cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-41452-2

Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans
Cited by: 21
Author(s): Jason P. Chan, Justin Wright, Hoi Tong Wong, Anastasia Ardasheva, Jamey T. Brumbaugh, Christopher J. McLimans, Regina Lamendella
Software Mentions: 5
Published: about 7 years ago

10.3390/cancers12051084

Multimodal Targeted Deep Sequencing of Circulating Tumor Cells and Matched Cell-Free DNA Provides a More Comprehensive Tool to Identify Therapeutic Targets in Metastatic Breast Cancer Patients
Cited by: 13
Author(s): Corinna Keup, Markus Storbeck, Siegfried Hauch, Peter F. Hahn, Markus Sprenger-Haussels, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir‐Bauer
Software Mentions: 5
Published: about 6 years ago

10.1007/s11104-017-3325-7

Impacts of peat bulk density, ash deposition and rainwater chemistry on establishment of peatland mosses
Cited by: 8
Author(s): Alice Noble, Sheila M. Palmer, David J. Glaves, Alistair Crowle, Joseph Holden
Software Mentions: 5
Published: almost 9 years ago

10.3389/fgene.2020.615680

Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma
Cited by: 5
Author(s): Miao Su, Kuangyuan Qiao, Xing Xie, Xinying Zhu, Fu-Lai Gao, Changjuan Li, Dongqiang Zhao
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-43091-z

A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model
Cited by: 10
Author(s): Tatjana Sajic, Rodolfo Ciuffa, Vera Lemos, Pan Xu, Valentina Leone, Chen Li, Evan G. Williams, Georgios Makris, Amir Banaei‐Esfahani, Mathias Heikenwälder, Kristina Schoonjans, Ruedi Aebersold
Software Mentions: 5
Published: about 7 years ago

10.3389/fpls.2019.00963

Identification of a Dominant Chlorosis Phenotype Through a Forward Screen of the Triticum turgidum cv. Kronos TILLING Population
Cited by: 17
Author(s): Sophie A Harrington, Nicolás Cobo, Miroslava Karafiátová, Jaroslav Doležel, Philippa Borrill, Cristóbal Uauy
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2021.569020

Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China
Cited by: 3
Author(s): Li Ma, Geng Wu, Jian Yang, Liuqin Huang, Dorji Phurbu, Wenjun Li, Hongchen Jiang
Software Mentions: 5
Published: almost 5 years ago

10.3390/plants10020267

Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover
Cited by: 5
Author(s): Axel J Giudicatti, Ariel Hernán Tomassi, Pablo Andrés Manavella, Agustín Lucas Arce
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-43907-y

Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño
Cited by: 31
Author(s): Allison R. Kolbe, Manuel Aira, María Gómez-Brandòn, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-019-44042-4

Refining the Genomic Region Containing a Major Locus Controlling Fruit Maturity in Peach
Cited by: 12
Author(s): Hanny Elsadr, Sherif M. Sherif, Travis Banks, Daryl J. Somers, Jayasankar Subramanian
Software Mentions: 5
Published: about 7 years ago

10.1155/2021/7391560

The Effect of Ferroptosis-Related Genes on Prognosis and Tumor Mutational Burden in Hepatocellular Carcinoma
Cited by: 8
Author(s): Hao Zhang, Renzheng Liu, Lin Sun, Weidong Guo, Xiao Hu
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-019-56472-1

Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia
Cited by: 8
Author(s): Mercedeh Movassagh, Cliff I. Oduor, Catherine S. Forconi, Ann M. Moormann, Jeffrey A. Bailey
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-019-57108-0

Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation
Cited by: 15
Author(s): Wilhelm Bertrams, Kathrin Griss, Maria Han, Kerstin Seidel, Andreas Klemmer, Alexandra Sittka-Stark, Stefan Hippenstiel, Norbert Suttorp, Florian Finkernagel, Jochen Wilhelm, Timm Greulich, Claus Vogelmeier, Julio Vera, Bernd Schmeck
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-019-57168-2

Competing Risk Analyses of Medullary Carcinoma of Breast in Comparison to Infiltrating Ductal Carcinoma
Cited by: 10
Author(s): Dongjun Dai, Rongkai Shi, Zhuo Wang, Yiwei Zhong, Vivian Y. Shin, Hongchuan Jin, Xian Wang
Software Mentions: 5
Published: over 6 years ago

10.3390/plants9070886

Gigaspora margarita and Its Endobacterium Modulate Symbiotic Marker Genes in Tomato Roots under Combined Water and Nutrient Stress
Cited by: 4
Author(s): Matteo Chialva, Luisa Lanfranco, Gianluca Guazzotti, Veronica Santoro, Mara Novero, Paola Bonfante
Software Mentions: 5
Published: almost 6 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

