cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1186/s12859-017-1936-x

Software for rapid time dependent ChIP-sequencing analysis (TDCA)
Cited by: 1
Author(s): Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David J. Vocadlo
Software Mentions: 9
Published: about 8 years ago

10.1371/journal.pntd.0006159

Barriers of attendance to dog rabies static point vaccination clinics in Blantyre, Malawi
Cited by: 30
Author(s): Stella Mazeri, Andrew D Gibson, Natascha Meunier, Barend M. deC. Bronsvoort, Ian Handel, Richard J. Mellanby, Luke Gamble
Software Mentions: 9
Published: about 8 years ago

10.1186/s12864-016-2886-9

OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis
Cited by: 32
Author(s): Alfredo Rago, Donald G. Gilbert, Jeong Hyeon Choi, Timothy B. Sackton, Xiaozhu Wang, Yogeshwar D. Kelkar, John H. Werren, John K. Colbourne
Software Mentions: 9
Published: over 9 years ago

10.3389/fpls.2019.00910

Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms
Cited by: 57
Author(s): Giovanni Del Frari, Alex Gobbi, Marie Rønne Aggerbeck, Helena Oliveira, Lars Hestbjerg Hansen, Ricardo B. Ferreira
Software Mentions: 9
Published: over 6 years ago

10.18632/aging.104064

Clinical and prognostic pan-cancer analysis of m6A RNA methylation regulators in four types of endocrine system tumors
Cited by: 29
Author(s): Kai Li, Hui Luo, Hui Luo, Xiao Zhu
Software Mentions: 9
Published: about 5 years ago

10.3389/fpls.2021.638738

Capturing and Selecting Senescence Variation in Wheat
Cited by: 11
Author(s): Elizabeth A. Chapman, Simon Orford, Jean-Luc Da Lage, Simon Griffiths
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12967-018-1608-2

NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome
Cited by: 13
Author(s): Luiza Handschuh, Paweł Wojciechowski, Maciej Kaźmierczak, Małgorzata Marcinkowska-Swojak, Magdalena Łuczak, Krzysztof Lewandowski, Mieczysław Komarnicki, Jacek Błażewicz, Marek Figlerowicz, Piotr Kozlowski
Software Mentions: 9
Published: over 7 years ago

10.1371/journal.pmed.1002362

Childhood adiposity and risk of type 1 diabetes: A Mendelian randomization study
Cited by: 86
Author(s): Jenny C Censin, Christoph Nowak, Nicholas Cooper, Peter Bergsten, John A. Todd, Tove Fall
Software Mentions: 9
Published: over 8 years ago

10.1186/s12967-021-02770-0

Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis
Cited by: 9
Author(s): Hui Zhang, Chang Xu, Shi Chen, Junying Zhang, Ting Qian, Zhuo Wang, Rong Ma, Jianzhong Wu, Feng Jiang, Jifeng Feng
Software Mentions: 9
Published: almost 5 years ago

10.1016/j.dib.2020.106651

Impact of malnutrition on survival in adult patients after elective cardiac surgery: Long-term follow up data
Cited by: 0
Author(s): Sergey Efremov, Tatiana Ionova, Tatiana Nikitina, Pavel E. Vedernikov, Timur Dzhumatov, Timofey S. Ovchinnikov, Abduvahhob A. Rashidov, Alexandr E Khomenko, Christian Stoppe, Daren K. Heyland, В. В. Ломиворотов
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pmed.1002686

Deep learning for chest radiograph diagnosis: A retrospective comparison of the CheXNeXt algorithm to practicing radiologists
Cited by: 755
Author(s): Pranav Rajpurkar, Jeremy Irvin, Robyn L. Ball, Kaylie Zhu, Brandon Yang, Hershel Mehta, Tony Duan, Daisy Yi Ding, Aarti Bagul, Curtis P. Langlotz, Bhavik N. Patel, Kristen W. Yeom, Katie Shpanskaya, Francis G. Blankenberg, Jayne Seekins, Timothy J. Amrhein, David A. Mong, Safwan Halabi, Evan J. Zucker, Andrew Y. Ng, Matthew P. Lungren
Software Mentions: 9
Published: about 7 years ago

