pypi: Archive | Projects | Ecosyste.ms: Papers

10.1186/s13321-020-00477-w

patRoon: open source software platform for environmental mass spectrometry based non-target screening
Cited by: 76
Author(s): Rick Helmus, Thomas L. ter Laak, Annemarie P. van Wezel, P. de Voogt, Emma L. Schymanski
Software Mentions: 20
Published: over 3 years ago

10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: about 3 years ago

10.3389/fimmu.2019.02887

Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo
Cited by: 29
Author(s): Hung Jen Chen, Andrew Y. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
Software Mentions: 13
Published: over 4 years ago

10.1093/aobpla/plz054

tealeaves: an R package for modelling leaf temperature using energy budgets
Cited by: 26
Author(s): Christopher D. Muir
Software Mentions: 12
Published: over 4 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: about 4 years ago

10.1038/s42003-018-0199-z

Improved reference genome for the domestic horse increases assembly contiguity and composition
Cited by: 137
Author(s): Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris Vermeesch, Brendan O’Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E. McCue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Edward Green, Donald C. Miller, Douglas F. Antczak, James N. MacLeod
Software Mentions: 9
Published: over 5 years ago

10.1016/j.mad.2021.111437

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice
Cited by: 6
Author(s): Matías Fuentealba, Daniel K. Fabian, Handan Melike Dönertaş, Janet Thornton, Linda Partridge
Software Mentions: 9
Published: about 3 years ago

10.1186/s13059-020-02141-w

Improved reference genome of the arboviral vector Aedes albopictus
Cited by: 61
Author(s): Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud‐Nissen, James K. Biedler, Flávia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna‐Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Д. А. Карагодин, James Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos Aris Papathanos, Ronald P. van Rij, Omar S. Akbari, Jeffrey R. Powell, Adam M. Phillippy, Mariangela Bonizzoni
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0254491

Learning epistatic gene interactions from perturbation screens
Cited by: 2
Author(s): Kieran Elmes, Fabian Schmich, Ewa Szczurek, Jeremy L. Jenkins, Niko Beerenwinkel, Alex Gavryushkin
Software Mentions: 9
Published: almost 3 years ago

10.12688/f1000research.22731.2

Fast analysis of scATAC-seq data using a predefined set of genomic regions
Cited by: 10
Author(s): Valentina Giansanti, Ming Tang, Davide Cittaro
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pcbi.1005727

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2015.00172

FAST: FAST Analysis of Sequences Toolbox
Cited by: 28
Author(s): Travis J Lawrence, Kyle T. Kauffman, Katherine C. H. Amrine, Dana L. Carper, Raymond S. Lee, Peter J. Becich, Claudia J. Canales, David H. Ardell
Software Mentions: 8
Published: about 9 years ago

10.1038/s41598-017-09064-w

Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching
Cited by: 27
Author(s): Douglas C. Wu, Alan M. Lambowitz
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2019.00182

Detection of Differentially Expressed Cleavage Site Intervals Within 3′ Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs
Cited by: 9
Author(s): Benjamin J. Harrison, Juw Won Park, Cynthia Gomes, Jeffrey C. Petruska, Matthew R. Sapio, Michael J. Iadarola, Julia H. Chariker, Eric C. Rouchka
Software Mentions: 8
Published: about 5 years ago

10.1038/s42003-021-02095-0

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Cited by: 28
Author(s): Mariana Galvão Ferrarini, Avantika Lal, Rita Rebollo, Andreas J. Gruber, Andrea Guarracino, Itziar Martinez Gonzalez, Taylor Floyd, Daniel Siqueira de Oliveira, Justin Shanklin, Ethan Beausoleil, Taneli Pusa, Brett E. Pickett, Vanessa Aguiar‐Pulido
Software Mentions: 7
Published: about 3 years ago