10.3389/fpls.2019.00214

Root-Associated Fungal Communities From Two Phenologically Contrasting Silver Fir (Abies alba Mill.) Groups of Trees
Cited by: 18
Author(s): Tina Unuk, Tijana Martinović, Domen Finžgar, Nataša Šibanc, Tine Grebenc, Hojka Kraigher
Software Mentions: 5
Published: over 7 years ago

10.3390/cancers11121951

Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia
Cited by: 17
Author(s): Antonella Padella, Giorgia Simonetti, Giulia Paciello, George Giotopoulos, Carmen Baldazzi, Simona Righi, Martina Ghetti, Anna Stengel, Viviana Guadagnuolo, Rossella De Tommaso, Cristina Papayannidis, Valentina Robustelli, Eugenia Franchini, Andrea Ghelli Luserna di Rorà, Anna Ferrari, Maria Chiara Fontana, Samantha Bruno, Emanuela Ottaviani, Simona Soverini, Clelia Tiziana Storlazzi, Claudia Haferlach, Elena Sabattini, Nicoletta Testoni, Ilaria Iacobucci, Brian J.P. Huntly, Elisa Ficarra, Giovanni Martinelli
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-60564-8

16S rRNA gene sequencing reveals an altered composition of the gut microbiota in chickens infected with a nephropathogenic infectious bronchitis virus
Cited by: 10
Author(s): Puzhi Xu, Yan Shi, Ping Liu, Yulin Yang, Changming Zhou, Guyue Li, Junrong Luo, Caiying Zhang, Cao H, Guoliang Hu, Xiaomin Guo
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-61216-7

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm
Cited by: 72
Author(s): Simone Scalabrin, Lucile Toniutti, Gabriele Di Gaspero, Davide Scaglione, Gabriele Magris, Michele Vidotto, Sara Pinosio, Frederica Cattonaro, Federica Magni, Irena Jurman, Mario Cerutti, F. S. Liverani, Luciano Navarini, Lorenzo Del Terra, Gloria Pellegrino, Manuela Rosanna Ruosi, Nicola Vitulo, Giorgio Valle, Alberto Pallavicini, G. Graziosi, Patricia E. Klein, Nolan Bentley, Seth C. Murray, William Solano, Amin Al Hakimi, Timothy Schilling, Christophe Montagnon, Michèle Morgante, Benoît Bertrand
Software Mentions: 5
Published: over 6 years ago

10.1177/0379572120973908

Changes in Retinol Binding Protein 4 Level in Undernourished Children After a Nutrition Intervention Are Positively Associated With Mother’s Weight but Negatively With Mother’s Height, Intake of Whole Milk, and Markers of Systemic Inflammation: Results From a Community-Based Intervention Study
Cited by: 0
Author(s): Subhasish Das, Amran Gazi, Mehedi Hasan, Shah Mohammad Fahim, Ashraful Alam, Md. Shabab Hossain, Mustafa Mahfuz, Tahmeed Ahmed
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.11422

The relationship between PLOD1 expression level and glioma prognosis investigated using public databases
Cited by: 5
Author(s): Lei Tian, Huandi Zhou, Guohui Wang, Wen Yan Wang, Yuehong Li, Xiaoying Xue
Software Mentions: 5
Published: about 5 years ago

10.3389/fmed.2021.716869

An Immune Signature Robustly Predicts Clinical Deterioration for Hepatitis C Virus-Related Early-Stage Cirrhosis Patients
Cited by: 1
Author(s): Cheng Guo, Chunyan Dong, Junjie Zhang, Rui Wang, Zhe Wang, Jie Zhou, Wei Wang, Bing Ji, Ben Ma, Yanli Ge, Zhirong Wang
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-63274-3

Epidemiological and aetiological characteristics of hand, foot, and mouth disease in Sichuan Province, China, 2011–2017
Cited by: 15
Author(s): Di Peng, Yue Ma, Yaqiong Liu, Qiang Lv, Fei Yin
Software Mentions: 5
Published: about 6 years ago

10.3389/fpls.2019.00156

Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens
Cited by: 12
Author(s): Anne L. Sternberger, Megan J. Bowman, Colin Kruse, Kevin L. Childs, Harvey E. Ballard, Sarah E. Wyatt
Software Mentions: 5
Published: over 7 years ago

10.3390/cancers13092115

Chromatin-Directed Proteomics Identifies ZNF84 as a p53-Independent Regulator of p21 in Genotoxic Stress Response
Cited by: 8
Author(s): Anna Strzeszewska-Potyrała, Karolina Staniak, Joanna Czarnecka‐Herok, Mahmoud-Reza Rafiee, Marcin Herok, Grażyna Mosieniak, Jeroen Krijgsveld, Ewa Sikora
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj.8172

Exploring profile and potential influencers of vaginal microbiome among asymptomatic pregnant Chinese women
Cited by: 10
Author(s): Yining He, Yun Huang, Zhengyin Zhang, Fei Yu, Yuejie Zheng
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-64393-7

Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study
Cited by: 13
Author(s): Manuela de Oliveira Ramalho, Christophe Duplais, Jérôme Orivel, Alain Déjean, Joshua C. Gibson, Andrew V. Suarez, Corrie S. Moreau
Software Mentions: 5
Published: about 6 years ago

10.7717/peerj.6964

Coastal fish assemblages and predation pressure in northern-central Chilean Lessonia trabeculata kelp forests and barren grounds
Cited by: 10
Author(s): Nicolás Riquelme-Pérez, Catalina A. Musrri, Wolfgang Stotz, Osvaldo Cerda, Oscar Pino-Olivares, Martín Thiel
Software Mentions: 5
Published: about 7 years ago

10.7717/peerj.1900

A comparison of species composition and community assemblage of secondary forests between the birch and pine-oak belts in the mid-altitude zone of the Qinling Mountains, China
Cited by: 13
Author(s): Zongzheng Chai, Dexiang Wang
Software Mentions: 5
Published: about 10 years ago

10.3389/fmicb.2018.02077

Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos
Cited by: 237
Author(s): Alba Pérez-Cataluña, Nuria Salas-Massó, Ana L. Diéguez, Sabela Balboa, Alberto Lema, Jesús L. Romalde, María José Figueras
Software Mentions: 5
Published: almost 8 years ago

10.3389/fgene.2018.00670

The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation
Cited by: 5
Author(s): Michael T. Zimmermann
Software Mentions: 5
Published: over 7 years ago

10.1093/femsec/fiy225

Highly competitive fungi manipulate bacterial communities in decomposing beech wood (Fagus sylvatica)
Cited by: 29
Author(s): Sarah Johnston, Jennifer Hiscox, Melanie Savoury, Lynne Boddy, Andrew J. Weightman
Software Mentions: 5
Published: over 7 years ago

10.3389/fpls.2020.01140

Development of a Novel Phenotypic Roadmap to Improve Blueberry Quality and Storability
Cited by: 10
Author(s): Brian Farneti, F. Emanuelli, Iuliia Khomenko, M. Ajelli, Franco Biasioli, L. Giongo
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-021-83030-5

Big trees drive forest structure patterns across a lowland Amazon regrowth gradient
Cited by: 9
Author(s): Tassiana Maylla Fontoura Caron, Victor Juan Ulises Rodriguez Chuma, Alexander Arévalo Sandi, D. Ryan Norris
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-83355-1

Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
Cited by: 10
Author(s): Calvin Sjaarda, Nazneen Rustom, Gerald A. Evans, David Huang, Santiago Pérez-Patrigeón, Melissa Hudson, Henry Wong, Zhengxin Sun, T Hugh Guan, Muhammad Ayub, Cláudio N. Soares, Robert I. Colautti, Prameet M. Sheth
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers13030365

Genome-Wide Circular RNA Expression Patterns Reflect Resistance to Immunomodulatory Drugs in Multiple Myeloma Cells
Cited by: 18
Author(s): Theresa Jakobsen, Mette Dahl, Konstantinos Dimopoulos, Kirsten Grønbæk, Jørgen Kjems, Lasse Sommer Kristensen
Software Mentions: 5
Published: over 5 years ago

10.1002/2211-5463.13085

IGLL5 is correlated with tumor‐infiltrating immune cells in clear cell renal cell carcinoma
Cited by: 11
Author(s): Zian Xia, Xingyuan Wang, Licheng Cai, Wengang Jian, Cheng Zhang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-81796-2

Characterising cancer-associated fibroblast heterogeneity in non-small cell lung cancer: a systematic review and meta-analysis
Cited by: 22
Author(s): Andrew J Irvine, Sara Waise, Edward W. Green, Beth Stuart, Gareth J. Thomas
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-83524-2

Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures
Cited by: 37
Author(s): Shashank Gupta, Malini Shariff, Gaura Chaturvedi, Arpit Sharma, Nitin Goel, Monika Yadav, Martin Steen Mortensen, Søren J. Sørensen, Mitali Mukerji, Nar Singh Chauhan
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12030702

STAT3 Mutation Is Associated with STAT3 Activation in CD30+ ALK− ALCL
Cited by: 16
Author(s): Emma Andersson, Oscar Brück, Till Braun, Susanna Mannisto, Leena Saikko, Sonja Lagström, Pekka Ellonen, Sirpa Leppä, Marco Herling, Panu E. Kovanen, Satu Mustjoki
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-84407-2

Premating barriers in young sympatric snail species
Cited by: 6
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Arseniy Lobov, Polina Tikanova, Egor A. Repkin, Irina Y. Babkina, Marina Panova, Natalia A. Mikhailova, Andrei I. Granovitch
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.11342

Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
Cited by: 6
Author(s): Qingqing Wang, Xiaoyan Yu, Zhewen Zheng, Fengxia Chen, Ningning Yang, Youwen Zhou
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-86135-z

