10.1038/s41598-021-81740-4

Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
Cited by: 3
Author(s): Ching-Tai Chen, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko, Wai-Kok Choong, Ting‐Yi Sung
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2020.00981

Metabolomic Markers of Colorectal Tumor With Different Clinicopathological Features
Cited by: 15
Author(s): Zhiping Long, Jianqiu Zhou, Kun Xie, Zhiyong Wu, Huihui Yin, Volontovich Daria, Jingshen Tian, Nannan Zhang, Liangliang Li, Yong Zhao, Wei Fan, Maoqing Wang, Yunfu Cui
Software Mentions: 5
Published: about 6 years ago

10.15252/msb.20177608

Landscape of nuclear transport receptor cargo specificity
Cited by: 79
Author(s): Marie‐Therese Mackmull, Bernd Klaus, Ivonne Heinze, Manopriya Chokkalingam, Andreas Beyer, Robert B. Russell, Alessandro Ori, Martin Beck
Software Mentions: 5
Published: over 8 years ago

10.1038/srep40170

Simultaneous abrupt shifts in hydrology and fish assemblage structure in a floodplain lake in the central Amazon
Cited by: 66
Author(s): Cristhiana Paula Röpke, Sidinéia Amadio, Jansen Zuanon, Efrem Jorge Gondim Ferreira, Cláudia Pereira de Deus, Tiago Pires, Kirk O. Winemiller
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2105-12-S9-S4

Fast and accurate methods for phylogenomic analyses
Cited by: 34
Author(s): Jimmy C. Yang, Tandy Warnow
Software Mentions: 5
Published: almost 15 years ago

10.1186/s12864-020-06795-5

Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality
Cited by: 27
Author(s): Alessandra Zombardo, Cristina Crosatti, Paolo Bagnaresi, Laura Bassolino, Noam Reshef, Sergio Puccioni, Primetta Faccioli, Alessio Tafuri, Massimo Delledonne, Aaron Fait, Paolo Storchi, Luigi Cattivelli, Erica Mica
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-019-6240-x

Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum
Cited by: 0
Author(s): Íria Gabriela Dias dos Santos, Tiago Antônio de Oliveira Mendes, Gerluza Aparecida Borges Silva, Amanda Maria Sena Reis, Cláudia Barros Monteiro-Vitorello, Patrícia Dayane Carvalho Schaker, Roberto Hirochi Herai, André Brait Carneiro Fabotti, Luiz Lehmann Coutinho, Érika Cristina Jorge
Software Mentions: 5
Published: over 6 years ago

10.1186/s13024-020-00405-4

Integrated analysis of the aging brain transcriptome and proteome in tauopathy
Cited by: 20
Author(s): Carl Grant Mangleburg, Timothy Wu, Hari Krishna Yalamanchili, Caiwei Guo, Yi-Cheng Hsieh, Duc Duong, Eric B. Dammer, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Zhandong Liu
Software Mentions: 5
Published: almost 6 years ago

10.1002/ece3.6650

A landscape‐scale assessment of the relationship between grassland functioning, community diversity, and functional traits
Cited by: 7
Author(s): Hanneke van ‘t Veen, Loïc Chalmandrier, Nadine Sandau, Michael P. Nobis, Patrice Descombes, Achilleas Psomas, Yann Hautier, Loïc Pellissier
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0129883

Regime Shift in an Exploited Fish Community Related to Natural Climate Oscillations
Cited by: 35
Author(s): Arnaud Auber, Morgane Travers-Trolet, Maria Ching Villanueva, Bruno Ernande
Software Mentions: 5
Published: about 11 years ago

10.1038/s41598-020-76991-6

Salivary microbiome composition changes after bariatric surgery
Cited by: 11
Author(s): Mária Džunková, Róbert Lipták, Barbora Vlková, Roman Gardlík, M Cierny, Andrés Moya, Peter Celec
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.21049

Proliferation-independent regulation of organ size by Fgf/Notch signaling
Cited by: 36
Author(s): Agnė Kozlovskaja-Gumbrienė, Yi Ren, Alexander Richard, Andy Aman, Ryan Jiskra, Danielle Nagelberg, Holger Knaut, Melainia McClain, Tatjana Piotrowski
Software Mentions: 5
Published: over 9 years ago