10.3389/fmicb.2020.01984

VHSV Single Amino Acid Polymorphisms (SAPs) Associated With Virulence in Rainbow Trout
Cited by: 12
Author(s): Valentina Panzarin, Argelia Cuenca, Michele Gastaldelli, Anna Luiza Farias Alencar, Francesco Pascoli, Thierry Morin, Yannick Blanchard, Jean-Yves Cabon, Lénaïg Louboutin, David Ryder, Miriam Abbadi, Anna Toffan, Carlos P. Dopazo, Stéphane Biacchesi, Michel Brémont, Niels Jørgen Olesen
Software Mentions: 7
Published: over 3 years ago

10.1038/s42003-020-01626-5

Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups
Cited by: 44
Author(s): Kaleb Z. Abram, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M. Wassenaar, Michael S. Robeson, David W. Ussery
Software Mentions: 7
Published: over 3 years ago

10.7150/jca.49707

Cancer-associated fibroblasts in gastric cancer affect malignant progression via the CXCL12-CXCR4 axis
Cited by: 20
Author(s): Qin Yan, Fang Wang, Hengli Ni, Yao Liu, Yuan Yin, Xinyi Zhou, Guihua Gao, Qing Li, Xiaowei Qi, Jianming Li
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0137222

Discovery of Intermediary Genes between Pathways Using Sparse Regression
Cited by: 1
Author(s): Kuo-ching Liang, Ashwini Patil, Kenta Nakai
Software Mentions: 7
Published: over 8 years ago

10.12688/f1000research.14880.4

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
Cited by: 0
Author(s): Syed Hussain Ather, Olaitan I. Awe, Thomas J. Butler, Tamiru Denka, Stephen A. Semick, Wanhu Tang, Ben Busby
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-81451-w

Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19
Cited by: 33
Author(s): Ilario De Toma, Mara Dierssen
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-019-2955-6

Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data
Cited by: 3
Author(s): Akio Miyao, Jianyu Song Kiyomiya, Kei Iida, Koji Doi, Hiroshi Yasue
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41597-020-0458-y

Epigenomic profiling of neuroblastoma cell lines
Cited by: 23
Author(s): Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M. Kendsersky, Karina L. Conkrite, Robyn T. Sussman, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Paolo Fortina, Sharon J. Diskin, John M. Maris, Jo Lynne Rokita
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pbio.3000559

Human sperm displays rapid responses to diet
Cited by: 102
Author(s): Daniel Nätt, Unn Kugelberg, Eduard Casas, Elizabeth Nedstrand, Stefan Zalavary, Pontus Henriksson, Carola Nijm, Julia Jäderquist, Johanna Sandborg, Eva Flinke, Rashmi Ramesh, Lovisa Örkenby, Filip Appelkvist, Thomas Lingg, Nicola Guzzi, Cristian Bellodi, Marie Löf, Tanya Vavouri, Anita Öst
Software Mentions: 6
Published: over 4 years ago

10.1093/gbe/evaa084

Paternally Inherited P-Element Copy Number Affects the Magnitude of Hybrid Dysgenesis in Drosophila simulans and D. melanogaster
Cited by: 14
Author(s): Antonio Serrato-Capuchina, Jeremy Wang, Eric J. Earley, David Peede, Kristin Isbell, Daniel R. Matute
Software Mentions: 6
Published: about 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: over 7 years ago

10.12688/f1000research.11355.2

Arkas: Rapid reproducible RNAseq analysis
Cited by: 9
Author(s): Anthony Colombo, Timothy J. Triche, Giridharan Ramsingh
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0221543

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
Cited by: 18
Author(s): Paltu Kumar Dhal, Gérmán A. Kopprio, Astrid Gärdes
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1004105

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers
Cited by: 173
Author(s): Christopher DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Z. Rassenti, Christian Barrett, Kristen Jepsen, Catriona Jamieson, Dennis A. Carson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 5
Published: about 9 years ago

10.1093/gigascience/giaa008

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms
Cited by: 77
Author(s): Patrick Browne, Tue Kjærgaard Nielsen, Witold Kot, Anni Aggerholm, M. Thomas P. Gilbert, Lara Puetz, Morten Rasmussen, Athanasios Zervas, Lars Hestbjerg Hansen
Software Mentions: 5
Published: over 4 years ago