Analysis of the response of the cell membrane of Saccharomyces cerevisiae during the detoxification of common lignocellulosic inhibitors
Cited by: 10
Author(s): Pau Cabañeros López, Chuantao Peng, Nils Arneborg, Helena Junicke, Krist V. Gernaey
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2018.00491

Dynamic Changes in the Global MicroRNAome and Transcriptome Identify Key Nodes Associated With Ovarian Development in Chickens
Cited by: 12
Author(s): Wenwen Wang, Keliang Wu, Meiting Jia, Siyuan Sun, Kang Li, Qin Zhang, Hui Tang
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-021-86294-z

Development of a novel transcription factors-related prognostic signature for serous ovarian cancer
Cited by: 5
Author(s): Lei He, Nayiyuan Wu, Zhaoyi Liu, Yongchang Chen, Quan Cheng, Jing Wang
Software Mentions: 5
Published: about 5 years ago

10.2196/28892

Mental Health and Behavior of College Students During the COVID-19 Pandemic: Longitudinal Mobile Smartphone and Ecological Momentary Assessment Study, Part II
Cited by: 25
Author(s): Dante L Mack, Alex W DaSilva, Courtney Rogers, Elin Hedlund, Eilis I Murphy, Vlado Vojdanovski, Jane Plomp, Weichen Wang, Subigya Nepal, Paul E. Holtzheimer, Dylan D. Wagner, Nicholas C. Jacobson, Meghan L. Meyer, Andrew T. Campbell, Jeremy F. Huckins
Software Mentions: 5
Published: about 5 years ago

10.3390/cancers12010075

A Case-Control Analysis of the Impact of Venous Thromboembolic Disease on Quality of Life of Patients with Cancer: Quality of Life in Cancer (Qca) Study
Cited by: 19
Author(s): Lucía Marín-Barrera, Andrés J. Muñoz Martín, Eduardo Ríos-Herranz, Ignacio García-Escobar, Carmen Beato, Carme Font, Estefania Oncala-Sibajas, Alfonso Revuelta-Rodriguez, Maria Carmen Areses, Victor Rivas-Jimenez, Maria Angeles Moreno-Santos, Aitor Ballaz-Quincoces, Juan-Bosco López-Sáez, Iria Gallego, Teresa Elías-Hernández, María Isabel Asensio-Cruz, Leyre Chasco-Eguilaz, Gonzalo Garcia-Gonzalez, Purificación Estévez-García, Remedios Otero, Jorge Lima-Alvarez
Software Mentions: 5
Published: over 6 years ago

10.3390/cancers11010101

SP1 and STAT3 Functionally Synergize to Induce the RhoU Small GTPase and a Subclass of Non-canonical WNT Responsive Genes Correlating with Poor Prognosis in Breast Cancer
Cited by: 16
Author(s): Emanuele Monteleone, Valeria Orecchia, Paola Corrieri, Davide Schiavone, Lidia Avalle, Enrico Moiso, Aurora Savino, Ivan Molineris, Paolo Provero, Valeria Poli
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.9350

Effects of microbial evolution dominate those of experimental host-mediated indirect selection
Cited by: 19
Author(s): Jigyasa Arora, Margaret A. Mars Brisbin, Alexander S. Mikheyev
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.62850

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Cited by: 24
Author(s): Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash Ahmed, Rubin Be, Troy J. Comi, Shounak Bhogale, Syed Sameed Husain, Charles Blatti, Martin Middendorf, Saurabh Sinha, Sriram Chandrasekaran, Gene E. Robinson
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.58533

A new role for histone demethylases in the maintenance of plant genome integrity
Cited by: 28
Author(s): Javier Antunez-Sanchez, Matthew Naish, Juan S. Ramirez-Prado, Sho Ohno, Ying Huang, Alexander Dawson, Korawit Opassathian, Deborah Manza‐Mianza, Federico Ariel, Cécile Raynaud, Anjar Tri Wibowo, Josquin Daron, Minako Ueda, David Latrasse, R. Keith Slotkin, Detlef Weigel, Moussa Benhamed, José Gutierrez-Marcos
Software Mentions: 5
Published: over 5 years ago

10.12688/f1000research.6536.1

A reanalysis of mouse ENCODE comparative gene expression data
Cited by: 90
Author(s): Yoav Gilad, Orna Mizrahi-Man
Software Mentions: 5
Published: about 11 years ago

10.7717/peerj.9368

Tip dating with fossil sites and stratigraphic sequences
Cited by: 7
Author(s): Benedict King, Martin Rücklin
Software Mentions: 5
Published: almost 6 years ago

10.3389/fpls.2020.00515

Temperature Variability at Local Scale in the Bordeaux Area. Relations With Environmental Factors and Impact on Vine Phenology
Cited by: 29
Author(s): Laure de Rességuier, Séverine Mary, Renan Le Roux, Théo Petitjean, Hervé Quénol, Cornelis van Leeuwen
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2021.706814

