cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-96236-4

A novel prognostic signature of immune-related lncRNA pairs in lung adenocarcinoma
Cited by: 5
Author(s): Yang Liu, Qiuhong Wu, Xuejiao Fan, Wen Li, Yong Li, Hui Zhu, Qinghua Zhou, Jinming Yu
Software Mentions: 10
Published: over 4 years ago

10.7554/eLife.10421

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain
Cited by: 115
Author(s): Claudia Scheckel, Elodie Drapeau, María A. Frías, Christopher Y. Park, John Fak, Ilana Zucker-Scharff, Yan Kou, Vahram Haroutunian, Avi Ma’ayan, Joseph D. Buxbaum, Robert B. Darnell
Software Mentions: 10
Published: about 10 years ago

10.1128/mSystems.00571-21

Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Cited by: 11
Author(s): Rachel E. Diner, Drishti Kaul, Ariel Rabines, Hong Zheng, Joshua A. Steele, John F. Griffith, Andrew E. Allen
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-020-76103-4

Phenotypic variation, functional traits repeatability and core collection inference in Synsepalum dulcificum (Schumach & Thonn.) Daniell reveals the Dahomey Gap as a centre of diversity
Cited by: 3
Author(s): Dèdéou Apocalypse Tchokponhoué, Enoch G. Achigan‐Dako, Sognigbé N’Danikou, Daniel Nyadanu, Rémi Kahane, Jacob S Houéto, V.N. Fassinou Hotegni, Alfred Odindo, Julia Sibiya
Software Mentions: 10
Published: over 5 years ago

10.3389/fonc.2020.01710

Prognostic Implications of Metabolism Related Gene Signature in Cutaneous Melanoma
Cited by: 14
Author(s): Furong Zeng, Juan Su, Cong Peng, Mengting Liao, Shuang Zhao, Ying Guo, Xiang Chen, Guangtong Deng
Software Mentions: 10
Published: over 5 years ago

10.3389/fvets.2020.00604

Autoregressive Models Applied to Time-Series Data in Veterinary Science
Cited by: 9
Author(s): Michael P. Ward, Rachel M Iglesias, Victoria Brookes
Software Mentions: 10
Published: over 5 years ago

10.7717/peerj.10264

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
Cited by: 6
Author(s): Elly Poretsky, Alisa Huffaker
Software Mentions: 10
Published: over 5 years ago

10.7554/eLife.36187

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Cited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: over 7 years ago

10.3389/fmicb.2021.679671

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt
Cited by: 4
Author(s): Junhyeong Kim, A. H. Goldstein, Romy Chakraborty, Kolby Jardine, Robert J. Weber, P. Sørensen, Wang Shi, Boris Faybishenko, Pawel K. Misztal, Eoin L. Brodie
Software Mentions: 10
Published: almost 5 years ago

10.1098/rsos.191333

Now or never: noticing occurs early in sustained inattentional blindness
Cited by: 4
Author(s): Katherine Wood, Daniel J. Simons
Software Mentions: 10
Published: over 6 years ago

10.3390/ijms20061510

Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR)
Cited by: 48
Author(s): Marta Majewska, Aleksandra Lipka, Łukasz Paukszto, J Jastrzebski, Karol Szeszko, Marek Gowkielewicz, Ewa Lepiarczyk, Marcin Jóźwik, Mariusz Majewski
Software Mentions: 10
Published: about 7 years ago

10.3389/fonc.2020.526577

Patient Stratification of Clear Cell Renal Cell Carcinoma Using the Global Transcription Factor Activity Landscape Derived From RNA-Seq Data
Cited by: 7
Author(s): Yanyan Zhu, Shundong Cang, Bowang Chen, Ye Gu, Miaomiao Jiang, Junya Yan, Fengmin Shao, Xiaoyun Huang
Software Mentions: 10
Published: over 5 years ago

10.1097/MD.0000000000026068

MiRNA-based model for predicting the TMB level in colon adenocarcinoma based on a LASSO logistic regression method
Cited by: 1
Author(s): Zhengtian Li, Lingling Jiang, Rong Zhao, Jun Huang, Weibo Yang, Zhenpei Wen, Bo Zhang, Gang Du
Software Mentions: 10
Published: almost 5 years ago

10.3389/fmicb.2020.01190

Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk
Cited by: 14
Author(s): Christopher Maier, Christopher Huptas, Mario von Neubeck, Stephen W. Scherer, Mareike Wenning, Genia Lücking
Software Mentions: 10
Published: almost 6 years ago