10.1038/srep29971

The impact of preconceptional obesity on trajectories of maternal lipids during gestation
Cited by: 26
Author(s): Latife Bozkurt, Christian Göbl, Anna-Theresa Hörmayer, Anton Luger, Giovanni Pacini, Alexandra Kautzky‐Willer
Software Mentions: 5
Published: almost 10 years ago

10.3390/ijms22179146

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses
Cited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12915-021-00996-4

Reorganization of the 3D chromatin architecture of rice genomes during heat stress
Cited by: 39
Author(s): Zhe Liang, Qian Zhang, Changmian Ji, Guihua Hu, Pingxian Zhang, Yifan Wang, Liwen Yang, Xiaofeng Gu
Software Mentions: 5
Published: over 5 years ago

10.1186/s40793-021-00382-1

Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed
Cited by: 5
Author(s): Leena Malayil, Suhana Chattopadhyay, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-019-2728-2

UTAP: User-friendly Transcriptome Analysis Pipeline
Cited by: 88
Author(s): Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-018-2122-5

IntEREst: intron-exon retention estimator
Cited by: 18
Author(s): Ali Oghabian, Dario Greco, Mikko J. Frilander
Software Mentions: 5
Published: over 8 years ago

10.3390/plants9121775

Compositional Analyses Reveal Relationships among Components of Blue Maize Grains
Cited by: 4
Author(s): Amol N. Nankar, M. Paul Scott, Richard C. Pratt
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-021-04106-7

EzMAP: Easy Microbiome Analysis Platform
Cited by: 0
Author(s): Gnanendra Shanmugam, Song Hee Lee, Junhyun Jeon
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-019-2749-x

Efficient proximal gradient algorithm for inference of differential gene networks
Cited by: 3
Author(s): Chen Wang, Feng Gao, Georgios B. Giannakis, Gennaro D’Urso, Xiaodong Cai
Software Mentions: 5
Published: about 7 years ago

10.1007/s11306-020-01686-y

A comparison of high-throughput plasma NMR protocols for comparative untargeted metabolomics
Cited by: 15
Author(s): Nikolaos G. Bliziotis, Udo F. H. Engelke, Ruud L. E. G. Aspers, Jasper Engel, Jaap Deinum, Henri J L M Timmers, Ron A. Wevers, Leo A. J. Kluijtmans
Software Mentions: 5
Published: about 6 years ago

10.1186/s12936-018-2612-y

Cryogenically preserved RBCs support gametocytogenesis of Plasmodium falciparum in vitro and gametogenesis in mosquitoes
Cited by: 9
Author(s): Ashutosh K. Pathak, Justine C. Shiau, Matthew B. Thomas, Courtney C. Murdock
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1004847

Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
Cited by: 40
Author(s): Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James Stevens
Software Mentions: 5
Published: over 10 years ago

10.1002/ece3.7638

Global change impacts on arid zone ecosystems: Seedling establishment processes are threatened by temperature and water stress
Cited by: 10
Author(s): Wolfgang Lewandrowski, Jason C. Stevens, Bruce L. Webber, Emma L. Dalziell, Melinda S. Trudgen, Amber Bateman, Todd E. Erickson
Software Mentions: 5
Published: about 5 years ago

10.1101/2021.01.15.426908

Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
Cited by: 2
Author(s): Jakub Jankowski, Hye Kyung Lee, Julia Wilflingseder, Lothar Hennighausen
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-21444-4

QFMatch: multidimensional flow and mass cytometry samples alignment
Cited by: 12
Author(s): Darya Orlova, Stephen Meehan, David R. Parks, Wayne A. Moore, Connor Meehan, Qian Zhao, Eliver Ghosn, Leonore A. Herzenberg, Guenther Walther
Software Mentions: 5
Published: over 8 years ago

10.3390/s19214652

Dark Field Microscopy-Based Biosensors for the Detection of E. coli in Environmental Water Samples
Cited by: 7
Author(s): Rita La Spina, Diana C. António, Cloé Desmet, Andrea Valsesia, Radoslaw Bombera, Hedvig Norlén, Teresa Lettieri, Pascal Colpo
Software Mentions: 5
Published: over 6 years ago