10.18632/oncotarget.27271

Single cell correlation analysis of liquid and solid biopsies in metastatic colorectal cancer
Cited by: 10
Author(s): Anna Sandström Gerdtsson, Jana-Aletta Thiele, Stephanie N. Shishido, Serena Zheng, Randolph Schaffer, Kelly Bethel, Steven A. Curley, Heinz‐Josef Lenz, Diana L. Hanna, Jorgé Nieva, Anand Kolatkar, C.B. Congregado Ruiz, Mariam Rodrı́guez-Lee, Gerard J. Oakley, Jerry S.H. Lee, James Hicks, Peter Kühn
Software Mentions: 9
Published: about 6 years ago

10.3390/ijms22116160

Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis
Cited by: 10
Author(s): Federico Martinez‐Seidel, Olga Beine-Golovchuk, Yin-Chen Hsieh, Kheloud El Eshraky, Michał Górka, Bo-Eng Cheong, Erika Vanessa Jiménez-Posada, Dirk Walther, Aleksandra Skirycz, Ute Roessner, Joachim Kopka, Alexandre Augusto Pereira Firmino
Software Mentions: 9
Published: over 4 years ago

10.3390/ijms22136855

Concentrated Raw Fibers Enhance the Fiber-Degrading Capacity of a Synthetic Human Gut Microbiome
Cited by: 3
Author(s): Alex Steimle, Mareike Neumann, Erica T. Grant, Jonathan D. Turner, Mahesh S. Desai
Software Mentions: 9
Published: over 4 years ago

10.3389/fonc.2021.698856

A Novel Ferroptosis-Related Gene Model for Overall Survival Predictions of Bladder Urothelial Carcinoma Patients
Cited by: 9
Author(s): Min Zhang, Xin Zhang, Minghang Yu, Wei Zhang, Di Zhang, Song Zeng, Xi Wang, Xiaosong Hu
Software Mentions: 9
Published: over 4 years ago

10.3390/ijms22073411

Insights of Phenolic Pathway in Fruits: Transcriptional and Metabolic Profiling in Apricot (Prunus armeniaca)
Cited by: 6
Author(s): Helena Gómez-Martínez, Francisco Gil-Muñoz, Almudena Bermejo, Elena Zuriaga, M. L. Badenes
Software Mentions: 9
Published: almost 5 years ago

10.1111/1755-0998.13030

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
Cited by: 26
Author(s): Lukas Weilguny, Robert Kofler
Software Mentions: 9
Published: over 6 years ago

10.3390/ijms22063200

Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens
Cited by: 4
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Przemysław Kołodziej, Jolanta Szymańska, Bartosz J. Płachno, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 9
Published: almost 5 years ago

10.1002/aps3.11344

A basic dd <scp>RAD</scp> seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
Cited by: 20
Author(s): Ingrid E. Jordon‐Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels
Software Mentions: 9
Published: almost 6 years ago

10.3389/fonc.2021.624395

Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers
Cited by: 12
Author(s): Xiaonan Liu, Pei Wang, Xufei Teng, Zhang Zhang, Shuhui Song
Software Mentions: 9
Published: almost 5 years ago

10.3390/ijms21145044

Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth
Cited by: 10
Author(s): Elena Spada, Luciano Calzari, Luigi Corsaro, Teresa Fazia, Monica Mencarelli, Anna Maria Di Blasio, Luisa Bernardinelli, G. Zangheri, Michele Vignali, Davide Gentilini
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.ppat.1009577

Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF
Cited by: 11
Author(s): Xiaogang Cheng, Ancy Joseph, Victor Castro, Alice Chen-Liaw, Zachary L. Skidmore, Takaharu Ueno, Jun–ichi Fujisawa, Daniel A. Rauch, Grant A. Challen, Michael P. Martinez, Patrick Green, Malachi Griffith, Jacqueline E. Payton, John Edwards, Lee Ratner
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0220770

Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application
Cited by: 40
Author(s): Edward Lopatto, Jinlyung Choi, Alfredo Colina, Lanying Ma, Adina Howe, Shannon M. Hinsa-Leasure
Software Mentions: 9
Published: over 6 years ago

10.3390/jintelligence6030030

The Relation of Personality and Intelligence—What Can the Brunswik Symmetry Principle Tell Us?
Cited by: 80
Author(s): André Kretzschmar, Marion Spengler, Anna‐Lena Schubert, Ricarda Steinmayr, Matthias Ziegler
Software Mentions: 9
Published: over 7 years ago

10.3389/fmolb.2021.567327

Molecular and Clinical Characterization of LIGHT/TNFSF14 Expression at Transcriptional Level via 998 Samples With Brain Glioma
Cited by: 3
Author(s): Ying Yang, Wen Lv, Shi‐Hai Xu, Fei Shi, Aijun Shan, Jin Wang
Software Mentions: 9
Published: over 4 years ago

10.3758/s13414-018-1538-3

Bottom-up attention capture with distractor and target singletons defined in the same (color) dimension is not a matter of feature uncertainty
Cited by: 11
Author(s): Hanna Weichselbaum, Ulrich Ansorge
Software Mentions: 9
Published: over 7 years ago

10.1128/AEM.00121-20

Assessment of Soil Features on the Growth of Environmental Nontuberculous Mycobacterial Isolates from Hawai'i
Cited by: 15
Author(s): Cody Glickman, Ravleen Virdi, Nabeeh A. Hasan, L. Elaine Epperson, Leeza Brown, Stephanie N. Dawrs, James Crooks, Edward D. Chan, Michael Strong, Stephen T. Nelson, Jennifer R. Honda
Software Mentions: 9
Published: over 5 years ago

10.1186/s12864-018-4870-z

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
Cited by: 11
Author(s): Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Software Mentions: 9
Published: over 7 years ago

10.1016/j.comppsych.2019.152143

Longitudinal population subgroups of CRP and risk of depression in the ALSPAC birth cohort
Cited by: 11
Author(s): Emanuele F. Osimo, Jan S̆tochl, Stanley Zammit, Glyn Lewis, Peter B. Jones, Golam M. Khandaker
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-021-81051-8

Summer weather conditions influence winter survival of honey bees (Apis mellifera) in the northeastern United States
Cited by: 37
Author(s): Martina Calovi, Christina M. Grozinger, Douglas A. Miller, Sarah C. Goslee
Software Mentions: 9
Published: about 5 years ago

10.3389/fmolb.2020.604252

Prognostic Model of Colorectal Cancer Constructed by Eight Immune-Related Genes
Cited by: 14
Author(s): Shuting Wen, Lina He, Zhuotai Zhong, Hong Mi, Fengbin Liu
Software Mentions: 9
Published: about 5 years ago

10.2196/10076

Key Elements of mHealth Interventions to Successfully Increase Physical Activity: Meta-Regression
Cited by: 56
Author(s): Lisa V. Eckerstorfer, Norbert K. Tanzer, Claudia Vogrincic-Haselbacher, Gayannée Kedia, Hilmar Brohmer, Isabelle Dinslaken, Katja Corcoran
Software Mentions: 9
Published: over 7 years ago

10.1186/s13040-021-00267-6

eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals
Cited by: 11
Author(s): Theodore G. Drivas, Anastasia Lucas, Marylyn D. Ritchie
Software Mentions: 9
Published: over 4 years ago

10.3390/ijerph18084052

The Impact of Temperature on the Risk of COVID-19: A Multinational Study
Cited by: 5
Author(s): Ya‐Chen Yang, Jason Lee
Software Mentions: 9
Published: almost 5 years ago