A Nomogram Integrating Ferroptosis- and Immune-Related Biomarkers for Prediction of Overall Survival in Lung Adenocarcinoma
Cited by: 2
Author(s): Mengyu Chai, Xiuchun Li, Yaxin Zhang, Yemeng Tang, Pingping Shu, Lin Jia, Ke–Qing Shi, Liangxing Wang, Xiaoying Huang
Software Mentions: 5
Published: almost 5 years ago

10.3390/cancers12113208

Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma
Cited by: 2
Author(s): Daniel A. Rodriguez, Margarita Dorantes Sánchez, Christina L. Decatur, Zélia M. Corrêa, Eden R. Martin, J. William Harbour
Software Mentions: 5
Published: over 5 years ago

10.12688/f1000research.55027.1

rmcorrShiny: A web and standalone application for repeated measures correlation
Cited by: 14
Author(s): Laura R. Marusich, Jonathan Z. Bakdash
Software Mentions: 5
Published: almost 5 years ago

10.7717/peerj.2387

Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea
Cited by: 33
Author(s): Beth L. Mindel, Francis Neat, Clive N. Trueman, Thomas J. Webb, Julia L. Blanchard
Software Mentions: 5
Published: almost 10 years ago

10.1038/s41598-021-86926-4

Assessing the effectiveness of two intervention methods for stony coral tissue loss disease on Montastraea cavernosa
Cited by: 32
Author(s): Erin N. Shilling, Ian R. Combs, Joshua D. Voss
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2020.01138

Bioinformatics Analysis of Gut Microbiota and CNS Transcriptome in Virus-Induced Acute Myelitis and Chronic Inflammatory Demyelination; Potential Association of Distinct Bacteria With CNS IgA Upregulation
Cited by: 11
Author(s): Seiichi Omura, Fumitaka Sato, Ah-Mee Park, Mitsugu Fujita, Sundar Khadka, Yumina Nakamura, Aoshi Katsuki, Kenji Nishio, Felicity N. E. Gavins, Ikuo Tsunoda
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12874-016-0229-9

Health Equity Assessment Toolkit (HEAT): software for exploring and comparing health inequalities in countries
Cited by: 64
Author(s): Ahmad Reza Hosseinpoor, Devaki Nambiar, Anne Schlotheuber, Daniel D. Reidpath, Zev Ross
Software Mentions: 5
Published: over 9 years ago

10.3390/cancers12010092

Human Tumor–Derived Matrix Improves the Predictability of Head and Neck Cancer Drug Testing
Cited by: 17
Author(s): Katja Tuomainen, Ahmed Al‐Samadi, Swapnil Potdar, Laura Turunen, Minna Turunen, Piia-Riitta Karhemo, Paula Bergman, Maija Risteli, Pirjo Åström, Riia Tiikkaja, Reidar Grénman, Krister Wennerberg, Outi Monni, Tuula Salo
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.58659

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation
Cited by: 22
Author(s): Bjoern Gaertner, Sebastiaan van Heesch, Valentin Schneider-Lunitz, Jana Felicitas Schulz, Franziska Witte, Susanne Blachut, Steven Nguyen, Richard L. Wong, Ileana Matta, Norbert Hübner
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.61968

Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species
Cited by: 36
Author(s): Arnaud Belcour, Clémence Frioux, Méziane Aïte, Anthony Bretaudeau, Falk Hildebrand, Anne Siegel
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12102959

De Novo A-to-I RNA Editing Discovery in lncRNA
Cited by: 15
Author(s): Domenico Alessandro Silvestris, Chiara Scopa, Sara Hanchi, Franco Locatelli, Angela Gallo
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2020.04.035