10.3390/metabo11080488

Investigating Global Lipidome Alterations with the Lipid Network Explorer
Cited by: 17
Author(s): Nikolai Köhler, Tim Rose, Lisa Falk, Josch Pauling
Software Mentions: 5
Published: almost 5 years ago

10.3390/proteomes8030015

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
Cited by: 9
Author(s): Subina Mehta, Caleb Easterly, Ray Sajulga, Robert Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed, Lloyd M. Smith, Thomas McGowan, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 5
Published: about 6 years ago

10.3325/cmj.2020.61.564

Bayesian meta-analysis now – let's do it
Cited by: 9
Author(s): Branimir K. Hackenberger
Software Mentions: 5
Published: over 5 years ago

10.1093/bioinformatics/btz284

clustermq enables efficient parallelization of genomic analyses
Cited by: 5
Author(s): Michaël Schubert
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pcbi.1004384

Ten Simple Rules for Experiments’ Provenance
Cited by: 10
Author(s): Toni Kazic
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0208371

Genetic resistance to DEHP-induced transgenerational endocrine disruption
Cited by: 17
Author(s): Ludwig Stenz, Rita Rahban, Julien Prados, Serge Nef, Ariane Paoloni-Giacobino
Software Mentions: 5
Published: about 7 years ago

10.1186/s12920-016-0201-x

Single and multi-subject clustering of flow cytometry data for cell-type identification and anomaly detection
Cited by: 7
Author(s): Maziyar Baran Pouyan, Vasu Jindal, Javad Birjandtalab, Mehrdad Nourani
Software Mentions: 5
Published: almost 10 years ago

10.1186/1471-2105-11-403

Data reduction for spectral clustering to analyze high throughput flow cytometry data
Cited by: 142
Author(s): Habil Zare, Parisa Shooshtari, Arvind Gupta, Ryan R. Brinkman
Software Mentions: 5
Published: almost 16 years ago

10.3389/fbioe.2020.598392

Phenotypic and Genomic Analysis of Clostridium beijerinckii NRRL B-598 Mutants With Increased Butanol Tolerance
Cited by: 6
Author(s): Maryna Vasylkivska, Barbora Branská, Karel Sedlář, Katerina Jureckova, Ivo Provazník, Petra Patáková
Software Mentions: 5
Published: over 5 years ago

10.1186/s12935-021-02042-3

Derivation and validation of a lipid-covered prognostic model for mature T-cell lymphomas
Cited by: 5
Author(s): Tianshi Lü, Lei Shi, Guanggang Shi, Yin Cai, Shunfeng Hu, Jiarui Liu, Shuai Ren, Xiangxiang Zhou, Xin Wang
Software Mentions: 5
Published: about 5 years ago

10.2196/15918

Enabling Agile Clinical and Translational Data Warehousing: Platform Development and Evaluation
Cited by: 5
Author(s): Helmut Spengler, C. Lang, Tanmaya Mahapatra, Ingrid Gatz, Klaus A. Kuhn, Fabian Praßer
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-021-81297-2

CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
Cited by: 3
Author(s): Victor Aprilyanto, Redi Aditama, Zulfikar Achmad Tanjung, Condro Utomo, Tony Liwang
Software Mentions: 5
Published: over 5 years ago

10.1098/rsos.202093

Habitat filtering differentially modulates phylogenetic and functional diversity relationships between predatory arthropods
Cited by: 4
Author(s): Aurélien Ridel, Denis Lafage, Pierre Devogel, Thomas Lacoue-Labarthe, Julien Pétillon
Software Mentions: 5
Published: about 5 years ago

10.1016/j.gpb.2019.08.002

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information
Cited by: 56
Author(s): Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, A. Ian Smith, Tatiana T. Marquez‐Lago, Jian Li, Jiangning Song
Software Mentions: 5
Published: over 6 years ago

10.1186/s12872-021-01961-3

Distinguishing cardiac myxomas from cardiac thrombi by a radiomics signature based on cardiovascular contrast-enhanced computed tomography images
Cited by: 3
Author(s): Wen-Lei Qian, Jiang Yu, Xi Liu, Yingkun Guo, Yuan Li, Xin Tang, Zhigang Yang
Software Mentions: 5
Published: over 5 years ago

