzam Taktak, Helen Kalirai
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-021-01090-1

Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs
Cited by: 16
Author(s): Chanenath Sriaporn, Kathleen A. Campbell, Martin J. Van Kranendonk, Kim M. Handley
Software Mentions: 5
Published: over 3 years ago

10.1053/j.gastro.2020.08.007

Alterations in Intestinal Microbiota of Children With Celiac Disease at the Time of Diagnosis and on a Gluten-free Diet
Cited by: 44
Author(s): Konstantina Zafeiropoulou, Ben Nichols, Mary Mackinder, Olga Biskou, Eleni Rizou, Antonia Karanikolou, Caspar Clark, Evan G. Buchanan, Tracey Cardigan, H. J. Duncan, David Wands, Julie A. Russell, Richard Hansen, Richard K. Russell, Paraic McGrogan, Christine Edwards, Umer Zeeshan Ijaz, Konstantinos Gerasimidis
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.1007099

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments
Cited by: 46
Author(s): Matthew L. Jenior, Thomas J. Moutinho, Bonnie V. Dougherty, Jason A. Papin
Software Mentions: 5
Published: over 4 years ago

10.1038/s41396-020-00794-w

Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity
Cited by: 17
Author(s): Sean Meaden, Loris Capria, Ellinor O. Alseth, Sylvain Gandon, Ambarish Biswas, Luca Lenzi, Stineke van Houte, Edze R. Westra
Software Mentions: 5
Published: about 4 years ago

10.1038/s41396-020-0701-8

Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers
Cited by: 85
Author(s): Shufeng Li, Haiying Wu, Liming Chen, Jiawen Wang, Maosheng Zheng, Sitong Liu, Qian Chen, Jinren Ni
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2016.01221

Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales
Cited by: 23
Author(s): John Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2019.01491

Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes
Cited by: 26
Author(s): Anisha M. Thanki, Nathan Brown, Andrew Millard, Martha R. J. Clokie
Software Mentions: 5
Published: over 5 years ago

10.3389/fmed.2020.00475

Impact of Gut Microbiome on Hypertensive Patients With Low-Salt Intake: Shika Study Results
Cited by: 7
Author(s): Satoshi Nagase, Shigehiro Karashima, Hiromasa Tsujiguchi, Hirohito Tsuboi, Sakae Miyagi, Mitsuhiro Kometani, Daisuke Aono, Takuya Higashitani, Masashi Demura, Hiroyuki Sakakibara, Akihiro Yoshida, Akinori Hara, Hiroyuki Nakamura, Yoshiyu Takeda, Hidetaka Nambo, Takashi Yoneda, Shigefumi Okamoto
Software Mentions: 5
Published: about 4 years ago

10.1186/s13024-018-0261-9

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model
Cited by: 37
Author(s): Lodewijk J.A. Toonen, Maurice Overzier, Melvin M. Evers, Leticia G. León, Sander A.J. van der Zeeuw, Hailiang Mei, Szymon M. Kiełbasa, Jelle J. Goeman, Kristina Hettne, Ólafur Þ. Magnússon, Marion Poirel, Alexandre Seyer, Peter A.C. ’t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 5
Published: over 6 years ago

10.3389/fmed.2020.00101

Distinct Skin Microbiome and Skin Physiological Functions Between Bedridden Older Patients and Healthy People: A Single-Center Study in Japan
Cited by: 16
Author(s): Satoshi Nagase, Kazuhiro Ogai, Tamae Urai, Katsushi Shibata, Emi Matsubara, Kanae Mukai, Miki Matsue, Yosai Mori, Miku Aoki, Defa Arisandi, Junko Sugama, Shigefumi Okamoto
Software Mentions: 5
Published: over 4 years ago

10.1007/s00442-019-04499-6

Resistance is futile: RNA-sequencing reveals differing responses to bat fungal pathogen in Nearctic Myotis lucifugus and Palearctic Myotis myotis
Cited by: 20
Author(s): Thomas M. Lilley, Jenni M. Prokkola, Anna Blomberg, Steve Paterson, Joseph S. Johnson, Gregory G. Turner, Tomáš Bartonička, Erik Bachorec, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-38198-8

Spectrum of Microbial Sequences and a Bacterial Cell Wall Antigen in Primary Demyelination Brain Specimens Obtained from Living Patients
Cited by: 12
Author(s): John D. Kriesel, Preetida J. Bhetariya, Zhengming Wang, David Renner, Cheryl A. Palmer, Kael F. Fischer
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-28720-3