10.1155/2020/5858092

Profiles of Immune Infiltration and Prognostic Immunoscore in Lung Adenocarcinoma
Cited by: 9
Author(s): Yanyan Li, Liping Tao, Weiyang Cai
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41396-020-00777-x

A network approach to elucidate and prioritize microbial dark matter in microbial communities
Cited by: 71
Author(s): Tatyana Zamkovaya, Jamie S. Foster, Valérie de Crécy‐Lagard, Ana Conesa
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-019-42533-y

MeshMonk: Open-source large-scale intensive 3D phenotyping
Cited by: 78
Author(s): Julie D. White, Alejandra Ortega-Castrillón, Harold Matthews, Arslan Zaidi, Omid Ekrami, Jonatan Snyders, Yi Fan, Tony Penington, Stefan Van Dongen, Mark D. Shriver, Peter Claes
Software Mentions: 10
Published: about 7 years ago

10.1093/plankt/fbaa017

Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea
Cited by: 11
Author(s): Laura Käse, Alexandra Kraberg, Katja Metfies, Stefan Neuhaus, Pim Sprong, Bernhard M. Fuchs, Maarten Boersma, Karen Helen Wiltshire
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41598-018-32681-y

Medicinal value of sunflower pollen against bee pathogens
Cited by: 77
Author(s): Jonathan J. Giacomini, Jessica Leslie, David R. Tarpy, Evan C. Palmer‐Young, Rebecca E. Irwin, Lynn S. Adler
Software Mentions: 10
Published: over 7 years ago

10.7717/peerj.11903

Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
Cited by: 10
Author(s): Patricia Sarcinelli Stelzer, Ana Carolina de Azevedo Mazzuco, L.E. de O. Gomes, João Luiz Martins, Sérgio A. Netto, Ângelo F. Bernardino
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-020-74909-w

Multi-strain volatile profiling of pathogenic and commensal cutaneous bacteria
Cited by: 19
Author(s): Shane Fitzgerald, Emer Duffy, Linda Holland, Aoife Morrin
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pntd.0008934

An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia
Cited by: 6
Author(s): Sam Stubbs, Edison Johar, Frilasita A. Yudhaputri, Benediktus Yohan, Marsha S. Santoso, Rahma Hayati, Dionisius Denis, Barbara Blacklaws, Ann M. Powers, R. Tedjo Sasmono, Khin Saw Aye Myint, Simon D. W. Frost
Software Mentions: 10
Published: over 5 years ago

10.1186/s40462-019-0175-3

Exploration during early life: distribution, habitat and orientation preferences in juvenile king penguins
Cited by: 14
Author(s): Florian Orgeret, Clara Péron, Manfred R. Enstipp, Karine Delord, Henri Weimerskirch, CA Bost
Software Mentions: 10
Published: over 6 years ago

10.1242/dev.193060

Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
Cited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: over 6 years ago

10.3389/fonc.2021.643465

Identification of the Roles of a Stemness Index Based on mRNA Expression in the Prognosis and Metabolic Reprograming of Pancreatic Ductal Adenocarcinoma
Cited by: 6
Author(s): Rong Tang, Xiaomeng Liu, Wei Wang, Jie Hua, Jin Xu, Chen Liang, Qingcai Meng, Jiang Liu, Bo Zhang, Xianjun Yu, Si Shi
Software Mentions: 10
Published: about 5 years ago

10.1093/bioinformatics/btv428

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Cited by: 1,079
Author(s): Tal Galili
Software Mentions: 10
Published: over 10 years ago

10.1128/mSphere.00743-20

Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull ( Chroicocephalus novaehollandiae ) Reveals the Acquisition of Multidrug Resistance Plasmids
Cited by: 17
Author(s): Max L. Cummins, Martina L. Sanderson-Smith, Peter Newton, Nicholas Carlile, David N. Phalen, Kimberly Maute, Leigh G. Monahan, Bethany J. Hoye, Steven P. Djordjevic
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pgen.1009376

Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae
Cited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: about 5 years ago

10.3389/fgene.2021.692953

Identification of the Real Hub Gene and Construction of a Novel Prognostic Signature for Pancreatic Adenocarcinoma Based on the Weighted Gene Co-expression Network Analysis and Least Absolute Shrinkage and Selection Operator Algorithms
Cited by: 15
Author(s): Qihang Yuan, Jie Ren, Zhizhou Wang, Ji Li, Dawei Deng, Dong Shang
Software Mentions: 10
Published: over 4 years ago