10.3390/plants10061092

Polymorphism in the Chloroplast ATP Synthase Beta-Subunit Is Associated with a Maternally Inherited Enhanced Cold Recovery in Cucumber
Cited by: 5
Author(s): Madeline W. Oravec, Michael J. Havey
Software Mentions: 5
Published: about 5 years ago

10.1186/1751-0473-3-13

Wndchrm – an open source utility for biological image analysis
Cited by: 193
Author(s): Lior Shamir, Nikita Orlov, D. Mark Eckley, Tomasz Macura, Josiah Johnston, Ilya G. Goldberg
Software Mentions: 5
Published: about 18 years ago

10.1155/2017/6218353

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers
Cited by: 105
Author(s): Luka Bolha, Metka Ravnik‐Glavač, Damjan Glavač
Software Mentions: 5
Published: over 9 years ago

10.3390/cells9061436

Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver
Cited by: 14
Author(s): Qinwei Kim-Wee Zhuang, José Héctor Gálvez, Qian Xiao, Najla AlOgayil, Jeffrey Hyacinthe, Teruko Taketo, Guillaume Bourque, Anna K. Naumova
Software Mentions: 5
Published: about 6 years ago

10.1126/sciadv.abh0534

Cell-free DNA TAPS provides multimodal information for early cancer detection
Cited by: 36
Author(s): Paulina Siejka-Zielińska, Jingfei Cheng, Felix Jackson, Yibin Liu, Zahir Soonawalla, Srikanth Reddy, Michael Silva, Luminita Puta, Misti McCain, Emma L. Culver, Noor Bekkali, Benjamin Schuster-Böckler, Pier Francesco Palamara, Derek A. Mann, Helen L. Reeves, Eleanor Barnes, Shivan Sivakumar, Chun-Xiao Song
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-017-17460-5

Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple
Cited by: 22
Author(s): Jiabin Wang, Zhiying Li, Ming Lei, Yuhua Fu, Jiaju Zhao, Meng-Fei Ao, Li Xu
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-017-14595-3

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Cited by: 27
Author(s): Zhifu Sun, Asha Nair, Xianfeng Chen, Naresh Prodduturi, Junwen Wang, Jean Pierre A. Kocher
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-020-02247-1

Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences
Cited by: 22
Author(s): Caroline Jane Ross, Aviv Rom, Amit Spinrad, Dikla Gelbard-Solodkin, Neta Degani, Igor Ulitsky
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.5887

Phenotypic plasticity, but not adaptive tracking, underlies seasonal variation in post‐cold hardening freeze tolerance of<i>Drosophila melanogaster</i>
Cited by: 9
Author(s): Helen M. Stone, Priscilla A. Erickson, Alan O. Bergland
Software Mentions: 5
Published: over 6 years ago

10.1002/eji.201948432

CD73 contributes to anti‐inflammatory properties of afferent lymphatic endothelial cells in humans and mice
Cited by: 10
Author(s): Dominik Eichin, Alberto Pessia, Akiko Takeda, Joni Laakkonen, Lydia Bellmann, Matti Kankainen, Beat A. Imhof, Patrizia Stoitzner, Jing Tang, Marko Salmi, Sirpa Jalkanen
Software Mentions: 5
Published: over 5 years ago

10.3390/insects12030219

Ant Diversity and Community Composition in Alpine Tree Line Ecotones
Cited by: 4
Author(s): Elia Guariento, Konrad Fiedler
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0252154

Hydrological and topographic determinants of biomass and species richness in a Mediterranean-climate shrubland
Cited by: 1
Author(s): Samantha Díaz de León-Guerrero, Rodrigo Méndez‐Alonzo, Stephen H. Bullock, Enrique R. Vivoni
Software Mentions: 5
Published: about 5 years ago

10.12688/f1000research.15433.1

Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets
Cited by: 5
Author(s): Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Héctor Corrada Bravo
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12864-021-07924-4

Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)
Cited by: 10
Author(s): Yan He, Hongyan Yu, Hongling Zhao, Hua Zhu, Qingjing Zhang, Anqi Wang, Yubang Shen, Xiaoyan Xu, Jiale Li
Software Mentions: 5
Published: almost 5 years ago

