Ecosyste.ms: Papers

10.1038/s41598-020-78469-x

Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
Cited by: 14
Author(s): Jacob Cardenas, Uthra Balaji, Jin Gu
Software Mentions: 23
Published: almost 4 years ago

10.3390/ijms22052244

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis
Cited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 3 years ago

10.1186/s40168-020-00961-3

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Cited by: 30
Author(s): Wang Ya, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Software Mentions: 15
Published: almost 4 years ago

10.1016/j.xpro.2021.100837

Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002
Cited by: 3
Author(s): Supreeta Vijayakumar, Claudio Angione
Software Mentions: 13
Published: almost 3 years ago

10.1371/journal.pgen.1006111

Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes
Cited by: 109
Author(s): Sébastian Lequime, Albin Fontaine, Meriadeg Ar Gouilh, Isabelle Moltini-Conclois, Louis Lambrechts
Software Mentions: 12
Published: over 8 years ago

10.1111/mec.13636

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event
Cited by: 34
Author(s): Kevin Schneider, Philipp Resl, Toby Spribille
Software Mentions: 11
Published: over 8 years ago

10.1002/ece3.6904

Light might suppress both types of sound‐evoked antipredator flight in moths
Cited by: 2
Author(s): Theresa Hügel, Holger R. Goerlitz
Software Mentions: 11
Published: about 4 years ago

10.3389/fgene.2019.00279

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: over 5 years ago

10.3389/fpsyg.2020.599788

Faster Visual Information Processing in Video Gamers Is Associated With EEG Alpha Amplitude Modulation
Cited by: 5
Author(s): Yannik Hilla, Jörg von Mankowski, Julia Föcker, Paul Sauseng
Software Mentions: 9
Published: almost 4 years ago

10.1186/s40168-018-0535-z

High-resolution ISR amplicon sequencing reveals personalized oral microbiome
Cited by: 30
Author(s): Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen, Eugene J. Leys
Software Mentions: 9
Published: about 6 years ago

10.1186/s40478-019-0851-y

Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas
Cited by: 12
Author(s): Ruslan Al‐Ali, Katharina Bauer, Jong‐Whi Park, Ruba Al-Abdulla, Valentina Fermi, Andreas von Deimling, Christel Herold‐Mende, Jan‐Philipp Mallm, Carl Herrmann, Wolfgang Wick, Şevin Turcan
Software Mentions: 9
Published: almost 5 years ago

10.3390/ijms21093139

The Dark Side of Orchid Symbiosis: Can Tulasnella calospora Decompose Host Tissues?
Cited by: 21
Author(s): Martino Adamo, Matteo Chialva, Jacopo Calevo, Silvia De Rose, Mariangela Girlanda, Silvia Perotto, Raffaella Balestrini
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.47859

Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction
Cited by: 15
Author(s): Shir Toubiana, Miriam Gagliardi, Mariarosaria Papa, Roberta Manco, Maty Tzukerman, Maria R. Matarazzo, Sara Selig
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0246052

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection
Cited by: 10
Author(s): Aleksandra Boba, Kamil Kostyń, Bartosz Kozak, Iwan Zalewski, Jan Szopa, Anna Kulma
Software Mentions: 8
Published: almost 4 years ago

10.1523/ENEURO.0339-19.2020

Function, Innervation, and Neurotransmitter Signaling in Mice Lacking Type-II Taste Cells
Cited by: 16
Author(s): Eric D. Larson, Aurélie Vandenbeuch, Catherine B. Anderson, Sue C. Kinnamon
Software Mentions: 8
Published: almost 5 years ago

10.1186/s13059-020-02195-w

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Cited by: 107
Author(s): Alon Shaiber, Amy Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch, A. Murat Eren
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0255169

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts
Cited by: 25
Author(s): Rafail Nikolaos Tasakis, Georgios Samaras, Anna Jamison, Michelle Lee, Alexandra Paulus, Gabrielle Whitehouse, Laurent Verkoczy, F. Nina Papavasiliou, Marilyn Diaz
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0244122