10.3389/fmicb.2020.00917

Changes in Faecal Microbiota Profiles Associated With Performance and Birthweight of Piglets
Cited by: 23
Author(s): Clare H. Gaukroger, Christopher J. Stewart, Sandra Edwards, John Walshaw, Ian Adams, Ι. Kyriazakis
Software Mentions: 10
Published: almost 6 years ago

10.1186/s12859-021-03967-2

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R
Cited by: 7
Author(s): Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina Kechris, Miranda Kroehl
Software Mentions: 10
Published: about 5 years ago

10.18632/aging.203257

Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastoma
Cited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: almost 5 years ago

10.3389/fmicb.2021.685263

Exploring the Potential of Micrococcus luteus Culture Supernatant With Resuscitation-Promoting Factor for Enhancing the Culturability of Soil Bacteria
Cited by: 9
Author(s): Marco Antonio Lopez Marin, Michal Strejcek, Petra Junková, Jáchym Šuman, Jiří Šantrůček, Ondřej Uhlík
Software Mentions: 10
Published: almost 5 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41598-021-94329-8

Combined detection of peripheral blood VEGF and inflammation biomarkers to evaluate the clinical response and prognostic prediction of non-operative ESCC
Cited by: 4
Author(s): Yuanyuan Ma, Xinyu Su, Xin Li, Xiaohui Zhi, Kan Jiang, Jianhong Xia, Hongliang Li, Yan Chen, Lixin Zhou
Software Mentions: 10
Published: over 4 years ago

10.3390/cancers13133371

Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis
Cited by: 7
Author(s): Aurora Savino, Niccolò De Marzo, Paolo Provero, Valeria Poli
Software Mentions: 10
Published: almost 5 years ago

10.1128/mSphere.00334-20

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake
Cited by: 13
Author(s): Myriam Labbé, Catherine Girard, Warwick F. Vincent, Alexander I. Culley
Software Mentions: 10
Published: almost 6 years ago

10.3389/fmicb.2019.01702

Experimental Inoculation of Coral Recruits With Marine Bacteria Indicates Scope for Microbiome Manipulation in Acropora tenuis and Platygyra daedalea
Cited by: 47
Author(s): Katarina Damjanovic, Madeleine Jh van Oppen, Patricia Menéndez, Linda L. Blackall
Software Mentions: 10
Published: over 6 years ago

10.1371/journal.pcbi.1007803

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Cited by: 9
Author(s): Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert
Software Mentions: 10
Published: almost 6 years ago

10.1186/s42523-021-00094-4

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales
Cited by: 23
Author(s): Connie A. Rojas, Santiago Ramírez‐Barahona, Kay E. Holekamp, Kevin R. Theis
Software Mentions: 10
Published: almost 5 years ago

10.1186/s12859-015-0613-1

tcR: an R package for T cell receptor repertoire advanced data analysis
Cited by: 199
Author(s): Vadim Nazarov, Mikhail V. Pogorelyy, Ekaterina A. Komech, Ivan V. Zvyagin, Dmitriy A. Bolotin, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov
Software Mentions: 10
Published: almost 11 years ago

10.1186/s12859-020-03549-8

BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
Cited by: 12
Author(s): Pirunthan Perampalam, Frederick A. Dick
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41598-021-89904-y

Feasibility of predicting allele specific expression from DNA sequencing using machine learning
Cited by: 5
Author(s): Zhenhua Zhang, Freerk van Dijk, Nigel Klein, Mariëlle van Gijn, Lude Franke, Richard J. Sinke, Morris A. Swertz, K. Joeri van der Velde
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41598-020-72047-x

Light intensity regulates flower visitation in Neotropical nocturnal bees
Cited by: 11
Author(s): Rodolfo Liporoni, Guaraci Duran Cordeiro, Paulo Inácio Prado, Clemens Schlindwein, Eric J. Warrant, Isabel Alves‐dos‐Santos
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-72369-w

Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology
Cited by: 10
Author(s): Natacha Nikolic, Iratxe Montes, Maxime Lalire, Alexis Puech, Nathalie Bodin, Sophie Arnaud‐Haond, Sven E. Kerwath, Emmanuel Corse, Philippe Gaspar, Stéphanie Hollanda, Jérôme Bourjea, Wendy West, Sylvain Bonhommeau
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-71663-x

