Ecosyste.ms: Papers

10.1186/s12864-016-2463-2

Improvement in detection of minor alleles in next generation sequencing by base quality recalibration
Cited by: 7
Author(s): Shengyu Ni, Mark Stoneking
Software Mentions: 3
Published: over 8 years ago

10.1038/srep38907

CircRNA accumulation in the aging mouse brain
Cited by: 270
Author(s): Hannah N. Gruner, Mariela Cortés-López, Daphne A. Cooper, Matthew Bauer, Pedro Miura
Software Mentions: 3
Published: almost 8 years ago

10.1038/srep39749

An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus
Cited by: 13
Author(s): James A. Cotton, Sascha Steinbiss, Toshiro Yokoi, Isheng Jason Tsai, Taisei Kikuchi
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-017-17081-y

Deep mutational scanning of S. pyogenes Cas9 reveals important functional domains
Cited by: 30
Author(s): Jeffrey M. Spencer, Xiaoliu Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-31074-5

Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis
Cited by: 13
Author(s): David J. X. Tan, Balaji Chattopadhyay, Kritika M. Garg, Emilie Cros, Per G. P. Ericson, Martin Irestedt
Software Mentions: 3
Published: about 6 years ago

10.3390/cells8101169

Aging Triggers H3K27 Trimethylation Hoarding in the Chromatin of Nothobranchius furzeri Skeletal Muscle
Cited by: 14
Author(s): Chiara Cencioni, Johanna Heid, Anna Krepelova, Seyed Mohammad Mahdi Rasa, Carsten Kuenne, Stefan Guenther, Mario Baumgart, Alessandro Cellerino, Francesco Neri, Francesco Spallotta, Carlo Gaetano
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-019-0311-3

Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta
Cited by: 21
Author(s): Robert Nowak, J Jastrzebski, Wiktor Kuśmirek, Rusłan Sałamatin, Małgorzata Rydzanicz, Agnieszka Sobczyk-Kopcioł, Anna Sulima-Celińska, Łukasz Paukszto, Karol G Makowczenko, Rafał Płoski, Vasyl V. Tkach, Katarzyna Basałaj, Daniel Młocicki
Software Mentions: 3
Published: almost 5 years ago

10.1093/cercor/bhv136

Hierarchical Organization of Auditory and Motor Representations in Speech Perception: Evidence from Searchlight Similarity Analysis
Cited by: 111
Author(s): Samuel Evans, Matthew H. Davis
Software Mentions: 3
Published: over 9 years ago

10.1073/pnas.2022702118

Photosynthesis-independent production of reactive oxygen species in the rice bundle sheath during high light is mediated by NADPH oxidase
Cited by: 24
Author(s): Haiyan Xiong, Lei Hua, Ivan Reyna-Llorens, Yi Shi, Kun-Ming Chen, Nicholas Smirnoff, Johannes Kromdijk, Julian M. Hibberd
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1004795

The Aspartate-Less Receiver (ALR) Domains: Distribution, Structure and Function
Cited by: 25
Author(s): Andrew J. Maule, David P. Wright, Joshua Weiner, Lu Han, Francis C. Peterson, Brian F. Volkman, N.R. Silvaggi, Andrew T. Ulijasz
Software Mentions: 3
Published: over 9 years ago

10.1111/j.1365-2052.2011.02273.x

Genome‐wide association analysis for feed efficiency in Angus cattle
Cited by: 89
Author(s): Megan M Rolf, Taylor Jf, Robert D. Schnabel, Stephanie McKay, Matthew McClure, S. L. Northcutt, M. S. Kerley, R. L. Weaber
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.ppat.1003037

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Cited by: 489
Author(s): Robin A. Ohm, Nicolas Feau, Bernard Henrissat, Conrad L. Schoch, Benjamin A. Horwitz, Kerrie Barry, Bradford Condon, Alex Copeland, Braham Dhillon, Fabian Glaser, Cedar Hesse, Idit Kosti, Kurt LaButti, Erika Lindquist, Susan Lucas, Asaf Salamov, Rosie E. Bradshaw, Lynda M. Ciuffetti, Richard Hamelin, G.H.J. Kema, Christopher B. Lawrence, James A. Scott, Joseph W. Spatafora, B. Gillian Turgeon, P.J.G.M. de Wit, Shaobin Zhong, Stephen B. Goodwin, Igor V. Grigoriev
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.ppat.1005166

Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Cited by: 12
Author(s): Seth B. Garren, Yuvabharath Kondaveeti, Michael O. Duff, Gordon G. Carmichael
Software Mentions: 3
Published: about 9 years ago

10.1016/j.xpro.2021.100544

Preparation of the intact rodent organ of Corti for RNAscope and immunolabeling, confocal microscopy, and quantitative analysis
Cited by: 1
Author(s): Daniël O. J. Reijntjes, J. Lukas Breitzler, Dora Persic, Sonja J. Pyott
Software Mentions: 3
Published: over 3 years ago

10.3390/jcm8091291

Identification of a Shared Microbiomic and Metabolomic Profile in Systemic Autoimmune Diseases
Cited by: 32
Author(s): Chiara Bellocchi, Álvaro Fernández-Ochoa, Gaia Montanelli, Barbara Vigone, Alessandro Santaniello, Rosa Quirantes-Piné, Isabel Borrás-Linares, Maria Gerosa, Carolina Artusi, Roberta Gualtierotti, Antonio Segura-Carrettero, Marta E. Alarcón‐Riquelme, Lorenzo Beretta
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1002962

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals
Cited by: 119
Author(s): Frank W. Albert, Mehmet Somel, Miguel Carneiro, Ayinuer Aximu‐Petri, Michael Halbwax, Olaf Thalmann, José Antonio Blanco‐Aguiar, I. Z. Plyusnina, Lyudmila N. Trut, Rafael Villafuerte, Nuno Ferrand, Sylvia Kaiser, Per Jensen, Svante Pääbo
Software Mentions: 3
Published: about 12 years ago

10.1128/JCM.01945-16

The EpiQuant Framework for Computing Epidemiological Concordance of Microbial Subtyping Data
Cited by: 2
Author(s): Benjamin M. Hetman, Steven K. Mutschall, James E. Thomas, Victor P. J. Gannon, Clifford G. Clark, Frank Pollari, Eduardo N. Taboada
Software Mentions: 3
Published: over 7 years ago

10.3390/insects12020167

A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
Cited by: 29
Author(s): John H. Boyle, Pasi Rastas, Xin Huang, Austin G. Garner, Indra Vythilingam, Peter Armbruster
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12862-015-0534-7

A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels
Cited by: 86
Author(s): Gianni Monaco, Sipko van Dam, João Luis Casal Novo Ribeiro, Anis Larbi, João Pedro de Magalhães
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pgen.1004223

Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species
Cited by: 87
Author(s): Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Manabu Kume, Seiichi Mori, Catherine L. Peichel, Atsushi Toyoda, Asao Fujiyama, Jun Kitano
Software Mentions: 3
Published: over 10 years ago

10.1016/j.celrep.2018.07.104

Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3′ End RNA-Seq
Cited by: 9
Author(s): Manfred Schmid, Agnieszka Tudek, Torben Heick Jensen
Software Mentions: 3
Published: over 6 years ago

10.3390/biomedicines8020019

A Multi-Omics Analysis of Bone Morphogenetic Protein 5 (BMP5) mRNA Expression and Clinical Prognostic Outcomes in Different Cancers Using Bioinformatics Approaches
Cited by: 23
Author(s): Md. Adnan Karim, Abdus Samad, Utpal Adhikari, Md. Ashraful Kader, Md. Masnoon Kabir, Md. Aminul Islam, Md. Nazmul Hasan
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.chom.2018.06.011

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales
Cited by: 124
Author(s): Talia L. Karasov, Juliana Almario, Claudia Friedemann, Wei Ding, Michael Giolai, Darren Heavens, Sonja Kersten, Derek S. Lundberg, Manuela Neumann, Julián Regalado, Richard A. Neher, Eric Kemen, Detlef Weigel
Software Mentions: 3
Published: over 6 years ago

10.1002/hbm.25418

Graph theoretical analysis of evoked potentials shows network influence of epileptogenic mesial temporal region
Cited by: 10
Author(s): Mark Hays, Christopher Coogan, Nathan E. Crone, Joon Y. Kang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1002864