10.2196/16442

Quality Awareness and Its Influence on the Evaluation of App Meta-Information by Physicians: Validation Study
Cited by: 8
Author(s): Urs‐Vito Albrecht, Theodor Framke, Ute von Jan
Software Mentions: 9
Published: about 6 years ago

10.3389/fonc.2020.573141

Significance of Tumor Mutation Burden in Immune Infiltration and Prognosis in Cutaneous Melanoma
Cited by: 57
Author(s): Kai Kang, Fucun Xie, Jianshan Mao, Yi Bai, Xiang Wang
Software Mentions: 9
Published: over 5 years ago

10.3390/ijerph18020658

Spatial-Temporal Modelling of Disease Risk Accounting for PM2.5 Exposure in the Province of Pavia: An Area of the Po Valley
Cited by: 3
Author(s): Leonardo Trivelli, Paola Borrelli, Ennio Cadum, Enrico Pisoni, Simona Villani
Software Mentions: 9
Published: about 5 years ago

10.3389/fmicb.2020.01536

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations
Cited by: 13
Author(s): Elias Broman, Xiaole Sun, Christian Stranne, Marco Salgado, Stefano Bonaglia, M. C. Geibel, Martin Jakobsson, Alf Norkko, Christoph Humborg, Francisco J. A. Nascimento
Software Mentions: 9
Published: over 5 years ago

10.3389/fpsyg.2021.636129

Psychological Differences Among Healthcare Workers of a Rehabilitation Institute During the COVID-19 Pandemic: A Two-Step Study
Cited by: 16
Author(s): Anna Panzeri, Silvia Rossi Ferrario, Paola Cerutti
Software Mentions: 9
Published: almost 5 years ago

10.3390/antiox10091424

S-Methyl-L-Ergothioneine to L-Ergothioneine Ratio in Urine Is a Marker of Cystine Lithiasis in a Cystinuria Mouse Model
Cited by: 2
Author(s): Miguel López de Heredia, Lourdes Muñoz, Ciriaco Carru, Salvatore Sotgia, Angelo Zinellu, C. Serra, Amadeu Llebaría, Yukio Kato, Virginia Nunes
Software Mentions: 9
Published: over 4 years ago

10.1128/mSystems.00897-19

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters
Cited by: 26
Author(s): Zachary Liechty, Christian Santos‐Medellín, Joseph Edwards, Bao‐Anh Thi Nguyen, David Mikhail, Shane Eason, Gregory C. Phillips, Venkatesan Sundaresan
Software Mentions: 9
Published: about 6 years ago

10.1186/s12864-018-5166-z

RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data
Cited by: 17
Author(s): Amanda Ernlund, Robert J. Schneider, Kelly V. Ruggles
Software Mentions: 9
Published: over 7 years ago

10.1042/BSR20201001

Identification of prognostic and metastasis-related alternative splicing signatures in hepatocellular carcinoma
Cited by: 11
Author(s): Runzhi Huang, Gaili Yan, Hao Sun, Jie Zhang, Dianwen Song, Rui Kong, Penghui Yan, Peng Hu, Aiqing Xie, Siqiao Wang, Juanwei Zhuang, Huabin Yin, Tong Meng, Zongqiang Huang
Software Mentions: 9
Published: over 5 years ago

10.3390/cancers13102498

Comparative Transcriptomics of Immune Checkpoint Inhibitor Myocarditis Identifies Guanylate Binding Protein 5 and 6 Dysregulation
Cited by: 16
Author(s): Daniel Finke, Markus Heckmann, Janek Salatzki, Johannes Riffel, Esther Herpel, Lucie Heinzerling, Benjamin Meder, Mirko Völkers, Oliver Müller, Norbert Frey, Hugo A. Katus, Florian Leuschner, Ziya Kaya, Lorenz Lehmann
Software Mentions: 9
Published: over 4 years ago