10.3390/ijms21020471

The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma
Cited by: 17
Author(s): Verena Boschert, Nicola Klenk, Alexander Abt, Sudha Janaki Raman, Markus Fischer, Roman C. Brands, Axel Seher, Christian Linz, Urs Müller‐Richter, Thorsten Bischler, Stefan Hartmann
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-016-2745-8

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
Cited by: 17
Author(s): Yongxian Yuan, Huaiqian Xu, Rufina Leung
Software Mentions: 5
Published: about 10 years ago

10.1002/ece3.4710

Unbalanced biparental care during colony foundation in two subterranean termites
Cited by: 17
Author(s): Lou Brossette, Joël Meunier, Simon Dupont, Anne‐Geneviève Bagnères, Christophe Lucas
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-021-04006-w

Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms
Cited by: 3
Author(s): Guoqing Han, Qi Li, Ying Li
Software Mentions: 5
Published: about 5 years ago

10.3389/frai.2020.584784

Using Word Embeddings to Learn a Better Food Ontology
Cited by: 7
Author(s): Jason Youn, Tarini Naravane, Ilias Tagkopoulos
Software Mentions: 5
Published: over 5 years ago

10.1186/s12885-019-6462-y

Systematical identifications of prognostic meaningful lung adenocarcinoma subtypes and the underlying mutational and expressional characters
Cited by: 6
Author(s): Zhenyang Lv, Ting Lei
Software Mentions: 5
Published: over 6 years ago

10.1016/j.prevetmed.2021.105395

Multiple model triangulation to identify factors associated with lameness in British sheep flocks
Cited by: 5
Author(s): Kate Lewis, Michael J. Green, Jessica D. Witt, Laura Green
Software Mentions: 5
Published: almost 5 years ago

10.3389/frai.2020.559617

An Interpretable Predictive Model of Vaccine Utilization for Tanzania
Cited by: 1
Author(s): R. Hariharan, Johnna Sundberg, Giacomo Gallino, Ashley Schmidt, Drew Arenth, Suvrit Sra, Benjamin Fels
Software Mentions: 5
Published: over 5 years ago

10.1016/j.isci.2021.103021

Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts
Cited by: 2
Author(s): Toni de-Dios, Pablo Carrión, Ïñigo Olalde, Laia Llovera Nadal, Esther Lizano, Dídac Pàmies, Tomàs Marqués-Bonet, François Balloux, Lucy van Dorp, Carles Lalueza‐Fox
Software Mentions: 5
Published: almost 5 years ago

10.1016/j.cmet.2018.07.005

A Role for p53 in the Adaptation to Glutamine Starvation through the Expression of SLC1A3
Cited by: 144
Author(s): Mylène Tajan, A. Höck, Julianna Blagih, Neil Robertson, Christiaan F. Labuschagne, Flore Kruiswijk, Timothy J. Humpton, Peter D. Adams, Karen H. Vousden
Software Mentions: 5
Published: over 7 years ago

10.18632/oncotarget.25350

High expression of nucleoporin 133 mRNA in bone marrow CD138+ cells is a poor prognostic factor in multiple myeloma
Cited by: 4
Author(s): Soushi Ibata, Masayoshi Kobune, Shohei Kikuchi, Masahiro Yoshida, Satoshi Miura, Hyogo Horiguchi, Kazuyuki Murase, Satoshi Iyama, Kohichi Takada, Koji Miyanishi, Junji Kato
Software Mentions: 5
Published: about 8 years ago

10.1186/s13148-021-01083-9

Estimands in epigenome-wide association studies
Cited by: 9
Author(s): Jochen Kruppa, Miriam Sieg, Gregor Richter, Anne Pohrt
Software Mentions: 5
Published: about 5 years ago

10.1186/s40064-015-1609-z

Structural homology guided alignment of cysteine rich proteins
Cited by: 16
Author(s): Thomas Shafee, Andrew Robinson, Nicole. Van Der Weerden, Marilyn A. Anderson
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-020-66374-2

Mutations in virus-derived small RNAs
Cited by: 6
Author(s): Deepti Nigam, Katherine LaTourrette, Hernán García-Ruíz
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-61558-2

Innovation in wild Barbary macaques (Macaca sylvanus)
Cited by: 16
Author(s): Federica Amici, Álvaro López Caicoya, Bonaventura Majolo, Anja Widdig
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0219962