Easyreporting simplifies the implementation of Reproducible Research layers in R software
Cited by: 0
Author(s): Dario Righelli, Claudia Angelini
Software Mentions: 8
Published: over 3 years ago

10.7717/peerj.6902

Optimizing <i>de novo</i> genome assembly from PCR-amplified metagenomes
Cited by: 26
Author(s): Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent Northen, Matthew B. Sullivan, V. I. Rich, Rex R. Malmstrom, Emiley A. Eloe‐Fadrosh
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.960

Swabs to genomes: a comprehensive workflow
Cited by: 30
Author(s): Madison I. Dunitz, Jenna M. Lang, Guillaume Jospin, Aaron E. Darling, Jonathan A. Eisen, David A. Coil
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pone.0179261

Monitoring of noble, signal and narrow-clawed crayfish using environmental DNA from freshwater samples
Cited by: 73
Author(s): Sune Agersnap, William Brenner Larsen, Steen Wilhelm Knudsen, David Strand, Philip Francis Thomsen, Martin Hesselsøe, Peter Mortensen, Trude Vrålstad, Peter Rask Møller
Software Mentions: 7
Published: over 7 years ago

10.1534/g3.120.401325

Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
Cited by: 17
Author(s): Alexander F. Gileta, Jianjun Gao, Apurva S. Chitre, Hannah Bimschleger, Celine L. St. Pierre, Shyam Gopalakrishnan, Abraham A. Palmer
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-021-92927-0

A new CAM6 + DART reanalysis with surface forcing from CAM6 to other CESM models
Cited by: 5
Author(s): K. Raeder, T. J. Hoar, Mohamad El Gharamti, Benjamin K. Johnson, Nancy Collins, Jeffrey L. Anderson, Jeff Steward, Mick Coady
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.62669

Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross
Cited by: 14
Author(s): Kaushik Renganaath, Rocky Cheung, Laura Day, Sriram Kosuri, Leonid Kruglyak, Frank W. Albert
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-020-70173-0

Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers
Cited by: 17
Author(s): Sofia Paraskevopoulou, Alice B. Dennis, Guntram Weithoff, Ralph Tiedemann
Software Mentions: 7
Published: over 4 years ago

10.1128/mBio.03396-20

Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes
Cited by: 21
Author(s): Rozlyn C.T. Boutin, Hind Sbihi, Ryan J. McLaughlin, Aria S. Hahn, Kishori M. Konwar, Rachelle Loo, Darlene Dai, Charisse Petersen, Fiona S. L. Brinkman, Geoffrey L. Winsor, Malcolm R. Sears, Theo J. Moraes, Allan B. Becker, Meghan B. Azad, Piush J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1006269

Evaluating reproducibility of AI algorithms in digital pathology with DAPPER
Cited by: 43
Author(s): Andrea Bizzego, Nicole Bussola, Marco Chierici, Valerio Maggio, Margherita Francescatto, Luca Cima, Marco Cristoforetti, Giuseppe Jurman, Cesare Furlanello
Software Mentions: 7
Published: over 5 years ago

10.1093/database/baz151

LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemia
Cited by: 13
Author(s): Abdul Rawoof, Guruprasadh Swaminathan, Shrish Tiwari, Rekha A. Nair, Lekha Dinesh Kumar
Software Mentions: 7
Published: almost 5 years ago

10.3389/fmolb.2020.598583

SARS-CoV-2 Proteins Exploit Host’s Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways
Cited by: 29
Author(s): A. A. Khan, Abul B.M.M.K. Islam
Software Mentions: 7
Published: almost 4 years ago

10.1128/mSphere.00737-20

Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus <i>Cryphonectria</i>
Cited by: 16
Author(s): Lea Stauber, Simone Prospero, Daniel Croll
Software Mentions: 7
Published: about 4 years ago

10.1186/s12859-021-04198-1

Comparative evaluation of full-length isoform quantification from RNA-Seq
Cited by: 12
Author(s): Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens, Gregory R. Grant
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0191557

Modelling human hard palate shape with Bézier curves
Cited by: 9
Author(s): Ruud Janssen, Scott R. Moisik, Dan Dediu
Software Mentions: 6
Published: almost 7 years ago