Genome-Wide Analysis of Germline Signaling Genes Regulating Longevity and Innate Immunity in the Nematode Pristionchus pacificus
Cited by: 24
Author(s): Robbie Rae, Amit Sinha, Ralf J. Sommer
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-018-36921-z

Whole Transcriptome Analysis of Renal Intercalated Cells Predicts Lipopolysaccharide Mediated Inhibition of Retinoid X Receptor alpha Function
Cited by: 13
Author(s): Vijay Saxena, James Fitch, John Ketz, Peter White, Amy Wetzel, Melinda A. Chanley, John David Spencer, Brian Becknell, Keith R. Pierce, Sam W. Arregui, Raoul D. Nelson, George J. Schwartz, Victoria M. Velazquez, Logan A. Walker, Xi Chen, Pearlly S. Yan, David S. Hains, Andrew L. Schwaderer
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41398-019-0538-y

Temporal dynamics of miRNAs in human DLPFC and its association with miRNA dysregulation in schizophrenia
Cited by: 24
Author(s): Zhonghua Hu, Shaojian Gao, Daniel M. Lindberg, Debabrata Panja, Yoshi Wakabayashi, Keshen Li, Joel E. Kleinman, Jun Zhu, Zheng Li
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0129016

De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes
Cited by: 22
Author(s): Yevgen Zolotarov, Martina V. Strömvik
Software Mentions: 3
Published: over 9 years ago

10.1093/gbe/evz053

Sex-Biased Gene Expression and Dosage Compensation on the<i>Artemia franciscana</i>Z-Chromosome
Cited by: 22
Author(s): Ann Kathrin Huylmans, Melissa A. Toups, Ariana Macon, William J Gammerdinger, Beatriz Vicoso
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1009270

Physiological and genetic convergence supports hypoxia resistance in high-altitude songbirds
Cited by: 10
Author(s): Ying Xiong, Liqing Fan, Yan Hao, Yalin Cheng, Ying Chang, Jing Wang, Haiyan Lin, Gang Song, Yanhua Qu, Fumin Lei
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-021-02449-1

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
Cited by: 12
Author(s): Deepak Thirunavukarasu, Lauren Y. Cheng, Ping Song, Sherry X. Chen, Mitesh J. Borad, Lawrence N. Kwong, Phillip James, Daniel J. Turner, David Y. Zhang
Software Mentions: 3
Published: about 3 years ago

10.1093/gbe/evw291

Variation in the intensity of selection on codon bias over time causes contrasting patterns of base composition evolution in <i>Drosophila</i>
Cited by: 26
Author(s): Benjamin C. Jackson, José Luis Campos, Penelope R. Haddrill, Brian Charlesworth, Kai Zeng
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13059-015-0749-3

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength
Cited by: 77
Author(s): Vihandha O. Wickramasinghe, Mar Gonzàlez-Porta, David Perera, Arthur R. Bartolozzi, Christopher R. Sibley, Martina Hallegger, Jernej Ule, John C. Marioni, Ashok R. Venkitaraman
Software Mentions: 3
Published: about 9 years ago

10.1186/1745-6150-3-22

Classifying transcription factor targets and discovering relevant biological features
Cited by: 10
Author(s): Dustin T. Holloway, Mark A. Kon, Charles DeLisi
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0059831

Construction of Customized Sub-Databases from NCBI-nr Database for Rapid Annotation of Huge Metagenomic Datasets Using a Combined BLAST and MEGAN Approach
Cited by: 48
Author(s): Ke Yu, Tong Zhang
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pcbi.1008732

Positive interactions within and between populations decrease the likelihood of evolutionary rescue
Cited by: 4
Author(s): Yaron Goldberg, Jonathan Friedman
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0044255

System Wide Analysis of the Evolution of Innate Immunity in the Nematode Model Species Caenorhabditis elegans and Pristionchus pacificus
Cited by: 49
Author(s): Amit Sinha, Robbie Rae, Igor Iatsenko, Ralf J. Sommer
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pcbi.1007074

Perturbing low dimensional activity manifolds in spiking neuronal networks
Cited by: 20
Author(s): Emil Wärnberg, Arvind Kumar
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-014-0551-7

Transcriptome-wide modulation of splicing by the exon junction complex
Cited by: 75
Author(s): Zhen Wang, Valentine Murigneux, Hervé Le Hir
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12915-021-00995-5