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
Cited by: 1,817
Author(s): Carly G.K. Ziegler, Samuel J. Allon, Sarah K. Nyquist, Ian Mbano, Vincent N. Miao, Constantine N. Tzouanas, Yuming Cao, Ashraf S. Yousif, Julia Bals, Blake M. Hauser, Jared Feldman, Christoph Muus, Marc H. Wadsworth, Samuel W. Kazer, Travis Hughes, Benjamin Doran, G. James Gatter, Marko Vukovic, Faith Taliaferro, Benjamin E. Mead, Zhiru Guo, Jennifer Wang, Delphine Gras, Magali Plaisant, Meshal Ansari, Ilias Angelidis, Heiko Adler, Jennifer M.S. Sucre, Chase J. Taylor, Brian M. Lin, Avinash Waghray, Vanessa Mitsialis, Daniel F. Dwyer, Kathleen M. Buchheit, Joshua A. Boyce, Nora A. Barrett, Tanya M. Laidlaw, Shaina L. Carroll, Lucrezia Colonna, Victor Tkachev, Christopher W. Peterson, Alison Yu, Hengqi Zheng, Hannah P. Gideon, Caylin G. Winchell, Philana Ling Lin, Colin D. Bingle, Scott B. Snapper, Jonathan A. Kropski, Fabian J. Theis, Herbert B. Schiller, Laure‐Emmanuelle Zaragosi, Pascal Barbry, Alasdair Leslie, Hans–Peter Kiem, JoAnne L. Flynn, Sarah M. Fortune, Bonnie Berger, Robert W. Finberg, Leslie S. Kean, Manuel Garber, Aaron Schmidt, Daniel Lingwood, Alex K. Shalek, José Ordovás-Montañés, Nicholas E. Banovich, Alvis Brāzma, Tushar J. Desai, Thao Duong, Oliver Eickelberg, Christine S. Falk, Michael Farzan, Ian A. Glass, Muzlifah Haniffa, Péter Horváth, Deborah T. Hung, Naftali Kaminski, Mark A. Krasnow, Malte Kühnemund, Robert Lafyatis, Haeock Lee, Sylvie Leroy, Sten Linnarson, Joakim Lundeberg, Kerstin B. Meyer, Alexander V. Misharin, Martijn C. Nawijn, M Nikolíc, Dana Pe’er, Joseph E. Powell, Stephen R. Quake, Jay Rajagopal, Purushothama Rao Tata, Emma L. Rawlins, Aviv Regev, Paul A. Reyfman, Mauricio Rojas, Orit Rosen, Kourosh Saeb‐Parsy, Christos Samakovlis, Herbert B. Schiller, Joachim L. Schultze, Max A. Seibold, Douglas P. Shepherd, Jason R. Spence, Avrum Spira, Xin Sun, Sarah A. Teichmann, Fabian J. Theis, Alexander M. Tsankov, Maarten van den Berge, Michael von Papen, Jeffrey A. Whitsett, Ramnik J. Xavier, Yan Xu, Kun Zhang
Software Mentions: 5
Published: about 6 years ago

10.3389/fonc.2021.637193

Oncogenic B-Myb Is Associated With Deregulation of the DREAM-Mediated Cell Cycle Gene Expression Program in High Grade Serous Ovarian Carcinoma Clinical Tumor Samples
Cited by: 5
Author(s): Audra N. Iness, Lisa Rubinsak, Steven J. Meas, Jessica Chaoul, Sadia Sayeed, Raghavendra Pillappa, Sarah M. Temkin, Mikhail G. Dozmorov, Larisa Litovchick
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.9893

Spatial ecology of little egret (Egretta garzetta) in Hong Kong uncovers preference for commercial fishponds
Cited by: 5
Author(s): Chun-Chiu Pang, Yik-Hei Sung, Yun-tak Chung, Hak-king Ying, Helen Hoi Ning Fong, Yat-tung Yu
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.8141

Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano
Cited by: 5
Author(s): Jenny Urbina, Tara Chestnut, Donelle Schwalm, Jenn Allen, Taal Levi
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-87564-6

The ANTsX ecosystem for quantitative biological and medical imaging
Cited by: 56
Author(s): Nicholas J. Tustison, Philip A. Cook, Andrew J. Holbrook, Hans J. Johnson, John Muschelli, Gabriel A. Devenyi, Jeffrey T. Duda, Sandhitsu R. Das, Nicholas Cullen, Daniel L. Gillen, Michael A. Yassa, James L. Stone, James C. Gee, Brian Avants
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj.8317

Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing
Cited by: 65
Author(s): Xiaowei Chen, Haixiang Sun, Fei Jiang, Yan Shen, Xin Li, HU Xue-ju, Xiao-Min Shen, Pingmin Wei
Software Mentions: 5
Published: over 6 years ago

10.3389/fonc.2021.643503

Transcriptome Analyses Identify a Metabolic Gene Signature Indicative of Antitumor Immunosuppression of EGFR Wild Type Lung Cancers With Low PD-L1 Expression
Cited by: 1
Author(s): Min Wang, Jie Zhu, Fang Zhao, Jiani Xiao
Software Mentions: 5
Published: almost 5 years ago

10.7717/peerj.7075

Visual complexity modelling based on image features fusion of multiple kernels
Cited by: 14
Author(s): Carlos Fernández-Lozano, Adrián Carballal, Penousal Machado, Andréa Cynthia Santos, Juan Romero
Software Mentions: 5
Published: almost 7 years ago

10.1002/ece3.7957

Drought has negative consequences on aphid fitness and plant vigor: Insights from a meta‐analysis
Cited by: 15
Author(s): Daniel J. Leybourne, Katharine Preedy, Tracy A. Valentine, Jorunn I. B. Bos, Alison J. Karley
Software Mentions: 5
Published: almost 5 years ago