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics
Cited by: 17
Author(s): Alexa A. Pragman, Katherine A. Knutson, Trevor Gould, Shane Hodgson, Richard E. Isaacson, Cavan Reilly, Chris H. Wendt
Software Mentions: 5
Published: almost 7 years ago

10.3390/microorganisms9051033

Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other
Cited by: 9
Author(s): A. K. Eskov, Aleksei Zverev, Evgeny Abakumov
Software Mentions: 5
Published: about 5 years ago

10.3390/microorganisms8081134

Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome
Cited by: 10
Author(s): Elena Biagi, Carlo Mengucci, Monica Barone, Gianfranco Picone, Alex Lucchi, Pietro Celi, Gilberto Litta, Marco Candela, Gerardo Manfreda, Patrizia Brigidi, Francesco Capozzi, Alessandra De Cesare
Software Mentions: 5
Published: almost 6 years ago

10.1534/g3.120.401452

Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
Cited by: 10
Author(s): Mariem Nsibi, Barbara Gouble, Sylvie Bureau, Timothée Flutre, Christopher Sauvage, Jean‐Marc Audergon, Jean‐Luc Regnard
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0125393

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation
Cited by: 45
Author(s): Samuel Gregory, Christopher Anderson, Marta Camps Arbestain, Patrick J. Biggs, Austen R. D. Ganley, Justin M. O’Sullivan, Michael T. McManus
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pone.0057170

General Patterns of Diversity in Major Marine Microeukaryote Lineages
Cited by: 51
Author(s): Massimo C. Pernice, Ramiro Logares, Laure Guillou, Ramón Massana
Software Mentions: 5
Published: over 13 years ago

10.3389/fonc.2020.01052

A Novel Method for Cancer Subtyping and Risk Prediction Using Consensus Factor Analysis
Cited by: 9
Author(s): Duc Tran, Hung Son Nguyen, Uyen Phuong Le, George Bebis, Hung N. Luu, Tin Nguyen
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0216471

NanoR: A user-friendly R package to analyze and compare nanopore sequencing data
Cited by: 17
Author(s): Davide Bolognini, Niccolò Bartalucci, Alessandra Mingrino, Alessandro M. Vannucchi, Alberto Magi
Software Mentions: 5
Published: about 7 years ago

10.3389/fpls.2019.00511

Activity in the Arbuscular Mycorrhizal Hyphosphere Warning Neighbouring Plants
Cited by: 8
Author(s): Carmina Cabral, Bernd Wollenweber, Carla António, Sabine Ravnskov
Software Mentions: 5
Published: about 7 years ago

10.1155/2019/2506843

Deciphering Immune-Associated Genes to Predict Survival in Clear Cell Renal Cell Cancer
Cited by: 30
Author(s): Daixing Hu, Mi Zhou, Xin Zhu
Software Mentions: 5
Published: over 6 years ago

10.3389/fonc.2021.629333

GEO Data Mining Identifies OLR1 as a Potential Biomarker in NSCLC Immunotherapy
Cited by: 6
Author(s): Bin Liu, Ziyu Wang, Meng Gu, Cong Zhao, Teng Ma, Jinghui Wang
Software Mentions: 5
Published: about 5 years ago

10.1098/rspb.2021.0454

Long-term exposure to artificial light at night in the wild decreases survival and growth of a coral reef fish
Cited by: 13
Author(s): Jules Schligler, Daphne Cortese, Ricardo Beldade, Stephen E. Swearer, Suzanne C. Mills
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0235066

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies
Cited by: 3
Author(s): Rose M. Collis, Patrick J. Biggs, Anne C. Midwinter, A. Springer Browne, David Wilkinson, Hamid Irshad, Nigel French, Gale Brightwell, Adrian L. Cookson
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pcbi.1009300

MicrobeTrace: Retooling molecular epidemiology for rapid public health response
Cited by: 17
Author(s): Ellsworth Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, S. P. Knyazev, Roxana Cintrón, William M. Switzer
Software Mentions: 5
Published: almost 5 years ago

10.1186/1759-8753-5-13

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
Cited by: 129
Author(s): Marc Bailly‐Bechet, Annabelle Haudry, Emmanuelle Lerat
Software Mentions: 5
Published: about 12 years ago