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: over 5 years ago

10.1186/s12918-015-0169-8

Increased robustness of early embryogenesis through collective decision-making by key transcription factors
Cited by: 8
Author(s): Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 10
Published: almost 11 years ago

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: over 5 years ago

10.3389/fmicb.2021.634503

Cottonseed Press Cake as a Potential Diet for Industrially Farmed Black Soldier Fly Larvae Triggers Adaptations of Their Bacterial and Fungal Gut Microbiota
Cited by: 26
Author(s): Dorothee Tegtmeier, Sabine Hurka, Patrick Klüber, Karina Brinkrolf, Philipp Heise, Andreas Vilcinskas
Software Mentions: 10
Published: about 5 years ago

10.1371/journal.pcbi.1009380

Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
Cited by: 11
Author(s): Rui Yin, Johnathan D. Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush, Brian G. Pierce
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-020-72272-4

Video-assisted thoracoscopic lobectomy is feasible for selected patients with clinical N2 non-small cell lung cancer
Cited by: 7
Author(s): Jae Kwang Yun, Geun Dong Lee, Sehoon Choi, Hyeong Ryul Kim, Yong Hee Kim, Seung-Il Park, Dong Kwan Kim
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pbio.3001053

Identification of 3′ UTR motifs required for mRNA localization to myelin sheaths in vivo
Cited by: 13
Author(s): Katie M. Yergert, Caleb A. Doll, Rebecca O’Rouke, Jacob H. Hines, Bruce Appel
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-70722-7

Active and social life is associated with lower non-social fearfulness in pet dogs
Cited by: 15
Author(s): Emma Hakanen, Salla Mikkola, Milla Salonen, Jenni Puurunen, Sini Sulkama, Cynthia Gobbi Alves Araújo, Hannes Lohi
Software Mentions: 10
Published: over 5 years ago

10.1172/jci.insight.138970

Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation program
Cited by: 21
Author(s): Farah Hasan, Yulun Chiu, Rebecca Shaw, Junmei Wang, Cassian Yee
Software Mentions: 10
Published: almost 5 years ago

10.7717/peerj.7907

motoRneuron: an open-source R toolbox for time-domain motor unit analyses
Cited by: 0
Author(s): Andrew J. Tweedell, Matthew S. Tenan
Software Mentions: 10
Published: over 6 years ago

10.1186/s40168-020-00895-w

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota
Cited by: 32
Author(s): Shashank Gupta, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Xuanji Li, Martin Steen Mortensen, Jakob Russel, Urvish Trivedi, Morten Arendt Rasmussen, Jakob Stokholm, Hans Bisgaard, Søren J. Sørensen
Software Mentions: 10
Published: over 5 years ago

10.7717/peerj.10118

High-throughput analysis of adaptation using barcoded strains ofSaccharomyces cerevisiae
Cited by: 8
Author(s): Vincent J. Fasanello, Ping Liu, Carlos A. Botero, Justin C. Fay
Software Mentions: 10
Published: over 5 years ago

10.1186/s12916-020-01595-w

Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection
Cited by: 30
Author(s): Guoxiang Xie, Xiaoning Wang, Runmin Wei, Jingye Wang, Aihua Zhao, Tianlu Chen, Yixing Wang, Hua Zhang, Zhun Xiao, Xin-Zhu Liu, Youping Deng, Linda L. Wong, Cynthia Rajani, Sandi A. Kwee, Hua Bian, Xin Gao, Ping Liu, Jia Wang
Software Mentions: 10
Published: almost 6 years ago

10.3389/fmicb.2020.00037

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Cited by: 164
Author(s): Arkadiy I. Garber, Kenneth H. Nealson, Akimitsu Okamoto, Sean M. McAllister, Clara S. Chan, Roman A. Barco, Nancy Merino
Software Mentions: 10
Published: about 6 years ago

10.3389/fimmu.2021.641495

Mitochondrial Reactive Oxygen Species Regulate Immune Responses of Macrophages to Aspergillus fumigatus
Cited by: 15
Author(s): Rémi Hatinguais, Arnab Pradhan, Gordon D. Brown, Alistair J. P. Brown, Adilia Warris, Elena Shekhova
Software Mentions: 10
Published: about 5 years ago