Plasmodium vinckei genomes provide insights into the pan-genome and evolution of rodent malaria parasites
Cited by: 8
Author(s): Abhinay Ramaprasad, Severina Klaus, Olga Douvropoulou, Richard Culleton, Arnab Pain
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0244110

Motion fluency effects on object preference is limited to learned context
Cited by: 0
Author(s): Jonathan Flavell, Bryony McKean
Software Mentions: 3
Published: almost 4 years ago

10.3390/genes8110310

Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies
Cited by: 18
Author(s): Tasha M. Santiago-Rodríguez, Gino Fornaciari, Stefania Luciani, Gary A. Toranzos, Isolina Marota, Valentina Giuffra, Raúl J. Cano
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0036456

Determining the Repertoire of Immunodominant Proteins via Whole-Genome Amplification of Intracellular Pathogens
Cited by: 12
Author(s): Michael J. Dark, Anna Lundgren, Anthony F. Barbet
Software Mentions: 3
Published: over 12 years ago

10.1093/aobpla/plaa003

Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas
Cited by: 17
Author(s): Amanda R. Silva, Luciana C. Resende‐Moreira, Carolina da Silva Carvalho, Éder Cristian Malta de Lanes, Mabel Ortiz-Vera, Pedro Lage Viana, Rodolfo Jaffé
Software Mentions: 3
Published: almost 5 years ago

10.1534/g3.120.401124

<i>Escherichia coli</i> with a Tunable Point Mutation Rate for Evolution Experiments
Cited by: 3
Author(s): Nicholas Sherer, Thomas E. Kuhlman
Software Mentions: 3
Published: over 4 years ago

10.3390/genes11070787

Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
Cited by: 11
Author(s): Cécile Fruchard, Hélène Badouin, David Latrasse, Ravi Suresh Devani, Aline Muyle, Bénédicte Rhoné, Susanne S. Renner, Anjan K. Banerjee, Abdelhafid Bendahmane, Gabriel Marais
Software Mentions: 3
Published: over 4 years ago

10.1186/1752-0509-1-56

Gene regulatory networks in lactation: identification of global principles using bioinformatics
Cited by: 124
Author(s): Danielle G. Lemay, Margaret C. Neville, Michael C. Rudolph, Katherine S. Pollard, J. Bruce German
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pcbi.1006933

An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis
Cited by: 12
Author(s): Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C Denis, George Kollias, Christoforos Nikolaou
Software Mentions: 3
Published: over 5 years ago

10.1534/g3.117.043471

Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm
Cited by: 34
Author(s): Mathieu Siol, Françoise Jacquin, Marianne Chabert-Martinello, Petr Smýkal, Marie‐Christine Le Paslier, Grégoire Aubert, Judith Burstin
Software Mentions: 3
Published: over 7 years ago

10.1534/g3.117.300318

Pas de deux: An Intricate Dance of Anther Smut and Its Host
Cited by: 5
Author(s): Su San Toh, Zehua Chen, Eric C. Rouchka, David J. Schultz, Christina A. Cuomo, Michael H. Perlin
Software Mentions: 3
Published: almost 7 years ago

10.1534/g3.115.019703

SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops
Cited by: 61
Author(s): Josh Clevenger, Peggy Ozias‐Akins
Software Mentions: 3
Published: about 9 years ago

10.1534/g3.115.017178

A Powerful New Quantitative Genetics Platform, Combining<i>Caenorhabditis elegans</i>High-Throughput Fitness Assays with a Large Collection of Recombinant Strains
Cited by: 99
Author(s): Erik C. Andersen, Tyler C. Shimko, Jonathan R. Crissman, Rajarshi Ghosh, Joshua S. Bloom, Hannah S. Seidel, Justin P. Gerke, Leonid Kruglyak
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pbio.2002690

Common genes associated with antidepressant response in mouse and man identify key role of glucocorticoid receptor sensitivity
Cited by: 26
Author(s): Tania Carrillo-Roa, Christiana Labermaier, Peter Weber, David P. Herzog, Caleb A. Lareau, Sara Santarelli, Klaus V. Wagner, Monika Rex‐Haffner, D. Harbich, Sebastian H. Scharf, Charles B. Nemeroff, Boadie W. Dunlop, W. Edward Craighead, Helen S. Mayberg, Mathias Schmidt, Manfred Uhr, Florian Holsboer, Inge Sillaber, Elisabeth B. Binder, Marianne B. Müller
Software Mentions: 3
Published: almost 7 years ago