10.3390/microorganisms8060906

Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature
Cited by: 23
Author(s): Francisco Luis Massello, Chia Sing Chan, Kok Gan Chan, Kian Mau Goh, Edgardo R. Donati, María Sofía Urbieta
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2019.00481

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype
Cited by: 40
Author(s): Gregory Bonito, Gian Maria Niccolò Benucci, Khalid Hameed, Deborah Weighill, Piet Jones, Ko‐Hsuan Chen, Daniel Jacobson, Christopher W. Schadt, Rytas Vilgalys
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-017-4031-9

unitas: the universal tool for annotation of small RNAs
Cited by: 83
Author(s): Daniel Gebert, Charlotte Hewel, David Rosenkranz
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giz066

PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning
Cited by: 102
Author(s): Zhencheng Fang, Jie Tan, Shu‐Fang Vivienne Wu, Mo Li, Congmin Xu, Zheng Xie, Huaiqiu Zhu
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0120117

The Level of Residual Dispersion Variation and the Power of Differential Expression Tests for RNA-Seq Data
Cited by: 1
Author(s): Gu Mi, Yanming Di
Software Mentions: 5
Published: about 9 years ago

10.1016/j.stem.2020.09.001

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder
Cited by: 86
Author(s): Hannah K. Long, Marco Osterwalder, Ian Welsh, Karissa Hansen, James O. J. Davies, Yiran E. Liu, Mervenaz Koska, Alexander T. Adams, Robert Aho, Neiha Arora, Kazuya Ikeda, Ruth M. Williams, Tatjana Sauka‐Spengler, Matthew H. Porteus, Tim Mohun, Diane E. Dickel, Tomek Swigut, Jim R. Hughes, Douglas R. Higgs, Axel Visel, Licia Selleri, Joanna Wysocka
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-021-01001-8

Evolution of the codling moth pheromone via an ancient gene duplication
Cited by: 9
Author(s): Jean-Marc Lassance, Bao‐Jian Ding, Christer Löfstedt
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pcbi.1000204

Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
Cited by: 151
Author(s): Duncan Hull, Steve Pettifer, Douglas B. Kell
Software Mentions: 5
Published: over 15 years ago

10.6026/97320630013101

optCluster: An R Package for Determining the Optimal Clustering Algorithm
Cited by: 36
Author(s): Michael Sekula, Somnath Datta, Susmita Datta
Software Mentions: 5
Published: about 7 years ago

10.1186/1471-2105-9-526

SNPFile – A software library and file format for large scale association mapping and population genetics studies
Cited by: 5
Author(s): Jesper Buus Nielsen, Thomas Mailund
Software Mentions: 5
Published: over 15 years ago

10.1038/s41598-021-92610-4

Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction
Cited by: 2
Author(s): Jun-Yan Hong, T.D.C.P. Gunasekara, Cheng He, Sanzhen Liu, Jianqin Huang, Hairong Wei
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13104-020-05180-5

A decision support system based on support vector machine for diagnosis of periodontal disease
Cited by: 31
Author(s): Maryam Farhadian, Parisa Shokouhi, Parviz Torkzaban
Software Mentions: 5
Published: almost 4 years ago

10.1111/1462-2920.15484

Effect of salinity on cable bacteria species composition and diversity
Cited by: 19
Author(s): Ann‐Sofie Dam, Ian P. G. Marshall, Nils Risgaard‐Petersen, Laurine D. W. Burdorf, Ugo Marzocchi
Software Mentions: 5
Published: about 3 years ago

10.1121/1.4976044

Language-independent talker-specificity in first-language and second-language speech production by bilingual talkers: L1 speaking rate predicts L2 speaking rate
Cited by: 26
Author(s): Ann R. Bradlow, Midam Kim, Michael Blasingame
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-018-2485-7

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Cited by: 590
Author(s): Michael J. Roach, Simon A. Schmidt, Anthony R. Borneman
Software Mentions: 4
Published: over 5 years ago