10.1038/s41598-019-46290-w

GeneHunt for rapid domain-specific annotation of glycoside hydrolases
Cited by: 14
Author(s): SC Nguyen, A. Flores, D. Talamantes, Furqan Dar, Adrian Roy L. Valdez, Jason P. Schwans, Renaud Berlemont
Software Mentions: 10
Published: almost 7 years ago

10.3389/fmicb.2020.597745

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce
Cited by: 15
Author(s): Saskia Windisch, Loreen Sommermann, Doreen Babin, Soumitra Paul Chowdhury, Rita Grosch, Narges Moradtalab, Frank Walker, Birgit Höglinger, Abbas El‐Hasan, Wolfgang Armbruster, Joseph Nesme, Søren J. Sørensen, Ingo Schellenberg, Joerg Geistlinger, Kornelia Smalla, Michael Rothballer, Uwe Ludewig, Günter Neumann
Software Mentions: 10
Published: over 5 years ago

10.1007/s00401-020-02224-9

Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt–Jakob disease
Cited by: 14
Author(s): Luke C. Dabin, Fernando Guntoro, Tracy Campbell, Tony Bélicard, Adam R. Smith, Rebecca G. Smith, Rachel Raybould, Jonathan M. Schott, Katie Lunnon, Peter Sarkies, John Collinge, Simon Mead, Emmanuelle Viré
Software Mentions: 10
Published: over 5 years ago

10.18632/aging.102434

Development and validation of a metastasis-associated prognostic signature based on single-cell RNA-seq in clear cell renal cell carcinoma
Cited by: 28
Author(s): Chuanjie Zhang, Hongchao He, Xin Hu, Ao Liu, Da Huang, Yu Xu, Lu Chen, Danfeng Xu
Software Mentions: 10
Published: over 6 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: about 5 years ago

10.1371/journal.pone.0250477

Geometric morphometric analysis of spore shapes improves identification of fungi
Cited by: 0
Author(s): Alexander Ordynets, Sarah Jayne Kessler, Ewald Langer
Software Mentions: 10
Published: over 4 years ago

10.1080/19336896.2020.1751574

Estimation of amyloid aggregate sizes with semi-denaturing detergent agarose gel electrophoresis and its limitations
Cited by: 10
Author(s): Polina Drozdova, Yury A. Barbitoff, М. В. Белоусов, Rostislav K. Skitchenko, Tatyana Rogoza, Jeremy Y Leclercq, Andrey V. Kajava, Andrew G. Matveenko, Galina A. Zhouravleva, Stanislav A. Bondarev
Software Mentions: 10
Published: over 6 years ago

10.1111/jcmm.15848

m6A RNA methylation regulators could contribute to the occurrence of chronic obstructive pulmonary disease
Cited by: 43
Author(s): Xinwei Huang, Dongjin Lv, Yao Xiao, Min Li, Hong Zhang
Software Mentions: 10
Published: over 5 years ago

10.1186/s12864-015-2356-9

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization
Cited by: 33
Author(s): Shanrong Zhao, Li Xi, Jie Quan, Hualin Simon Xi, Ying Zhang, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 10
Published: over 10 years ago

10.1111/jcmm.16619

Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinoma
Cited by: 17
Author(s): Ping Yu, L. Tong, Yujia Song, Hui Qü, Ying Chen
Software Mentions: 10
Published: almost 5 years ago

10.1098/rspb.2021.0343

A multi-faceted comparative perspective on elevational beta-diversity: the patterns and their causes
Cited by: 17
Author(s): Yuanbao Du, Liqing Fan, Zaifu Xu, Zhixin Wen, Tianlong Cai, Anderson Feijó, Junhua Hu, Fumin Lei, Qisen Yang, Huijie Qiao
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41598-019-45491-7

The future of coffee and cocoa agroforestry in a warmer Mesoamerica
Cited by: 58
Author(s): Kauê de Sousa, Maarten van Zonneveld, Milena Holmgren, Roeland Kindt, Jenny C. Ordóñez
Software Mentions: 10
Published: almost 7 years ago

10.3389/fgene.2021.695130

A Novel Signature Constructed by Immune-Related LncRNA Predicts the Immune Landscape of Colorectal Cancer
Cited by: 7
Author(s): Mengyu Sun, Tongyue Zhang, Yijun Wang, Wenjie Huang, Limin Xia
Software Mentions: 10
Published: over 4 years ago