10.1093/aobpla/plz019

Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F1 hybrid
Cited by: 5
Author(s): Wei Lun Ng, Wei Wu, Peishan Zou, Renchao Zhou
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0204629

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing
Cited by: 64
Author(s): Simon Poirier, Olivier Rué, R. Peguilhan, Gwendoline Coeuret, Monique Zagorec, Marie‐Christine Champomier‐Vergès, Valentin Loux, Stéphane Chaillou
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0147229

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing
Cited by: 30
Author(s): James A. Stapleton, Jeongwoon Kim, John Hamilton, Ming Wu, Luiz Irber, Rohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R. Burton, C. Titus Brown, Christina Chan, C. Robin Buell, Timothy A. Whitehead
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2021.703283

Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil
Cited by: 10
Author(s): Rama Harinath Reddy Dadu, Ido Bar, Rebecca Ford, Prabhakaran Thanjavur Sambasivam, Janine Croser, Federico M. Ribalta, Sukhjiwan Kaur, Shimna Sudheesh, Dorin Gupta
Software Mentions: 3
Published: about 3 years ago

10.3389/fpls.2017.00391

Phylogeny Predicts the Quantity of Antimalarial Alkaloids within the Iconic Yellow Cinchona Bark (Rubiaceae: Cinchona calisaya)
Cited by: 35
Author(s): Carla Maldonado, Christopher J. Barnes, Claus Cornett, Else Holmfred, Steen Honoré Hansen, Claes Persson, Alexandre Antonelli, Nina Rønsted
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-016-0858-5

Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease
Cited by: 43
Author(s): Federico Martinelli, Russell L. Reagan, David Dolan, Veronica Fileccia, Abhaya M. Dandekar
Software Mentions: 3
Published: over 8 years ago

10.1111/pbi.12772

A toolkit for <i>Nannochloropsis oceanica </i><scp>CCMP</scp>1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long‐chain polyunsaturated fatty acid production
Cited by: 101
Author(s): Eric Poliner, Jane A. Pulman, Krzysztof Zienkiewicz, Kevin L. Childs, Christoph Benning, Eva M. Farré
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0222323

Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation
Cited by: 16
Author(s): Mariana E. Kirst, Dawn Baker, Eric Li, Mutasim Abu-Hasan, Gary P. Wang
Software Mentions: 3
Published: about 5 years ago

10.1111/pbi.12940

Chromosome‐based survey sequencing reveals the genome organization of wild wheat progenitor <i>Triticum dicoccoides</i>
Cited by: 27
Author(s): Bala Anı Akpınar, Sezgi Biyiklioglu, Burcu Alptekin, M. Havránková, Jan Vrána, Jaroslav Doležel, Assaf Distelfeld, Pilar Hernández, Hikmet Budak
Software Mentions: 3
Published: over 6 years ago

10.3389/fped.2021.618009

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation
Cited by: 33
Author(s): Marielle Nguyen, Heaven Holdbrooks, Prasanthi K. Mishra, Maria Abrantes, Sherri Eskew, Mariajamiela Garma, Cyr-Geraurd Oca, Carrie McGuckin, Cynthia B. Hein, Ryan D. Mitchell, Sufyan Kazi, Stephanie Chew, Giorgio Casaburi, Heather K. Brown, Steven A. Frese, Bethany M. Henrick
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0177742

Using NextRAD sequencing to infer movement of herbivores among host plants
Cited by: 18
Author(s): Zhen F. Fu, Brendan Epstein, Joanna L. Kelley, Qi Zheng, Alan O. Bergland, Carmen I. Castillo Carrillo, Andrew S. Jensen, Jennifer Dahan, Alexander V. Karasev, William E. Snyder
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0054664

Whole Genome Gene Expression Analysis Reveals Casiopeína-Induced Apoptosis Pathways
Cited by: 31
Author(s): Alejandra Idan Valencia-Cruz, Laura Uribe-Figueroa, Rodrigo Galindo‐Murillo, Karol Baca-López, Anllely Grizett Gutiérrez, Adriana Vázquez-Aguirre, Lena Ruíz-Azuara, Enrique Hernández‐Lemus, Carmen Mejía
Software Mentions: 3
Published: almost 12 years ago