10.1093/database/baw145

Text mining resources for the life sciences
Cited by: 34
Author(s): Piotr Przybyła, Matthew Shardlow, Sophie Aubin, Robert Bossy, Richard Eckart de Castilho, Stelios Piperidis, John McNaught, Sophia Ananiadou
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-020-3427-8

Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data
Cited by: 33
Author(s): Aaron Smith, Jonathan R. Walsh, John M. Long, Craig B. Davis, Peter V. Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek, Charles K. Fisher
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-015-1954-x

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
Cited by: 8
Author(s): David Wragg, Andrew S. Mason, Lejun Yu, Richard Kuo, Raman Akinyanju Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang-Yeon Cho, Stephen J. Kemp, David W. Burt, Olivier Hanotte
Software Mentions: 4
Published: over 8 years ago

10.1111/all.14694

Comparative proteomics of common allergenic tree pollens of birch, alder, and hazel
Cited by: 5
Author(s): Barbara Darnhofer, Tamara Tomin, Laura Liesinger, Matthias Schittmayer, Peter Valentin Tomazic, Ruth Birner‐Gruenberger
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-018-0568-3

Fecal source identification using random forest
Cited by: 85
Author(s): Adélaïde Roguet, A. Murat Eren, Ryan J. Newton, Sandra L. McLellan
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0227076

All of gene expression (AOE): An integrated index for public gene expression databases
Cited by: 29
Author(s): Hidemasa Bono
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0231759

Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation
Cited by: 19
Author(s): J M Bowen, Paul Cormican, S.J. Lister, Matthew S. McCabe, Carol-Anne Duthie, R. Roehe, Richard J. Dewhurst
Software Mentions: 4
Published: about 4 years ago

10.1186/1471-2164-12-402

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
Cited by: 2,222
Author(s): Nabil-Fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour, Scott A. Beatson
Software Mentions: 4
Published: almost 13 years ago

10.1093/gigascience/giz052

Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection
Cited by: 8
Author(s): Toshio Ohta, Tomoya Tanjo, Osamu Ogasawara
Software Mentions: 4
Published: about 5 years ago

10.3390/genes10090714

NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements
Cited by: 13
Author(s): Ryan Connor, Rodney Brister, Jan P. Buchmann, Ward Deboutte, Robert A. Edwards, Joan Martí-Carreras, Michael J. Tisza, Vadim Zalunin, Juan S. Andrade-Martínez, Adrian Cantu, Michael D’Amour, Alexandre Efremov, Lydia Fleischmann, Laura Milena Forero‐Junco, Sanzhima Garmaeva, Melissa Giluso, Cody Glickman, Margaret Henderson, Benjamin P. Kellman, David M. Kristensen, Carl Leubsdorf, Kyle Levi, Shane Levi, Suman B. Pakala, Vikas Peddu, Alise J. Ponsero, Eldred A. Ribeiro, Farrah Roy, Lindsay Rutter, Surya Saha, Migun Shakya, Ryan C. Shean, Matthew Miller, Benjamin J. Tully, Christopher J R Turkington, Ken Youens‐Clark, Bert Vanmechelen, Ben Busby
Software Mentions: 4
Published: over 4 years ago

10.1128/AEM.02343-19

Reintroducing mothur: 10 Years Later
Cited by: 132
Author(s): Patrick D. Schloss
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2014.00223

Characterizing the avian gut microbiota: membership, driving influences, and potential function
Cited by: 297
Author(s): David W. Waite, Michael W. Taylor
Software Mentions: 4
Published: about 10 years ago

10.1186/s13059-020-02012-4

REPIC: a database for exploring the N6-methyladenosine methylome
Cited by: 65
Author(s): Shun Liu, Allen Zhu, Chuan He, Mengjie Chen
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2018.01534

Jellyfish Life Stages Shape Associated Microbial Communities, While a Core Microbiome Is Maintained Across All
Cited by: 24
Author(s): Michael D. Lee, Joshua D. Kling, Rubén Araya, Janja Ceh
Software Mentions: 4
Published: almost 6 years ago

10.1007/s00239-020-09939-z

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila
Cited by: 51
Author(s): Brennen Heames, Julia Schmitz, Erich Bornberg‐Bauer
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1000832