10.1099/mgen.0.000552

Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen
Cited by: 6
Author(s): Josephine Grützke, Mayada Gwida, Carlus Deneke, Holger Brendebach, Michaela Projahn, Alexander Schattschneider, Dirk Hofreuter, Maged El-Ashker, Burkhard Malorny, Sascha Al Dahouk
Software Mentions: 10
Published: almost 5 years ago

10.18632/aging.202174

Periodontitis in elderly patients with type 2 diabetes mellitus: impact on gut microbiota and systemic inflammation
Cited by: 18
Author(s): Jinyou Li, Haifeng Lü, Hengchao Wu, Shunmei Huang, Lufang Chen, Qifeng Gui, Wenjing Zhou, Yichen Yang, Yue Wu, Hua Zhang, Qin Zhang, Yunmei Yang
Software Mentions: 10
Published: over 5 years ago

10.1186/s12864-021-07388-6

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: about 5 years ago

10.1172/jci.insight.147535

The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2–infected patients by sex and age
Cited by: 12
Author(s): Paula Paccielli Freire, Amélia Pasqual Marques, G. Baiocchi, Lena F. Schimke, Dennyson Leandro M. Fonseca, Ranieri Coelho Salgado, Igor Salerno Filgueiras, Sarah M.S. Napoleao, Desirée Rodrigues Plaça, Karen Tiemi Akashi, Thiago Dominguez Crespo Hirata, Nadia El Khawanky, Lasse Melvær Giil, Gustavo Cabral-Miranda, Robson Francisco Carvalho, Luís Carlos S. Ferreira, Antônio Condino‐Neto, Helder I. Nakaya, Igor Jurišica, Hans D. Ochs, Niels Olsen Saraiva Câmara, Vera Lúcia Garcia Calich, Otávio Cabral-Marques
Software Mentions: 10
Published: almost 5 years ago

10.1172/jci.insight.145854

Cell-autonomous retinoic acid receptor signaling has stage-specific effects on mouse enteric nervous system
Cited by: 6
Author(s): Tao Gao, Elizabeth C. Wright-Jin, Rajarshi Sengupta, Jessica B. Anderson, Robert O. Heuckeroth
Software Mentions: 10
Published: almost 5 years ago

10.3389/fcell.2021.731790

Identification and Validation of a Nine-Gene Amino Acid Metabolism-Related Risk Signature in HCC
Cited by: 34
Author(s): Yajuan Zhao, Junli Zhang, Shuhan Wang, Qianqian Jiang, Ke Xu
Software Mentions: 10
Published: over 4 years ago

10.1093/gigascience/giaa060

SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
Cited by: 35
Author(s): Wenxi Wang, Zihao Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Mingming Xin, Huiru Peng, Yingyin Yao, Qixin Sun, Weilong Guo
Software Mentions: 10
Published: almost 6 years ago

10.1186/s12864-019-6181-4

Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)
Cited by: 12
Author(s): Jianjun Fu, Wenbin Zhu, Lanmei Wang, Ming Luo, Fei Song, Zaijie Dong
Software Mentions: 10
Published: over 6 years ago

10.3390/microorganisms9071487

Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
Cited by: 20
Author(s): Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja‐Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman‐Yassky, Tove Agner
Software Mentions: 10
Published: almost 5 years ago

10.1093/gigascience/giz064

TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer
Cited by: 6
Author(s): Amartya Singh, Gyan Bhanot, Hossein Khiabanian
Software Mentions: 10
Published: almost 7 years ago

10.1186/s40360-021-00505-x

Causal inference multiple imputation investigation of the impact of cannabinoids and other substances on ethnic differentials in US testicular cancer incidence
Cited by: 26
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 10
Published: almost 5 years ago

10.1093/aje/kwaa127

Conditional Cash Transfer Program and Leprosy Incidence: Analysis of 12.9 Million Families From the 100 Million Brazilian Cohort
Cited by: 15
Author(s): Júlia Moreira Pescarini, Elizabeth Williamson, Maria Yury Ichihara, Rosemeire Leovigildo Fiaccone, Laura Forastiere, Anna Ramond, Joilda Silva Nery, Maria Lúcia Fernandes Penna, Agostino Strina, Sandra Reis, Liam Smeeth, Laura C. Rodrigues, Elizabeth B Brickley, Gerson Oliveira Penna, Marcos Barreto
Software Mentions: 10
Published: almost 6 years ago