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus
Cited by: 9
Author(s): Inga Reich, Umer Zeeshan Ijaz, Michael J. Gormally, Cindy J. Smith
Software Mentions: 5
Published: over 6 years ago

10.1038/srep30349

Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil
Cited by: 92
Author(s): Johnny R. Soares, Noriko A. Cassman, Anna M. Kielak, Agata Pijl, Janaína Braga do Carmo, Késia Silva Lourenço, Hendrikus J. Laanbroek, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-017-03232-8

Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
Cited by: 14
Author(s): Stephen Byrne, Philip G. Conaghan, Susanne Barth, Sai Krishna Arojju, Michael D. Casler, Thibauld Michel, Janaki Velmurugan, Dan Milbourne
Software Mentions: 5
Published: over 7 years ago

10.1080/19490976.2020.1785252

The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide
Cited by: 34
Author(s): Chenchen Ma, S. S. Wasti, Shi Huang, Zhen Zeng, Rajeev Mishra, Shuaiming Jiang, Zhengkai You, Yixuan Wu, Haibo Chang, Yuanyuan Wang, Dongxue Huo, Congfa Li, Zhihong Sun, Zheng Sun, Jiachao Zhang
Software Mentions: 5
Published: over 4 years ago

10.3390/microorganisms9071457

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants
Cited by: 7
Author(s): Julia Hassa, Johanna Klang, Dirk Benndorf, Marcel Pohl, Benedikt Hülsemann, Torsten Mächtig, Mathias Effenberger, Alfred Pühler, Andreas Schlüter, Susanne Theuerl
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-020-02148-3

Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease
Cited by: 17
Author(s): Xiaofeng Dong, Jordana Muñoz-Basagoiti, Natasha Y. Rickett, Georgios Pollakis, William A. Paxton, Stephan Günther, Romy Kerber, Lisa F. P. Ng, Michael J. Elmore, N’Faly Magassouba, Miles W. Carroll, David A. Matthews, Julian A. Hiscox
Software Mentions: 5
Published: about 4 years ago

10.1186/s40168-021-01134-6

SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities
Cited by: 4
Author(s): Raminta Kazlauskaite, Bachar Cheaib, Chloe Heys, Umer Ijaz, Stephanie Connelly, William T. Sloan, Julie Russel, Laura Rubio, John Sweetman, Alex Kitts, Philip McGinnity, Philip Lyons, Martin S. Llewellyn
Software Mentions: 5
Published: about 3 years ago

10.1074/mcp.RA120.002175

Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment
Cited by: 3
Author(s): Kathryn M. Huson, Erwan Atcheson, Nicola A.M. Oliver, Philip M. Best, J.P. Barley, R.E.B. Hanna, Tom N. McNeilly, Yongxiang Fang, Sam Haldenby, Steve Paterson, Mark W. Robinson
Software Mentions: 5
Published: almost 4 years ago

10.3390/foods10061431

Synergistic Effects of the Jackfruit Seed Sourced Resistant Starch and Bifidobacterium pseudolongum subsp. globosum on Suppression of Hyperlipidemia in Mice
Cited by: 8
Author(s): Zhen Zeng, Yuanyuan Wang, Yanjun Zhang, Kaining Chen, Haibo Chang, Chenchen Ma, Shuaiming Jiang, Dongxue Huo, Wenjun Liu, Rajesh Jha, Jiachao Zhang
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.705712

Dual Transcriptomic Analyses Unveil Host–Pathogen Interactions Between Salmonella enterica Serovar Enteritidis and Laying Ducks (Anas platyrhynchos)
Cited by: 1
Author(s): Yu Zhang, Lina Song, Li-e Hou, Zhen Cao, Wanwipa Vongsangnak, Guoqiang Zhu, Qi Xu, Guohong Chen
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giaa043

Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle
Cited by: 27
Author(s): Suk-Kyung Lim, Dong‐Jun Kim, Dong Chan Moon, Youna Cho, Mina Rho
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-82951-5

Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury
Cited by: 10
Author(s): J. Russell Huie, Adam R. Ferguson, Nikos Kyritsis, Jonathan Z. Pan, Karen Irvine, Jessica L. Nielson, Patrick G. Schupp, Michael C. Oldham, John C. Gensel, Amity Lin, Mark R. Segal, Rajiv R. Ratan, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.dib.2018.11.034

Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection
Cited by: 4
Author(s): Mostafa Abdelrahman, Mai Mitoma, Takao Ikeuchi, Motoyuki Mori, Kyoko Murakami, Yukio Ozaki, Masaru Matsumoto, Atsuko Uragami, Akira Kanno
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.118.200880

Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog
Cited by: 1
Author(s): Megan L. Civitello, Robert D. Denton, Michael Zasloff, John H. Malone
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13148-020-00966-7

DNA methylation signatures to predict the cervicovaginal microbiome status
Cited by: 3
Author(s): Nuno R. Nené, James E. Barrett, Allison Jones, Iona Evans, Daniel Reisel, John F. Timms, Tobias Paprotka, Andreas Leimbach, D. Franchi, Nicoletta Colombo, Line Bjørge, Michal Zikán, David Cibula, Martin Widschwendter
Software Mentions: 4
Published: almost 4 years ago

10.1002/ece3.6042

Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol
Cited by: 22
Author(s): Maurício M. Zenker, Alexandre Specht, Vera G. Fonseca
Software Mentions: 4
Published: over 4 years ago

10.1186/2049-2618-2-1

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
Cited by: 314
Author(s): Brandon Brooks, Brian Firek, Christopher S. Miller, Itai Sharon, Brian C. Thomas, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 4
Published: almost 11 years ago

10.1186/s40168-019-0776-5

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities
Cited by: 55
Author(s): Eslam O. Osman, David J. Suggett, Christian R. Voolstra, D. Tye Pettay, Dave R. Clark, Claudia Pogoreutz, Eugenia M. Sampayo, Mark E. Warner, David J. Smith
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40168-018-0408-5

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline
Cited by: 44
Author(s): Martin Broberg, James Doonan, Filip Mundt, Sandra Denman, James E. McDonald
Software Mentions: 4
Published: almost 7 years ago

10.1534/g3.116.032805

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
Cited by: 45
Author(s): Daniel González-Ibeas, Pedro Manuel Martínez-García, Randi Famula, Annette Delfino-Mix, Kristian Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, Jill L. Wegrzyn
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13075-015-0677-3

Use of RNA sequencing to evaluate rheumatic disease patients
Cited by: 23
Author(s): Ευγενία Γιαννοπούλου, Olivier Elemento, Lionel B. Ivashkiv
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0172605

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred
Cited by: 28
Author(s): Umer Zeeshan Ijaz, Christopher Quince, Laura Hanske, Nicholas J. Loman, Szymon T. Calus, Martin Bertz, Christine Edwards, Daniel R. Gaya, Richard Hansen, Paraic McGrogan, Richard K. Russell, Konstantinos Gerasimidis
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-015-1635-9

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection
Cited by: 72
Author(s): James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Igseo Choi, Hua Bao, Arun Kommadath, Nick V. L. Serão, Nicholas Boddicker, Samuel M. Abrams, Martine Schroyen, Hyelee Loyd, Christopher K. Tuggle, Graham Plastow, Leluo Guan, Paul Stothard, Joan K. Lunney, Peng Liu, Susan Carpenter, Raymond R. R. Rowland, Jack C. M. Dekkers, James M. Reecy
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-015-2114-z

Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
Cited by: 9
Author(s): Gareth D. Weedall, Helen Irving, Margaret Hughes, Charles S. Wondji
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0091918

RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence
Cited by: 34
Author(s): Bouabid Badaoui, Teresa Rutigliano, Anna Anselmo, Merijn Vanhee, Hans Nauwynck, Elisabetta Giuffra, Sara Botti
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0177739

Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid
Cited by: 15
Author(s): Wang Hai, Shengyan Li, Shouzhen Teng, Haisheng Liang, Hongjia Xin, Hongjiang Gao, Dafang Huang, Zhihong Lang
Software Mentions: 4
Published: over 7 years ago

10.3389/fnmol.2017.00185

Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq
Cited by: 18
Author(s): Shannon Farris, Yu Wang, James M. Ward, Serena M. Dudek
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0241889

Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide
Cited by: 2
Author(s): Takahiro Yamagishi, Haruyo Yamaguchi, Shigekatsu Suzuki, Mayumi Yoshikawa, Ian Jameson, Maike Lorenz, David R. Nobles, Christine Campbell, Masanori Seki, Masanobu Kawachi, Hiroshi Yamamoto
Software Mentions: 4
Published: about 4 years ago

10.1186/s40168-020-00867-0

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Cited by: 394
Author(s): Kristopher Kieft, Zhichao Zhou, Karthik Anantharaman
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0227882

Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq
Cited by: 5
Author(s): Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp
Software Mentions: 4
Published: almost 5 years ago

Projects: pypi: Sickle

Papers Mentioning Sickle 740