10.1111/1755-0998.13060

Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists
Cited by: 60
Author(s): Luís P. da Silva, Vanessa A. Mata, Pedro Lopes, Paulo Pereira, Simon Jarman, Ricardo Lopes, Pedro Beja
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0188972

Adiposity QTL Adip20 decomposes into at least four loci when dissected using congenic strains
Cited by: 4
Author(s): Cailu Lin, Brad D. Fesi, Michael Marquis, Natalia P. Bosak, Anna Lysenko, Mohammed Amin Koshnevisan, Fujiko Duke, Maria L. Theodorides, Theodore M. Nelson, Amanda H. McDaniel, Mauricio Avigdor, Charles J. Arayata, Lauren Shaw, Alexander A. Bachmanov, Danielle R. Reed
Software Mentions: 6
Published: almost 7 years ago

10.1523/ENEURO.0066-20.2020

Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth
Cited by: 33
Author(s): Jeremy S. Toma, Konstantina Karamboulas, Matthew Carr, Adelaida Kolaj, Scott A. Yuzwa, Neemat Mahmud, Mekayla Storer, David R. Kaplan, Freda D. Miller
Software Mentions: 6
Published: over 4 years ago

10.1534/g3.119.400180

Hybrid Assembly of the Genome of the Entomopathogenic Nematode <i>Steinernema carpocapsae</i> Identifies the X-Chromosome
Cited by: 12
Author(s): Lorrayne Serra, Marissa Macchietto, Aide Macias-Muñoz, Cassandra McGill, Isaryhia Rodriguez, Bryan Rodriguez, Rabi Murad, A Mortazavi
Software Mentions: 6
Published: over 5 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

10.7554/eLife.02535

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species
Cited by: 111
Author(s): Molly Schumer, Rongfeng Cui, Daniel L. Powell, Rebecca Dresner, Gil G. Rosenthal, Peter Andolfatto
Software Mentions: 6
Published: over 10 years ago

10.1186/s12864-018-5266-9

Host microRNA analysis in cyprinid Herpesvirus-3 (CyHV-3) infected common carp
Cited by: 10
Author(s): M. Reichert, Anna Łukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj‐Paluch, Magdalena Stachnik, Ewa Borzym
Software Mentions: 6
Published: almost 6 years ago

10.1002/2211-5463.13057

Long noncoding RNAs implicated in embryonic development in <i>Ybx1</i> knockout zebrafish
Cited by: 5
Author(s): Chen Huang, Bo Zhu, Dongliang Leng, Wei Ge, Xiaohua Douglas Zhang
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007800

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
Cited by: 30
Author(s): Avtar Roopra
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1008309

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
Cited by: 34
Author(s): Filip Stefaniak, Janusz Bujnicki
Software Mentions: 6
Published: almost 4 years ago

10.1186/1751-0473-6-4

Parallel biocomputing
Cited by: 0
Author(s): Kenneth S Kompass, Thomas J. Hoffmann, John S. Witte
Software Mentions: 6
Published: over 13 years ago

10.1128/mBio.02634-20

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study
Cited by: 22
Author(s): Nastassia V. Patin, Angela Peña-Gonzalez, Janet K. Hatt, Christine L. Moe, Amy Kirby, Konstantinos T. Konstantinidis
Software Mentions: 6
Published: almost 4 years ago

10.1002/ece3.6471

Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids
Cited by: 12
Author(s): Anna F. Feller, Oliver M. Selz, Matthew D. McGee, Joana I. Meier, Salome Mwaiko, Ole Seehausen
Software Mentions: 6
Published: over 4 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: almost 6 years ago

10.3390/microorganisms8101554

HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts
Cited by: 6
Author(s): Soukaina Timouma, Jean-Marc Schwartz, Daniela Delneri
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-019-45714-x

Transcriptome Analysis of Long-lived Drosophila melanogaster E(z) Mutants Sheds Light on the Molecular Mechanisms of Longevity
Cited by: 30
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Nadezhda Zemskaya, Liubov Koval, Eugenia V. Schegoleva, Zulfiya G. Guvatova, George S. Krasnov, Ilya Solovev, Maksim A. Sheptyakov, Alex Zhavoronkov, Anna V. Kudryavtseva
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.3000675