10.3389/fimmu.2018.02547

Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation
Cited by: 36
Author(s): Athina Soragia Gkazi, Ben Margetts, Teresa Attenborough, Lana Mhaldien, Joseph F. Standing, Theres Oakes, James Heather, John Booth, Marlène Pasquet, Robert Chiesa, Paul Veys, Nigel Klein, Benjamin M. Chain, Robin E. Callard, Stuart Adams
Software Mentions: 5
Published: over 7 years ago

10.1111/mec.13769

The genetic architecture of resistance to virus infection inDrosophila
Cited by: 50
Author(s): Rodrigo Cogni, Chuan Cao, Jonathan P. Day, Calum Bridson, Francis M. Jiggins
Software Mentions: 5
Published: almost 10 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

10.1007/s00122-021-03828-9

Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation
Cited by: 6
Author(s): Caijin Chen, Anthony J. Travis, Mahmud Hossain, Rafiqul Islam, Adam H. Price, Gareth J. Norton
Software Mentions: 5
Published: about 5 years ago

10.1007/s10126-021-10033-8

Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
Cited by: 5
Author(s): Magnus Alm Rosenblad, Anna Abramova, Ulrika Lind, Pall I. Olason, Stefania Giacomello, Björn Nystedt, Anders Blomberg
Software Mentions: 5
Published: about 5 years ago

10.1186/s12974-019-1418-3

Correlation of alteration of HLA-F expression and clinical characterization in 593 brain glioma samples
Cited by: 36
Author(s): Enshan Feng, Tingyu Liang, Xiaoyong Wang, Juan Du, Kai Tang, Xiaoxuan Wang, Fang Wang, Guoxiang You
Software Mentions: 5
Published: over 7 years ago

10.7150/thno.51795

Genome-wide CRISPR/Cas9 knockout screening uncovers a novel inflammatory pathway critical for resistance to arginine-deprivation therapy
Cited by: 11
Author(s): Cheng‐Ying Chu, Yi‐Ching Lee, Cheng-Han Hsieh, Chi‐Tai Yeh, Tsu‐Yi Chao, Po-Hung Chen, I-Hsuan Lin, Tsung‐Han Hsieh, Jing Wen Shih, Chia‐Hsiung Cheng, Che-Chang Chang, Po-Chuan Lin, Yuan‐Li Huang, Tsung-Ming Chen, Yun Yen, David K. Ann, Hsing-Jien Kung
Software Mentions: 5
Published: over 5 years ago

10.1186/s12911-020-1115-2

A prognostic index based on a fourteen long non-coding RNA signature to predict the recurrence-free survival for muscle-invasive bladder cancer patients
Cited by: 3
Author(s): Xiaolong Zhang, Meng Zhang, Xuanping Zhang, Xiaoyan Zhu, Jiayin Wang
Software Mentions: 5
Published: almost 6 years ago

10.7150/thno.60031

Astrocytic YAP protects the optic nerve and retina in an experimental autoimmune encephalomyelitis model through TGF-β signaling
Cited by: 27
Author(s): Wei Qian, Xuemeng Miao, Jingjing Zhang, Ludan Xiang, Xiuchun Li, Xiaomei Bao, Siyu Du, Mianxian Wang, Shuangda Miao, Yiren Fan, Wei Wang, Xingxing Xu, Xiya Shen, Dongren Yang, Xiwu Wang, Yuanyuan Fang, Li‐Xin Hu, Xuyi Pan, Haoru Dong, Hui Wang, Ying Wang, Jia Li, Zhihui Huang
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.63930

An in vitro stem cell model of human epiblast and yolk sac interaction
Cited by: 16
Author(s): Kirsty Mackinlay, Bailey A. T. Weatherbee, Viviane Souza Rosa, Charlotte E. Handford, George R. Hudson, Tim Coorens, Lygia V. Pereira, Sam Behjati, Ludovic Vallier, Marta Shahbazi, Magdalena Zernicka‐Goetz
Software Mentions: 5
Published: almost 5 years ago

10.1111/1759-7714.14002

Significance of tumor mutation burden and immune infiltration in thymic epithelial tumors
Cited by: 8
Author(s): Zi-Ming Wang, Qiang Xu, David Kaul, Mahmoud Ismail, Harun Badakhshi
Software Mentions: 5
Published: about 5 years ago

10.1038/s41418-021-00784-1

Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment
Cited by: 58
Author(s): Safae Terrisse, Lisa Derosa, Valerio Iebba, François Ghiringhelli, Inês Vaz-Luís, Guido Kroemer, Marine Fidelle, Stergios Christodoulidis, Nicola Segata, Andrew Maltez Thomas, Anne‐Laure Martin, Aude Sirven, Sibille Everhard, Fanny Aprahamian, Nitharsshini Nirmalathasan, Romy Aarnoutse, Marjolein L. Smidt, Janine Ziemons, Carlos Caldas, Sibylle Loibl, Carsten Denkert, Sylvère Durand, Claudia Iglesias, Filippo Pietrantonio, Bertrand Routy, Fabrice André, Edoardo Pasolli, Suzette Delaloge, Laurence Zitvogel
Software Mentions: 5
Published: about 5 years ago