10.1186/1745-6150-9-20

A new rhesus macaque assembly and annotation for next-generation sequencing analyses
Cited by: 150
Author(s): Aleksey V. Zimin, Adam Cornish, Mnirnal D Maudhoo, Robert Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T. Meehan, Kristin Wipfler, Steven E. Bosinger, Zachary P. Johnson, Gregory K. Tharp, Guillaume Marçais, Michael R. Roberts, Betsy Ferguson, Howard S. Fox, Todd J. Treangen, Steven L. Salzberg, James A. Yorke, Robert B. Norgren
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0236126

Impact of processing method on donated human breast milk microRNA content
Cited by: 24
Author(s): Urszula Smyczyńska, Marcin A. Bartłomiejczyk, Marcin Stańczak, Paweł Sztromwasser, Aleksandra Wesołowska, Olga Barbarska, Emilia Pawlikowska, Wojciech Fendler
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2229-13-228

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing
Cited by: 40
Author(s): Jin Zhang, Tracey A. Ruhlman, Jeffrey P. Mower, Robert K. Jansen
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0229326

Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak
Cited by: 1
Author(s): Marjolein J Poen, Anne Pohlmann, Clara Amid, Theo M. Bestebroer, Sharon M Brookes, Ian H. Brown, Helen Everett, Claudia M. E. Schapendonk, Rachel D Scheuer, Saskia L. Smits, Martin Beer, Ron A. M. Fouchier, Richard J. Ellis
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1006157

Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids
Cited by: 86
Author(s): Andreas F. Kautt, Gonzalo Machado‐Schiaffino, Axel Meyer
Software Mentions: 3
Published: over 8 years ago

10.3389/fonc.2020.00757

Integration of Digital Pathologic and Transcriptomic Analyses Connects Tumor-Infiltrating Lymphocyte Spatial Density With Clinical Response to BRAF Inhibitors
Cited by: 9
Author(s): Artūras Žiemys, Michelle Kim, Alexander M. Menzies, James S. Wilmott, Georgina V. Long, Richard A. Scolyer, Larry Kwong, Ashley M. Holder, Genevieve M. Boland
Software Mentions: 3
Published: over 4 years ago

10.1534/g3.119.400972

Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon
Cited by: 21
Author(s): Garrett J. McKinney, Megan V. McPhee, Carita E. Pascal, James E. Seeb, Lisa W. Seeb
Software Mentions: 3
Published: over 4 years ago

10.1093/gigascience/giz069

Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa)
Cited by: 36
Author(s): Aki Ohdera, Cheryl Lewis Ames, Rebecca B. Dikow, Ehsan Kayal, Marta Chiodin, Ben Busby, Sean La, Stacy Pirro, Allen G. Collins, Mónica Medina, Joseph F. Ryan
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0049455

Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species
Cited by: 104
Author(s): Susan Joseph, Prerak Desai, Yongmei Ji, Craig Cummings, Pei-Ju Rita Shih, Lovorka Degoricija, Alain Rico, Pius Brzoska, Stephen E. Hamby, Naqash Masood, Sumyya Hariri, Hana Sonbol, Nadia Chuzhanova, Michael McClelland, Manohar R. Furtado, Stephen Forsythe
Software Mentions: 3
Published: about 12 years ago

10.3389/fmicb.2017.02485

Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors
Cited by: 66
Author(s): Raymond Kiu, Shabhonam Caim, Sarah Alexander, Purnima Pachori, Lindsay J. Hall
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0149531

Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage
Cited by: 34
Author(s): Sigisfredo Garnica, Kai Riess, Max Emil Schön, Franz Oberwinkler, Sabrina Setaro
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2017.01695

AR-13, a Celecoxib Derivative, Directly Kills Francisella In Vitro and Aids Clearance and Mouse Survival In Vivo
Cited by: 4
Author(s): Ky V. Hoang, Haley E. Adcox, James Fitch, David Gordon, Heather M. Curry, Larry S. Schlesinger, Peter White, John S. Gunn
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2016.00941