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Cited by: 35
Author(s): Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-020-66224-1

Genomic deregulation of PRMT5 supports growth and stress tolerance in chronic lymphocytic leukemia
Cited by: 5
Author(s): Ann-Kathrin Schnormeier, Claudia Pommerenke, Maren Kaufmann, Hans Drexler, Max Koeppel
Software Mentions: 6
Published: over 4 years ago

10.1186/1471-2342-8-10

Internet Image Viewer (iiV)
Cited by: 9
Author(s): Joel T. Lee, Kristin Munch, John V. Carlis, José V. Pardo
Software Mentions: 6
Published: over 16 years ago

10.1371/journal.pone.0097379

Direct Sequencing from the Minimal Number of DNA Molecules Needed to Fill a 454 Picotiterplate
Cited by: 12
Author(s): Mária Džunková, Marc García-Garcerá, Llúcia Martínez-Priego, Giussepe D’Auria, Francesc Calafell, Andrés Moya
Software Mentions: 6
Published: over 10 years ago

10.1093/jxb/erab072

Dynamic histone acetylation in floral volatile synthesis and emission in petunia flowers
Cited by: 19
Author(s): Ryan M. Patrick, Xing-Qi Huang, Natalia Dudareva, Ying Liu
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13007-020-00591-8

The BELT and phenoSEED platforms: shape and colour phenotyping of seed samples
Cited by: 18
Author(s): Keith Halcro, Kaitlin McNabb, Ashley Lockinger, Didier Socquet-Juglard, Kirstin E. Bett, Scott D. Noble
Software Mentions: 6
Published: over 4 years ago

10.3389/fcimb.2018.00020

Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals
Cited by: 20
Author(s): Lisandra Aguilar-Bultet, Pamela Nicholson, Lorenz Rychener, Margaux Dreyer, Bulent Gözel, Francesco C. Origgi, Anna Oevermann, Joachim Frey, Laurent Falquet
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-021-07912-8

Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilience
Cited by: 8
Author(s): Kyu-Sang Lim, Jian Cheng, Austin M. Putz, Qian Dong, Xue Bai, Hamid Beiki, Christopher K. Tuggle, Michael K. Dyck, Pig Gen Canada, Frédéric Fortin, John C. S. Harding, Graham Plastow, Jack C. M. Dekkers
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0051292

Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes
Cited by: 9
Author(s): Francesco Lescai, Silvia Bonfiglio, Chiara Bacchelli, Estelle Chanudet, Aoife Waters, Sanjay M. Sisodiya, Dalia Kasperavičiūtė, Julie Williams, Denise Harold, John Hardy, Robert Kleta, Sebahattin Çırak, Richard Williams, John C. Achermann, John Anderson, David P. Kelsell, Tom Vulliamy, Henry Houlden, Nicholas W. Wood, Una Marie Sheerin, Gian Paolo Tonini, Donna S. Mackay, Khalid Hussain, Jane C. Sowden, Veronica A. Kinsler, Justyna Osinska, Tony Brooks, Mike Hubank, Philip L. Beales, Elia Stupka
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12915-020-00940-y

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses
Cited by: 14
Author(s): Andra Waagmeester, Egon Willighagen, Andrew I. Su, Martina Kutmon, José Emilio Labra Gayo, Daniel Fernández-Álvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. Koehorst
Software Mentions: 5
Published: almost 4 years ago

10.1093/gbe/evab099

Rampant Genome-Wide Admixture across the <i>Heliconius</i> Radiation
Cited by: 28
Author(s): Krzysztof M. Kozak, Mathieu Joron, W. Owen McMillan, Chris D. Jiggins
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0255433

Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa
Cited by: 5
Author(s): Stephen Osei-Wusu, Isaac Darko Otchere, Portia Morgan, Abdul Basit Musah, Ishaque Mintah Siam, Diana Asema Asandem, Theophilus Afum, Prince Asare, Adwoa Asante-Poku, Kwadwo Asamoah Kusi, Sébastien Gagneux, Dorothy Yeboah-Manu
Software Mentions: 5
Published: about 3 years ago

10.3390/genes12060842

De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis
Cited by: 5
Author(s): J.M. Córdoba, Emilie Perez, Mick Van Vlierberghe, Amandine Bertrand, Valérian Lupo, Pierre Cardol, Denis Baurain
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-017-0412-4

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution
Cited by: 96
Author(s): Damien J. Lightfoot, David E. Jarvis, Thiruvarangan Ramaraj, R. Lee, Eric N. Jellen, Peter J. Maughan
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-015-0840-9

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
Cited by: 126
Author(s): Xiaomin Bao, Adam J. Rubin, Kun Qu, Jiajing Zhang, Paul G. Giresi, Howard Y. Chang, Paul A. Khavari
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12864-017-4351-9

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
Cited by: 3
Author(s): David Martín‐Gálvez, Denis Dunoyer de Segonzac, Man Chun John, Anne E. Kwitek, David Thybert, Paul Flicek
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12935-019-0731-3

Potential new biomarkers for endometrial cancer
Cited by: 37
Author(s): Michelle H. Townsend, Zac E. Ence, Abigail M. Felsted, Alyssa Parker, Stephen R. Piccolo, Richard A. Robison, Kim L. O’Neill
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-021-08036-9

Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires
Cited by: 5
Author(s): Robert J. Dixon, Stephen G. Preston, Stefan Dascalu, Patrik G. Flammer, Steven R. Fiddaman, Kirstie McLoughlin, Amy Boyd, Jiřı́ Volf, Ivan Rychlı́k, Michael B. Bonsall, Bernd Kaspers, Adrian L. Smith
Software Mentions: 5
Published: about 3 years ago

10.1186/2047-217X-1-3

Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers
Cited by: 40
Author(s): Gareth A. Wilson, Pawandeep Dhami, Andrew Feber, Daniel Cortázar, Yuka Suzuki, Reiner Schulz, Primo Schär, Stephan Beck
Software Mentions: 5
Published: over 12 years ago

10.1186/s12864-019-5613-5

Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes
Cited by: 25
Author(s): Isabelle Rosinski‐Chupin, Elisabeth Sauvage, Agnès Fouet, Claire Poyart, Philippe Glaser
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2016.00398

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow
Cited by: 48
Author(s): Anna Lopatina, Sofia Medvedeva, Sergey Shmakov, Maria D. Logacheva, В. А. Крыленков, Konstantin Severinov
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.05255

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Cited by: 402
Author(s): Manu Dubin, Pei Zhang, Dong Meng, Marie Stanislas Remigereau, Edward J. Osborne, Francesco Paolo Casale, Philipp Drewe, André Kahles, Géraldine Jean, Bjarni J. Vilhjálmsson, Joanna Jagoda, Selen Irez, Viktor Voronin, Qiang Song, Quan Long, Gunnar Rätsch, Oliver Stegle, Richard M. Clark, Magnus Nordborg
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0176596

Evolution of microRNA in primates
Cited by: 31
Author(s): Jennifer C. McCreight, Sean E. Schneider, Damien B. Wilburn, Willie J. Swanson
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-021-04317-y

OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow
Cited by: 12
Author(s): Jochen Bathke, Gesine Lühken
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.02075

Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis
Cited by: 14
Author(s): Gi Yoon Shin, Jeffrey K. Schachterle, Divine Yufetar Shyntum, Lucy N. Moleleki, Teresa A. Coutinho, George W. Sundin
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2017.01566

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes
Cited by: 75
Author(s): Anne-Mette Bjerregaard, Morten Nielsen, Vanessa Isabell Jurtz, Carolina Barra, Sine Reker Hadrup, Zoltán Szállási, Aron C. Eklund
Software Mentions: 5
Published: about 7 years ago