10.7717/peerj.3391

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates
Cited by: 15
Author(s): Dariya K. Sydykova, Claus O. Wilke
Software Mentions: 5
Published: about 9 years ago

10.1093/ve/vez060

Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses
Cited by: 23
Author(s): Vincent Loiseau, Elisabeth A. Herniou, Yannis Moreau, Nicolas Lévêque, Carine Meignin, Laurent Daeffler, Brian A. Federici, Richard Cordaux, Clément Gilbert
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-018-0430-7

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore
Cited by: 41
Author(s): Angélique Gobet, Laëtitia Mest, Morgan Perennou, Simon M. Dittami, Claire Caralp, Céline Coulombet, Sylvain Huchette, Sabine Roussel, Gurvan Michel, Catherine Leblanc
Software Mentions: 5
Published: over 8 years ago

10.1099/mgen.0.000224

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Cited by: 110
Author(s): Sergio Arredondo-Alonso, Malbert R. C. Rogers, Johanna C. Braat, Tess D. Verschuuren, Janetta Top, Jukka Corander, Rob J. L. Willems, Anita C. Schürch
Software Mentions: 5
Published: over 7 years ago

10.3390/cells9051288

Computational Tools and Resources Supporting CRISPR-Cas Experiments
Cited by: 34
Author(s): Paweł Śledziński, Mateusz Nowaczyk, Marta Olejniczak
Software Mentions: 5
Published: about 6 years ago

10.3389/fonc.2020.00368

Expression Profile and Prognostic Values of HOXA Family Members in Laryngeal Squamous Cell Cancer
Cited by: 20
Author(s): Jinyun Li, Meng Ye, Chongchang Zhou
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-020-02188-9

Convergent network effects along the axis of gene expression during prostate cancer progression
Cited by: 14
Author(s): Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C. Toussaint, Christine Fritz, Chunhui Yuan, Hao Chen, Niels J. Rupp, Ailsa J. Christiansen, Dorothea Rutishauser, Jan H. Rüschoff, Christian Daniel Fankhauser, Karim Saba, Cédric Poyet, Thomas Hermanns, Kathrin Oehl, Ariane L. Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti, Qiushi Zhang, Yi Zhu, María Rodríguez Martínez, Matteo Manica, Michael C. Haffner, Ruedi Aebersold, Peter J. Wild, Andreas Beyer
Software Mentions: 5
Published: over 5 years ago

10.1186/s13104-017-2616-7

fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data
Cited by: 6
Author(s): Damien M. O’Halloran
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-018-1490-5

A comparative study of endoderm differentiation in humans and chimpanzees
Cited by: 31
Author(s): Lauren E. Blake, Samantha M. Thomas, John Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad, Bryan J. Pavlovic
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.68967

Spatially patterned excitatory neuron subtypes and projections of the claustrum
Cited by: 17
Author(s): Sarah R. Erwin, Brianna N. Bristow, Kaitlin E Sullivan, Rennie M Kendrick, Brian A. Marriott, Lihua Wang, Jody Clements, Andrew L. Lemire, Jesse Jackson, Mark S. Cembrowski
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2020.01212

Diverse Microbial Composition of Sourdoughs From Different Origins
Cited by: 50
Author(s): Andrea Comasio, Marko Verce, Simon Van Kerrebroeck, Luc De Vuyst
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.cell.2017.07.025

Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient
Cited by: 338
Author(s): Alejandro Jiménez-Sánchez, Danish Memon, Stephane Pourpe, Harini Veeraraghavan, Yanyun Li, Hebert Alberto Vargas, Michael B. Gill, Kay J. Park, Oliver Zivanovic, Jason Konner, Jacob Ricca, Dmitriy Zamarin, Tyler Walther, Carol Aghajanian, Jedd D. Wolchok, Evis Sala, Taha Merghoub, Alexandra Snyder, Martin L. Miller
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-15-71

Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian
Cited by: 37
Author(s): Derek Stefanik, Tristan Lubinski, Brian R. Granger, Allyson L. Byrd, Adam M. Reitzel, Lukas DeFilippo, Allison Lorenc, John R. Finnerty
Software Mentions: 5
Published: over 12 years ago