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field
Cited by: 23
Author(s): Donato Giovannelli, Giuseppe d’Errico, Federica Fiorentino, Daniele Fattorini, Francesco Regoli, Lorenzo Angeletti, Tatjana Bakran‐Petricioli, Costantino Vetriani, Mustafa Yücel, Marco Taviani, Elena Manini
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0236684

Distinct patterns of activity in individual cortical neurons and local networks in primary somatosensory cortex of mice evoked by square-wave mechanical limb stimulation
Cited by: 2
Author(s): Mischa V Bandet, Bin Dong, Ian R. Winship
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2017.01008

Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants
Cited by: 44
Author(s): Christopher J. Stewart, Nicholas D. Embleton, Elizabeth Clements, Pamela N. Luna, Daniel P. Smith, Tatiana Fofanova, Andrew Nelson, Gillian Taylor, Caroline Orr, Joseph F. Petrosino, Janet Berrington, Stephen Cummings
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0216565

Faecal microbiota changes associated with the moult fast in chinstrap and gentoo penguins
Cited by: 7
Author(s): Won Young Lee, Hyunjun Cho, Min‐Cheol Kim, Binu M. Tripathi, Jin-Woo Jung, Hosung Chung, Jeong-Hoon Kim
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers11101410

An IKK/NF-κB Activation/p53 Deletion Sequence Drives Liver Carcinogenesis and Tumor Differentiation
Cited by: 3
Author(s): Michael Svinarenko, Sarah‐Fee Katz, Umesh Tharehalli, Medhanie Mulaw, Harald J. Maier, Yoshiaki Sunami, Sarah Fischer, Yuexin Chen, Sabine Heurich, Lena Erkert, Andrea Tannapfel, Thomas Wirth, Reinhold Schirmbeck, Thomas Seufferlein, André Lechel
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.3819

Human agency beliefs influence behaviour during virtual social interactions
Cited by: 24
Author(s): Nathan Caruana, Dean Spirou, Jon Brock
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2016.01759

Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates
Cited by: 32
Author(s): Taya Forde, Karin Orsel, Ruth N. Zadoks, Roman Biek, Layne G. Adams, Sylvia Checkley, Tracy Davison, Jeroen De Buck, Mathieu Dumond, Brett Elkin, Laura Finnegan, Bryan Macbeth, Cait Nelson, Amanda Niptanatiak, Shane Sather, Helen Schwantje, Frank van der Meer, Susan Kutz
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0083504

RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Cited by: 43
Author(s): Stefano Capomaccio, Nicola Vitulo, Andrea Verini-Supplizi, Gianni Barcaccia, Alessandro Albiero, Michela D’Angelo, Davide Campagna, Giorgio Valle, Michela Felicetti, Maurizio Silvestrelli, Katia Cappelli
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0074256

Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms
Cited by: 90
Author(s): Federico Martinelli, Russell L. Reagan, Sandra L. Uratsu, My L. Phu, Ute Albrecht, Wenwei Zhao, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 3
Published: about 11 years ago

10.3389/fmicb.2020.00377

A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC)
Cited by: 14
Author(s): Barbara K. Zehentner, Zachary Ardern, Michaela Kreitmeier, Stephen W. Scherer, Klaus Neuhaus
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.631250

Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
Cited by: 12
Author(s): Dayong Han, Pei‐Jie Han, Karl Rumbold, Anbessa Dabassa Koricha, Shoufu Duan, Liang Song, Junyan Shi, Kuan Li, Qiming Wang, Feng‐Yan Bai
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-017-3574-0

The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases
Cited by: 33
Author(s): Lucas Luciano Maldonado, Juliana de Assis, Flávio Marcos Gomes Araújo, Anna C. M. Salim, Natalia Macchiaroli, Marcela Alejandra Cucher, Federico Camicia, Adolfo Fox, Mara Cecília Rosenzvit, Guilherme Oliveira, Laura Kamenetzky
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0156723

Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
Cited by: 76
Author(s): Xuke Lu, Xiugui Chen, Mingchun Mu, Junjuan Wang, Xiaoge Wang, Delong Wang, Zujun Yin, Weili Fan, Shuai Wang, Lixue Guo, Wuwei Ye
Software Mentions: 3
Published: over 8 years ago