10.1128/mSystems.00081-18

Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality
Cited by: 16
Author(s): Sara R. Selitsky, David Marron, Lisle E. Mose, Joel S. Parker, Dirk P. Dittmer
Software Mentions: 9
Published: over 7 years ago

10.3390/cancers13061189

Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers
Cited by: 10
Author(s): Siddesh Southekal, Nitish K. Mishra, Chittibabu Guda
Software Mentions: 9
Published: almost 5 years ago

10.1128/mBio.00399-21

Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System
Cited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-021-94996-7

Avian vampire fly (Philornis downsi) mortality differs across Darwin’s finch host species
Cited by: 3
Author(s): Lauren K. Common, Petra Sumasgutner, Rachael Y. Dudaniec, Diane Colombelli‐Négrel, Sonia Kleindorfer
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-021-93800-w

Year-round high abundances of the world’s smallest marine vertebrate (Schindleria) in the Red Sea and worldwide associations with lunar phases
Cited by: 4
Author(s): Vanessa Robitzch, Víctor Molina-Valdivia, Jaiber J. Solano‐Iguaran, Mauricio F. Landaeta, Michael L. Berumen
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0177276

Succinct workflows for circulating tumor cells after enrichment: From systematic counting to mutational profiling
Cited by: 11
Author(s): Vernon G. Wong, Josephine Mun Yee Ko, Chi-Tat Lam, Maria Li Lung
Software Mentions: 9
Published: almost 9 years ago

10.1038/s41598-021-93699-3

Analysing omics data sets with weighted nodes networks (WNNets)
Cited by: 1
Author(s): Gabriele Tosadori, Dario Di Silvestre, Fausto Spoto, Pierluigi Mauri, Carlo Laudanna, Giovanni Scardoni
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0193164

Mosquito pornoscopy: Observation and interruption of Aedes aegypti copulation to determine female polyandric event and mixed progeny
Cited by: 10
Author(s): Danilo O. Carvalho, Samira Chuffi, Rafaella Sayuri Ioshino, I. C. S. Marques, Regina Fini, Maria Karina Costa, Helena Rocha Corrêa de Araújo, André Luis Costa-da-Silva, Bianca Burini Kojin, Margareth Lara Capurro
Software Mentions: 9
Published: almost 8 years ago

10.1186/s12866-021-02211-4

Microbiome characterization of defensive tissues in the model anemone Exaiptasia diaphana
Cited by: 10
Author(s): Justin Maire, Linda L. Blackall, Madeleine J. H. van Oppen
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-021-92648-4

Transmitting silks of maize have a complex and dynamic microbiome
Cited by: 5
Author(s): Eman M. Khalaf, Anuja Shrestha, Jeffrey Rinne, Michael D. J. Lynch, Charles Shearer, Victor Limay-Rios, L. M. Reid, Manish N. Raizada
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-021-92629-7

A cohort study to investigate sex-specific differences in ANCA-associated glomerulonephritis outcomes
Cited by: 8
Author(s): Jennifer Scott, Carolina Canepa, Antonia Buettner, Louise Ryan, Bróna Moloney, Sarah Cormican, Cathal Walsh, Arthur White, Alan D. Salama, Mark A. Little
Software Mentions: 9
Published: over 4 years ago

10.1186/s12862-020-01671-y

Sex determination systems in reptiles are related to ambient temperature but not to the level of climatic fluctuation
Cited by: 12
Author(s): Paola Cornejo‐Páramo, Andrés Lira‐Noriega, Ciro Ramírez-Suástegui, Fausto Méndez-de-la-Cruz, Tamás Székely, Araxi O. Urrutia, Diego Cortez
Software Mentions: 9
Published: over 5 years ago

10.3390/ijms21134763

The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose
Cited by: 15
Author(s): Michal Šíma, Kristýna Vrbová, Táňa Závodná, K. Hoňková, Irena Chvojková, Antonín Ambrož, Jǐŕı Kléma, Andrea Rössnerová, Kateřina Poláková, Tomáš Malina, Jan Belza, Jan Topinka, Pavel Rőssner
Software Mentions: 9
Published: over 5 years ago