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
Cited by: 238
Author(s): Michael J. Clark, Nils Homer, Brian D. O’Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, Stanley F. Nelson
Software Mentions: 4
Published: over 14 years ago

10.1186/s13058-018-0933-y

HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors
Cited by: 44
Author(s): Anneleen Daemen, Gerard Manning
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2018.00020

Improved circRNA Identification by Combining Prediction Algorithms
Cited by: 123
Author(s): Thomas B. Hansen
Software Mentions: 4
Published: about 6 years ago

10.3389/fimmu.2020.01859

Transcriptional Profiling of CD8+ CMV-Specific T Cell Functional Subsets Obtained Using a Modified Method for Isolating High-Quality RNA From Fixed and Permeabilized Cells
Cited by: 3
Author(s): Zachary R. Healy, Kent J. Weinhold, David M. Murdoch
Software Mentions: 4
Published: over 3 years ago

10.1098/rsos.181453

Behavioural and transcriptional changes in post-mating females of an egg parasitoid wasp species
Cited by: 19
Author(s): Pengcheng Liu, Dejun Hao
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.7548

Genome-resolved insights into a novelSpiroplasmasymbiont of the Wheat Stem Sawfly (Cephus cinctus)
Cited by: 11
Author(s): Carl J. Yeoman, Laura M. Brutscher, Özcan C. Esen, Furkan Ibaoglu, Curtis Fowler, A. Murat Eren, Kevin W. Wanner, David K. Weaver
Software Mentions: 4
Published: over 4 years ago

10.1111/tpj.14179

Computational aspects underlying genome to phenome analysis in plants
Cited by: 47
Author(s): Anthony Bolger, Hendrik Poorter, Kathryn Dumschott, Marie E. Bolger, Daniel Arend, Sonia Osorio, Heidrun Gundlach, Klaus Mayer, Matthias Lange, Uwe Scholz, Björn Usadel
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.10221.1

Integration of EGA secure data access into Galaxy
Cited by: 6
Author(s): Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, J. Dylan Spalding, Sanne Abeln
Software Mentions: 4
Published: over 7 years ago

10.1016/j.ajhg.2019.03.025

Cell-Type Heterogeneity in Adipose Tissue Is Associated with Complex Traits and Reveals Disease-Relevant Cell-Specific eQTLs
Cited by: 76
Author(s): Craig A. Glastonbury, Alexessander Couto Alves, Julia S. El-Sayed Moustafa, Kerrin S. Small
Software Mentions: 4
Published: almost 5 years ago

10.1136/rmdopen-2020-001324

Current status of use of high throughput nucleotide sequencing in rheumatology
Cited by: 2
Author(s): Sebastian Boegel, John C. Castle, Andreas Schwarting
Software Mentions: 4
Published: over 3 years ago

10.1016/j.jbc.2021.100743

From integrative structural biology to cell biology
Cited by: 38
Author(s): Andrej Šali
Software Mentions: 3
Published: over 3 years ago

10.1016/j.dib.2019.104172

Data describing the effects of depletion of Myoparr, myogenin, Ddx17, and hnRNPK in differentiating C2C12 cells
Cited by: 3
Author(s): Keisuke Hitachi, Kunihiro Tsuchida
Software Mentions: 3
Published: almost 5 years ago

10.1093/gigascience/giab017

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis
Cited by: 10
Author(s): Anton Zamyatin, Pavel Avdeyev, Jiangtao Liang, Atashi Sharma, Chujia Chen, Varvara Lukyanchikova, Nikita Alexeev, Zhijian Tu, Max A. Alekseyev, Igor V. Sharakhov
Software Mentions: 3
Published: about 3 years ago

10.1186/s12866-016-0694-7

Influence of periparturient and postpartum diets on rumen methanogen communities in three breeds of primiparous dairy cows
Cited by: 24
Author(s): Laura M. Cersosimo, Melissa L. Bainbridge, Jana Kraft, André Denis G. Wright
Software Mentions: 3
Published: about 8 years ago