10.1016/j.molcel.2018.09.033

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: over 7 years ago

10.18632/oncotarget.11772

Hypoxia-responsive miR-210 promotes self-renewal capacity of colon tumor-initiating cells by repressing ISCU and by inducing lactate production
Cited by: 47
Author(s): Pit Ullmann, Komal Qureshi-Baig, Fabien Rodriguez, Aurélien Ginolhac, Yannic Nonnenmacher, Dominik Ternes, Jil Weiler, Karoline Gäbler, Christelle Bahlawane, Karsten Hiller, Serge Haan, Elisabeth Letellier
Software Mentions: 5
Published: almost 10 years ago

10.3389/fmicb.2018.00973

A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains
Cited by: 15
Author(s): Xiangchen Li, Wenjun Tong, Lina Wang, Siddiq Ur Rahman, Gehong Wei, Shiheng Tao
Software Mentions: 5
Published: about 8 years ago

10.3390/toxins13050318

Risky Business: The Function of Play in a Venomous Mammal—The Javan Slow Loris (Nycticebus javanicus)
Cited by: 6
Author(s): Meg Barrett, Marco Campera, Thaís Q. Morcatty, Ariana Weldon, Katherine Hedger, Keely Q. Maynard, Muhammad Ali Imron, K. A. I. Nekaris
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2016.00772

Molecular Evidence for Metabolically Active Bacteria in the Atmosphere
Cited by: 72
Author(s): Ann M. Klein, Brendan J. M. Bohannan, Daniel A. Jaffe, David A. Levin, Jessica L. Green
Software Mentions: 5
Published: about 10 years ago

10.3390/toxins13080552

Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells
Cited by: 4
Author(s): Ilse Vanhoutte, Caroline De Tender, Kristel Demeyere, Mohamed F. Abdallah, Sarah Ommeslag, Pieter Vermeir, Sarah De Saeger, Jane Debode, Evelyne Meyer, Siska Croubels, Kris Audenaert, Leen De Gelder
Software Mentions: 5
Published: almost 5 years ago

10.1007/s00227-017-3279-6

Life-history responses to changing temperature and salinity of the Baltic Sea copepod Eurytemora affinis
Cited by: 22
Author(s): Konrad Karlsson, Simona Puiac, Monika Winder
Software Mentions: 5
Published: over 8 years ago

10.1093/molbev/msx270

Faster Evolving Primate Genes Are More Likely to Duplicate
Cited by: 35
Author(s): Áine O’Toole, Laurence D. Hurst, Aoife McLysaght
Software Mentions: 5
Published: over 8 years ago

10.1186/s12868-021-00635-2

Early postnatal irradiation‐induced age‐dependent changes in adult mouse brain: MRI based characterization
Cited by: 5
Author(s): Bo Ren, Isaac Huen, Zi Jun Wu, Hong Wang, Meng Yun Duan, Ilonka Guenther, Kritika Prakash, Feng Ru Tang
Software Mentions: 5
Published: about 5 years ago

10.1038/s41398-019-0384-y

Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism
Cited by: 63
Author(s): Manav Kapoor, Jen Chyong Wang, Sean P. Farris, Yunlong Liu, Jeanette N. McClintick, Ishaan Gupta, Jacquelyn L. Meyers, Sarah Bertelsen, Michael J. Chao, John I. Nürnberger, Jay A. Tischfield, Oscar Harari, Zeran Li, Victor Hesselbrock, Lance O. Bauer, Towfique Raj, Bernice Porjesz, Arpana Agrawal, Tatiana Foroud, Howard J. Edenberg, R. Dayne Mayfield, Alison Goate
Software Mentions: 5
Published: over 7 years ago

10.3389/fnins.2020.620723

Spatiotemporal Processing of Bimodal Odor Lateralization in the Brain Using Electroencephalography Microstates and Source Localization
Cited by: 2
Author(s): Christine Ida Hucke, Rebekka Heinen, Marlene Pacharra, Edmund Wascher, Christoph van Thriel
Software Mentions: 5
Published: over 5 years ago

10.1167/tvst.8.5.4

A Method to Calibrate the Carbon Dioxide (Chemical) Stimuli of Pneumatic Esthesiometer Externally
Cited by: 1
Author(s): Varadharajan Jayakumar, Trefford Simpson
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13100-020-00224-w

Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains
Cited by: 14
Author(s): Mahoko Takahashi Ueda, Kirill Kryukov, Satomi Mitsuhashi, Hiroaki Mitsuhashi, Tadashi Imanishi, So Nakagawa
Software Mentions: 5
Published: almost 6 years ago

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