10.3389/fmicb.2020.587972

DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil
Cited by: 11
Author(s): Julian Yu, Michael J. Pavia, Lauren M. Deem, Susan E. Crow, Jonathan Deenik, C. Ryan Penton
Software Mentions: 9
Published: about 5 years ago

10.1186/s12862-019-1406-3

Specificity of resistance and geographic patterns of virulence in a vertebrate host-parasite system
Cited by: 9
Author(s): Agnes Piecyk, Olivia Roth, Martin Kalbe
Software Mentions: 9
Published: almost 7 years ago

10.1371/journal.pone.0247790

Parasitism and host behavior in the context of a changing environment: The Holocene record of the commercially important bivalve Chamelea gallina, northern Italy
Cited by: 3
Author(s): John Warren Huntley, Daniele Scarponi
Software Mentions: 9
Published: almost 5 years ago

10.3390/cancers11081057

Mining of Self-Organizing Map Gene-Expression Portraits Reveals Prognostic Stratification of HPV-Positive Head and Neck Squamous Cell Carcinoma
Cited by: 21
Author(s): Laura D. Locati, Mara Serena Serafini, Maria Federica Iannò, Andrea Carenzo, Ester Orlandi, Carlo Resteghin, Stefano Cavalieri, Paolo Bossi, Silvana Canevari, Lisa Licitra, Loris De Cecco
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-021-81773-9

Verifying explainability of a deep learning tissue classifier trained on RNA-seq data
Cited by: 26
Author(s): Melvyn Yap, Rebecca L. Johnston, Helena Foley, Samual MacDonald, Olga Kondrashova, Khoa Tran, Kátia Nones, Lambros T. Koufariotis, Cameron Bean, John V. Pearson, Maciej Trzaskowski, Nicola Waddell
Software Mentions: 9
Published: about 5 years ago

10.1093/molbev/msaa266

Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes
Cited by: 10
Author(s): Rhett M. Rautsaw, Tristan D. Schramer, Rachel Acuña, Lindsay N Arick, Mark DiMeo, Kathryn P. Mercier, Michael Schrum, Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Christopher L. Parkinson
Software Mentions: 9
Published: over 5 years ago

10.1186/s12862-021-01806-9

The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)
Cited by: 8
Author(s): Polina Drozdova, Alena Kizenko, Alexandra Saranchina, Anton Gurkov, Maria Firulyova, E. B. Govorukhina, Maxim A. Timofeyev
Software Mentions: 9
Published: almost 5 years ago

10.3389/fmicb.2020.575707

Evaluating the Potential Antibiotic Resistance Status in Environment Based on the Trait of Microbial Community
Cited by: 9
Author(s): Zhiguo Su, Bei Huang, Quanquan Mu, Donghui Wen
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2021.663617

Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment
Cited by: 10
Author(s): Fangfang Xu, Jiacheng Shen, Shaohua Xu
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-020-76792-x

Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific
Cited by: 3
Author(s): Hillary A. Smith, Jessica A. Conlan, F. Joseph Pollock, Naohiro Wada, Amanda Shore, Julia Yun-Hsuan Hung, Greta S. Aeby, Bette L. Willis, David S. Francis, David G. Bourne
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-020-76603-3

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots
Cited by: 230
Author(s): Joachim Goedhart, Martijn S. Luijsterburg
Software Mentions: 9
Published: about 5 years ago

10.1534/g3.120.401436

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat
Cited by: 18
Author(s): Sophie A Harrington, Anna E Backhaus, Ajit Singh, Keywan Hassani‐Pak, Cristóbal Uauy
Software Mentions: 9
Published: over 5 years ago