10.3390/microorganisms9020346

Gut Microbiota Profile and Changes in Body Weight in Elderly Subjects with Overweight/Obesity and Metabolic Syndrome
Cited by: 13
Author(s): Alessandro Atzeni, Serena Galiè, Jananee Muralidharan, Nancy Babió, Francisco J. Tinahones, Jesús Vioque, Dolores Corella, Olga Castañer, Josep Vidal, Isabel Moreno-Indias, Laura Torres-Collado, Rebeca Fernández-Carrión, Montserrat Fitó, Romina Olbeyra, Miguel Ángel Martínez‐González, Mònica Bulló, Jordi Salas‐Salvadó
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.51243

Global genome diversity of the Leishmania donovani complex
Cited by: 77
Author(s): Susanne U. Franssen, Caroline Durrant, Olivia Stark, Bettina A. Moser, Tim Downing, Hideo Imamura, Jean Claude Dujardin, Mandy Sanders, Isabel Maurício, Michael A. Miles, Lionel F. Schnur, Charles L. Jaffe, Abedelmajeed Nasereddin, Henk D. F. H. Schallig, Matthew Yeo, Tapan Bhattacharyya, Mohammad Zahangir Alam, Matthew Berriman, Thierry Wirth, Gabriele Schönian, James A. Cotton
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2020.01009

RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development
Cited by: 22
Author(s): Siyuan Xing, Ranran Liu, Guiping Zhao, Lu Liu, M.A.M. Groenen, Ole Madsen, Maiqing Zheng, Xinting Yang, R.P.M.A. Crooijmans, Jie Wen
Software Mentions: 5
Published: about 4 years ago

10.1186/s12870-018-1316-3

UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study
Cited by: 43
Author(s): Peng Qi, Davis Gimode, Dipnarayan Saha, Stephan Schröder, Debkanta Chakraborty, Xuewen Wang, Mathews M. Dida, Russell L. Malmberg, Katrien M. Devos
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms22179470

Mammalian and Invertebrate Models as Complementary Tools for Gaining Mechanistic Insight on Muscle Responses to Spaceflight
Cited by: 13
Author(s): Thomas J. Cahill, Henry Cope, Joseph J. Bass, Eliah Overbey, Rachel Gilbert, Willian A. da Silveira, Amber M. Paul, Tejaswini Mishra, Raúl Herranz, Sigrid Reinsch, Sylvain V. Costes, Gary Hardiman, Nathaniel J. Szewczyk, Candice Tahimic
Software Mentions: 5
Published: about 3 years ago

10.1186/s12870-018-1467-2

WRKY transcription factors in legumes
Cited by: 51
Author(s): Hui Song, Weihong Sun, Guofeng Yang, Juan Sun
Software Mentions: 5
Published: about 6 years ago

10.1186/s12859-018-2013-9

TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association
Cited by: 8
Author(s): Seo Won Choi, Jin Wu Nam
Software Mentions: 5
Published: almost 7 years ago

10.1099/mgen.0.000190

Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections
Cited by: 32
Author(s): Cosmika Goswami, Stephen Fox, Matthew T. G. Holden, Martin Connor, Alistair Leanord, Thomas J. Evans
Software Mentions: 5
Published: over 6 years ago

10.1121/10.0003529

Remote sociophonetic data collection: Vowels and nasalization over video conferencing apps
Cited by: 21
Author(s): Valerie Freeman, Paul De Decker
Software Mentions: 5
Published: almost 4 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

10.15252/embr.201846960

Nucleosome dynamics of human iPSC during neural differentiation
Cited by: 5
Author(s): Janet Harwood, Nicholas A. Kent, Nicholas Denby Allen, Adrian J. Harwood
Software Mentions: 5
Published: over 5 years ago

10.1111/pbi.13085

Development of an integrated 200K <scp>SNP</scp> genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (<i>Pyrus</i>)
Cited by: 43
Author(s): Xiaolong Li, Jugpreet Singh, Mengfan Qin, Siwei Li, Xun Zhang, Mingyue Zhang, Awais Khan, Shaoling Zhang
Software Mentions: 5
Published: almost 6 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