10.1186/s12879-019-4566-2

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia
Cited by: 12
Author(s): Allison Black, Louise H. Moncla, Katherine Laiton‐Donato, Barney Potter, Lissethe Pardo, Angélica Rico, Catalina Tovar, Diana Patricia Rojas, Ira M. Longini, M. Elizabeth Halloran, Dioselina Peláez-Carvajal, Juan David Ramírez, Marcela Mercado-Reyes, Trevor Bedford
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0191241

A portable prototype magnetometer to differentiate ischemic and non-ischemic heart disease in patients with chest pain
Cited by: 8
Author(s): Shima Ghasemi-Roudsari, Abbas Al-Shimary, Benjamin T. H. Varcoe, Rowena Byrom, Lorraine Kearney, Mark T. Kearney
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.celrep.2020.108401

Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma
Cited by: 12
Author(s): Marian F. Laughery, Alexander Brown, Kaitlynne A. Bohm, Smitha Sivapragasam, Haley S. Morris, Mila Tchmola, Angelica D. Washington, Debra Mitchell, Stephen J. Mather, Ewa Malc, Piotr A. Mieczkowski, Steven A. Roberts, John J. Wyrick
Software Mentions: 3
Published: about 4 years ago

10.1128/IAI.00331-18

Genome Plasticity of <i>agr</i> -Defective Staphylococcus aureus during Clinical Infection
Cited by: 45
Author(s): Deena R. Altman, Mitchell J. Sullivan, Kieran I. Chacko, Divya Balasubramanian, Theodore R. Pak, William E. Sause, Krishan Kumar, Robert Sebra, Gintaras Deikus, Oliver Attie, Hannah Rose, Martha Lewis, Yi Fulmer, Ali Kashif Bashir, Andrew Kasarskis, Eric E. Schadt, Anthony R. Richardson, Victor J. Torres, Bo Shopsin, Harm van Bakel
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-016-3009-3

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat
Cited by: 79
Author(s): Siyuan Zhan, Yao Dong, Wei Zhao, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0159177

Immunophenotypic and Ultrastructural Analysis of Mast Cells in Hermansky-Pudlak Syndrome Type-1: A Possible Connection to Pulmonary Fibrosis
Cited by: 11
Author(s): Arnold S. Kirshenbaum, Glenn Cruse, Avanti Desai, Geethani Bandara, Maarten Leerkes, Chyi‐Chia Richard Lee, Elizabeth R. Fischer, Kevin O’Brien, Bernadette R. Gochuico, Kelly D. Stone, William A. Gahl, Dean D. Metcalfe
Software Mentions: 3
Published: over 8 years ago

10.3390/v11050481

Attenuation of Bluetongue Virus (BTV) in an in ovo Model Is Related to the Changes of Viral Genetic Diversity of Cell-Culture Passaged BTV
Cited by: 4
Author(s): Fabian Z. X. Lean, Matthew J. Neave, John R. White, Jean Payne, Teresa Eastwood, Jemma Bergfeld, Antonio Di Rubbo, Vittoria Stevens, Kelly R. Davies, Joanne M. Devlin, David T. Williams, John Bingham
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0006777

Parsing Social Network Survey Data from Hidden Populations Using Stochastic Context-Free Grammars
Cited by: 20
Author(s): Art F. Y. Poon, Kimberly C. Brouwer, Steffanie A. Strathdee, Michelle Firestone-Cruz, Remedios Lozada, Sergei L. Kosakovsky Pond, Douglas D. Heckathorn, Simon D. W. Frost
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2105-15-90

Consistency of metagenomic assignment programs in simulated and real data
Cited by: 18
Author(s): Koldo Garcia-Etxebarria, Marc García-Garcerá, Francesc Calafell
Software Mentions: 3
Published: over 10 years ago

10.3389/fimmu.2021.643189

Plasticity of the Immune System in Children Following Treatment Interruption in HIV-1 Infection
Cited by: 2
Author(s): Katrine Schou Sandgaard, Ben Margetts, Teresa Attenborough, Triantafylia Gkouleli, Stuart Adams, Mette Holm, Diana Gibb, Deena L. Gibbons, Carlo Giaquinto, Anita De Rossi, Alasdair Bamford, Paolo Palma, Benny Chain, Athina Soragia Gkazi, Nigel Klein
Software Mentions: 3
Published: over 3 years ago