10.1080/19490976.2021.1919464

A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects
Cited by: 6
Author(s): Marta Pérez, Alexandra Ntemiri, Huizi Tan, Hugh M. B. Harris, Henrik Munch Roager, Céline Ribière, Paul W. O’Toole
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-14-S14-S5

A cross disciplinary study of link decay and the effectiveness of mitigation techniques
Cited by: 29
Author(s): Jason Hennessey, Xijin Ge
Software Mentions: 3
Published: over 10 years ago

10.1080/19490976.2021.1930872

A microbial signature following bariatric surgery is robustly consistent across multiple cohorts
Cited by: 14
Author(s): Farnaz Fouladi, Ian M. Carroll, Thomas J. Sharpton, Emily C. Bulik-Sullivan, Leslie J. Heinberg, Kristine J. Steffen, Anthony A. Fodor
Software Mentions: 3
Published: over 3 years ago

10.1093/gigascience/giy070

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data
Cited by: 21
Author(s): Lukas M. Simon, Sebastian Karg, Alexander J. Westermann, Marion Engel, Ali H. A. Elbehery, Burkhard A. Hense, Matthias Heinig, Li Deng, Fabian J. Theis
Software Mentions: 3
Published: almost 6 years ago

10.1007/s00018-021-03865-z

Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data
Cited by: 14
Author(s): Robin Herbrechter, Nadine Hube, Raoul Buchholz, Andreas Reiner
Software Mentions: 3
Published: almost 3 years ago

10.1186/s12864-015-2240-7

Transcriptional cellular responses in midgut tissue of Aedes aegypti larvae following intoxication with Cry11Aa toxin from Bacillus thuringiensis
Cited by: 24
Author(s): Pablo Emiliano Cantón, Angeles Cancino-Rodezno, Sarjeet S. Gill, Mário Soberón, Alejandra Bravo
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-021-02490-0

STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions
Cited by: 35
Author(s): Kenneth S. Katz, Oleg Shutov, Richard T. Lapoint, Michael Kimelman, J. Rodney Brister, Christopher D. O’Sullivan
Software Mentions: 3
Published: over 2 years ago

10.1016/j.gpb.2017.01.001

GSA: Genome Sequence Archive *
Cited by: 465
Author(s): Yanqing Wang, Fuhai Song, Junwei Zhu, Sisi Zhang, Yadong Yang, Tingting Chen, Bixia Tang, Lili Dong, Nan Ding, Qian Zhang, Zhouxian Bai, Xunong Dong, Huanxin Chen, Mingyuan Sun, Shuang Zhai, Yuan Sun, Lei Yu, Lan Li, Jingfa Xiao, Xiangdong Fang, Hongxing Lei, Zhang Zhang, Wenming Zhao
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giaa138

iGenomics: Comprehensive DNA sequence analysis on your Smartphone
Cited by: 17
Author(s): Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz
Software Mentions: 3
Published: over 3 years ago

10.1007/s10278-018-0097-4

Reengineering Workflow for Curation of DICOM Datasets
Cited by: 16
Author(s): William Bennett, Kirk E. Smith, Quasar Jarosz, Tracy S. Nolan, Walter Bosch
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-014-0572-2

De novo assembly of bacterial transcriptomes from RNA-seq data
Cited by: 764
Author(s): Brian Tjaden
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0218085

De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages
Cited by: 23
Author(s): C. Rozenfeld, José Blanca, Víctor Gallego, Victor García‐Carpintero, J.G. Herranz-Jusdado, Luz Pérez, Juan F. Asturiano, Joaquı́n Cañizares, David S. Peñaranda
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-016-1118-6

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Cited by: 91
Author(s): Abhinav Nellore, Andrew E. Jaffe, Jean‐Philippe Fortin, José Alquicira-Hernández, Leonardo Collado‐Torres, Siruo Wang, Robert A. Phillips, Nishika Karbhari, Kasper D. Hansen, Ben Langmead, Jeffrey T. Leek
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-019-6223-y

Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process
Cited by: 23
Author(s): Rannyele Passos Ribeiro, Guillermo Ponz‐Segrelles, Christoph Bleidorn, M. Teresa Aguado
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0240178

Occurrence of Brucella ceti in striped dolphins from Italian Seas
Cited by: 14
Author(s): Giuliano Garofolo, A. Petrella, Giuseppe Lucifora, Gabriella Di Francesco, Giovanni Di Guardo, Alessandra Pautasso, Barbara Iulini, Katia Varello, Federica Giorda, Maria Goria, Alessandro Dondo, Simona Zoppi, Cristina Esmeralda Di Francesco, Stefania Giglio, Furio Ferringo, Luigina Serrecchia, Mattia Anna Rita Ferrantino, Katiuscia Zilli, Anna Janowicz, Manuela Tittarelli, Walter Mignone, Cristina Casalone, Carla Grattarola
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0173392

Developing a benchmark for emotional analysis of music
Cited by: 118
Author(s): Anna Aljanaki, Yi Yang, Mohammad Soleymani
Software Mentions: 3
Published: about 7 years ago

10.1186/s13059-019-1883-0

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads
Cited by: 11
Author(s): Laura H. Tung, Mingfu Shao, Carl Kingsford
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2017.02366

Combination of Classifiers Identifies Fungal-Specific Activation of Lysosome Genes in Human Monocytes
Cited by: 3
Author(s): J. Saraiva, Cristina Zubiría-Barrera, Tilman E. Klassert, Maximilian Julius Lautenbach, Markus Blaess, Ralf A. Claus, Hortense Slevogt, Rainer König
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0226708

Wattpad as a resource for literary studies. Quantitative and qualitative examples of the importance of digital social reading and readers’ comments in the margins
Cited by: 32
Author(s): Federico Pianzola, Simone Rebora, Gerhard Lauer
Software Mentions: 3
Published: over 4 years ago

10.1186/gb-2012-13-4-r31

Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Cited by: 33
Author(s): Marieke Simonis, Santosh S. Atanur, Sam E.V. Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Gamé, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven J.M. Jones, Michal Pravenec, Tim Aitman, Edwin Cuppen
Software Mentions: 3
Published: over 12 years ago

10.1002/mp.14322

FAIR‐compliant clinical, radiomics and DICOM metadata of RIDER, interobserver, Lung1 and head‐Neck1 TCIA collections
Cited by: 16
Author(s): Petros Kalendralis, Zhenwei Shi, Alberto Traverso, Ananya Choudhury, Matthijs Sloep, Ivan Zhovannik, Martijn P.A. Starmans, Detlef Grittner, Peter Feltens, R. Monshouwer, Stefan Klein, Rianne Fijten, Hugo J.W.L. Aerts, André Dekker, Johan van Soest, Leonard Wee
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2020.579802

A Biological Inventory of Prophages in A. baumannii Genomes Reveal Distinct Distributions in Classes, Length, and Genomic Positions
Cited by: 32
Author(s): Belinda Loh, Jiayuan Chen, Prasanth Manohar, Yunsong Yu, Xiaoting Hua, Sebastian Leptihn
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0253830

High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
Cited by: 20
Author(s): Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin O. Borevitz, Benjamin Schwessinger
Software Mentions: 3
Published: almost 3 years ago

10.1186/s12864-016-3287-9

AnnoLnc: a web server for systematically annotating novel human lncRNAs
Cited by: 43
Author(s): Mei Hou, Xing Tang, Feng Tian, Fang-Yuan Shi, Fenglin Liu, Ge Gao
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0233170

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing
Cited by: 10
Author(s): William Taylor, John Pearson, Allison L. Miller, Sebastian Schmeier, Frank Frizelle, Rachel Purcell
Software Mentions: 3
Published: about 4 years ago

10.1186/s12862-017-1066-0

Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)
Cited by: 51
Author(s): Jessica A. Goodheart, Adam L. Bazinet, Ángel Valdés, Allen G. Collins, Michael P. Cummings
Software Mentions: 3
Published: over 6 years ago

Projects: pypi: Archive

Papers Mentioning Archive 363