10.3389/pore.2021.594649

Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis
Cited by: 7
Author(s): Xi Zhang, Junjun Zhang, Yang Liu, Jie Li, Juan Tan, Zewen Song
Software Mentions: 10
Published: about 5 years ago

10.3389/fimmu.2016.00372

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts
Cited by: 52
Author(s): Chaim A. Schramm, Zizhang Sheng, Zhenhai Zhang, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
Software Mentions: 10
Published: over 9 years ago

10.1093/femsec/fiab127

Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost
Cited by: 1
Author(s): Gilda Varliero, Muhammad Rafiq, Swati Singh, Annabel Summerfield, Fotis Sgouridis, Donald A. Cowan, Gary Barker
Software Mentions: 10
Published: over 4 years ago

10.1007/s11357-021-00424-z

Impact of COVID-19 on ischemic stroke care in Hungary
Cited by: 5
Author(s): Péter Pál Böjti, G. Szilágyi, Balázs Dobi, Rita Stang, I Szikora, Balázs Kis, Ákos Kornfeld, Csaba Óváry, Lóránd Eröss, Péter Banczerowski, Wojciech Kuczyński, Dániel Bereczki
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-019-46168-x

Cytotoxic unsaturated electrophilic compounds commonly target the ubiquitin proteasome system
Cited by: 16
Author(s): Karthik Selvaraju, Arjan Mofers, Paola Pellegrini, Johannes Salomonsson, Alexandra Ahlner, Vivian Morad, Ellin-Kristina Hillert, Belén Espinosa, Elias S.J. Arnér, Lasse Jensen, Jonas Malmström, Maria V. Turkina, Pádraig D’Arcy, Michael A. Walters, Maria Sunnerhagen, Stig Linder
Software Mentions: 10
Published: almost 7 years ago

10.3389/fimmu.2021.622563

9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Cited by: 17
Author(s): Kexin Yan, Yuxiu Lu, Zhangyong Yan, Yutao Wang
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: about 6 years ago

10.1186/s13071-020-04461-z

Oviposition of Aedes japonicus japonicus (Diptera: Culicidae) and associated native species in relation to season, temperature and land use in western Germany
Cited by: 12
Author(s): Linus Früh, Helge Kampen, Marcel B. Koban, Nadja Pernat, Günter A. Schaub, Doreen Werner
Software Mentions: 10
Published: over 5 years ago

10.1007/s00253-021-11449-x

Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota
Cited by: 6
Author(s): Alice Checcucci, Diana Luise, Monica Marianna Modesto, Federico Correa, Paolo Bosi, Paola Mattarelli, Paolo Trevisi
Software Mentions: 10
Published: over 4 years ago

10.1186/s12864-015-2250-5

Leveraging global gene expression patterns to predict expression of unmeasured genes
Cited by: 3
Author(s): James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty
Software Mentions: 10
Published: over 10 years ago

10.1111/eva.13143

Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus )
Cited by: 20
Author(s): Laura Benestan, Quentin Rougemont, Caroline Senay, Éric Normandeau, Éric Parent, Rick M. Rideout, Louis Bernatchez, Yvan Lambert, Céline Audet, Gérard Parent
Software Mentions: 10
Published: over 5 years ago

10.1002/cam4.4071

Integrative analysis of immune molecular subtypes and microenvironment characteristics of bladder cancer
Cited by: 5
Author(s): Jinlong Cao, Jianpeng Li, Xin Yang, Pan Li, Zhiqiang Yao, Dali Han, Lijun Ying, Lijie Wang, Junqiang Tian
Software Mentions: 10
Published: almost 5 years ago

10.1534/g3.120.401309

CeMbio - TheCaenorhabditis elegansMicrobiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: over 5 years ago

10.3389/fpsyg.2020.555576

Trail Pheromone Does Not Modulate Subjective Reward Evaluation in Lasius niger Ants
Cited by: 3
Author(s): Felix B. Oberhauser, Stephanie Wendt, Tomer J. Czaczkes
Software Mentions: 10
Published: over 5 years ago

10.1534/g3.120.401534

A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts
Cited by: 3
Author(s): Matthew Chung, Preston J. Basting, Rayanna S. Patkus, Alexandra Grote, Ashley N. Luck, Elodie Ghedin, Barton E. Slatko, Michelle L. Michalski, Jeremy M. Foster, Casey M. Bergman, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 5 years ago

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Papers Mentioning ggplot2 11,441