10.3389/fpls.2017.02185

Morphometrics Reveals Complex and Heritable Apple Leaf Shapes
Cited by: 43
Author(s): Zoë Migicovsky, Mao Li, Daniel H. Chitwood, Sean Myles
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0140829

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud
Cited by: 99
Author(s): Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor V. Makunin, Derek Benson, Mark L. Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie
Software Mentions: 4
Published: about 9 years ago

10.1186/s12859-017-2000-6

A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy
Cited by: 53
Author(s): Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers, Matthew E. Hudson
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-021-02333-y

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean
Cited by: 28
Author(s): Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu, Li D
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-15-37

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
Cited by: 74
Author(s): Jorge F. Vázquez-Castellanos, Rodrigo García-López, Vicente Pérez‐Brocal, Miguel Pignatelli, Andrés Moya
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12915-019-0659-z

Biological and RNA regulatory function of MOV10 in mammalian germ cells
Cited by: 18
Author(s): Kaiqiang Fu, Suwen Tian, Huanhuan Tan, Caifeng Wang, Hanben Wang, Min Wang, Yuan‐Yuan Wang, Zhen Chen, Yanfeng Wang, Qiuling Yue, Qiushi Xu, Shuya Zhang, Haixin Li, Jie Xie, Mingyan Lin, Mengcheng Luo, Feng Chen, Lan Ye, Ke Zheng
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ajhg.2015.07.007

Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability
Cited by: 51
Author(s): Stephen R.F. Twigg, Jennifer Forecki, Jacqueline A.C. Goos, Ivy C.A. Richardson, A. Jeannette M. Hoogeboom, Ans M.W. van den Ouweland, Sigrid Swagemakers, Maarten H. Lequin, Daniel Van Antwerp, Simon J. McGowan, Isabelle Westbury, Kerry A. Miller, Steven A. Wall, Peter J. van der Spek, Irene M.J. Mathijssen, Erwin Pauws, Christa Merzdorf, Andrew O.M. Wilkie
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0090706

A Bulk Segregant Gene Expression Analysis of a Peach Population Reveals Components of the Underlying Mechanism of the Fruit Cold Response
Cited by: 36
Author(s): Clara Pons, Cristina Martí, Javier Forment, Carlos H. Crisosto, Abhaya M. Dandekar, Antonio Granell
Software Mentions: 4
Published: over 10 years ago

10.1186/s12859-016-0982-0

Modeling the integration of bacterial rRNA fragments into the human cancer genome
Cited by: 5
Author(s): Karsten B. Sieber, Pawel Gajer, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 8 years ago

10.3390/genes12010044

Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data
Cited by: 12
Author(s): Claudio Cucini, Pietro Paolo Fanciulli, Francesco Frati, Peter Convey, Francesco Nardi, Antonio Carapelli
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12711-021-00668-5

A near complete genome for goat genetic and genomic research
Cited by: 11
Author(s): Ran Li, Peng Yang, Xuelei Dai, Hojjat Asadollahpour Nanaei, Wenwen Fang, Zhirui Yang, Yi Cai, Zhuqing Zheng, Xihong Wang, Yu Jiang
Software Mentions: 4
Published: about 3 years ago

10.1534/g3.117.039396

Comparative Genomics of the Ectomycorrhizal Sister Species <i>Rhizopogon vinicolor</i> and <i>Rhizopogon vesiculosus</i> (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type <i>B</i> Locus
Cited by: 16
Author(s): Alija B. Mujic, Alan Kuo, Andrew Tritt, Anna Lipzen, Cindy Chen, Jenifer Johnson, Aarti Sharma, Kerrie Barry, Igor V. Grigoriev, Joseph W. Spatafora
Software Mentions: 4
Published: over 7 years ago

10.3389/fpsyg.2020.02154

HIIT the Road Jack: An Exploratory Study on the Effects of an Acute Bout of Cardiovascular High-Intensity Interval Training on Piano Learning
Cited by: 3
Author(s): Dana Swarbrick, Alex Kiss, Sandra E. Trehub, Luc Tremblay, David A. Alter, Joyce L. Chen
Software Mentions: 4
Published: about 4 years ago