10.15252/msb.20198849

High‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network
Cited by: 24
Author(s): Antje Dittmann, Norman J. Kennedy, Nina L Soltero, Nader Morshed, Miyeko Mana, Ömer H. Yılmaz, Roger J. Davis, Forest M. White
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-020-76315-8

Robustly forecasting maize yields in Tanzania based on climatic predictors
Cited by: 18
Author(s): Rahel Laudien, Bernhard Schauberger, David Makowski, Christoph Gornott
Software Mentions: 9
Published: over 5 years ago

10.18632/aging.203455

Construction of an immune-related lncRNA signature as a novel prognosis biomarker for LUAD
Cited by: 9
Author(s): Hang Chen, Wei Shen, Saiqi Ni, Menglu Sang, Shibo Wu, Yinyu Mu, Kaitai Liu, Ni Li, Linwen Zhu, Guodong Xu
Software Mentions: 9
Published: over 4 years ago

10.1186/s12885-020-6638-5

Multiple m6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis
Cited by: 33
Author(s): Nanfang Qu, Sanyu Qin, Xuemei Zhang, Xiaotong Bo, Zhengchun Liu, Chao Tan, Guiqiong Wen, Haixing Jiang
Software Mentions: 9
Published: almost 6 years ago

10.15698/mic2021.08.757

Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes
Cited by: 13
Author(s): Maria Paula Rueda‐Mejia, Lukas Nägeli, Stefanie Lutz, Richard D. Hayes, Adithi R. Varadarajan, Igor V. Grigoriev, Christian H. Ahrens, Florian M. Freimoser
Software Mentions: 9
Published: over 4 years ago

10.1186/s12885-021-07807-7

Molecular subtypes based on DNA methylation predict prognosis in lung squamous cell carcinoma
Cited by: 10
Author(s): Xiushen Li, Kechao Nie, Zhihua Zheng, Ruisheng Zhou, Yu‐Sheng Huang, Zeng Jie Ye, Fan He, Ying Tang
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0149237

Optimizing Viral Discovery in Bats
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Author(s): Caroline Young, Kevin J. Olival
Software Mentions: 9
Published: about 10 years ago

10.3389/fimmu.2018.02074

Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vκ Gene Rearrangement in Pre-B Cells and Pro-B Cells
Cited by: 13
Author(s): Eden Kleiman, Salvatore Loguercio, Ann J. Feeney
Software Mentions: 9
Published: over 7 years ago

10.18632/aging.102424

The construction and analysis of tumor-infiltrating immune cell and ceRNA networks in recurrent soft tissue sarcoma
Cited by: 29
Author(s): Runzhi Huang, Tong Meng, Rui Chen, Penghui Yan, Jie Zhang, Peng Hu, Xiaolong Zhu, Huabin Yin, Dianwen Song, Zongqiang Huang
Software Mentions: 9
Published: about 6 years ago

10.7717/peerj.4473

pcr: an R package for quality assessment, analysis and testing of qPCR data
Cited by: 72
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 9
Published: almost 8 years ago

10.3389/fgene.2020.00785

Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer
Cited by: 3
Author(s): Zihu Guo, Han Liang, Yingxue Fu, Ziyin Wu, Yaohua Ma, Yueping Liu, Haiqing Wang, Li Jiang, Shengnan Liang, Zhenzhong Wang, Furong Li, Wei Xiao, Jingbo Wang, Yonghua Wang
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-020-62842-x

A year in the life of a North Atlantic seabird: behavioural and energetic adjustments during the annual cycle
Cited by: 28
Author(s): Ruth E. Dunn, Sarah Wanless, Francis Daunt, Michael Harris, Jonathan A. Green
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-020-62186-6

Site-specific molecular analysis of the bacteriota on worn spectacles
Cited by: 4
Author(s): Birgit Fritz, Melanie März, Severin Weis, Siegfried Wahl, Focke Ziemssen, Markus Egert
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-020-65087-w

Expression of genes of the Pho regulon is altered in Streptomyces coelicolor
Cited by: 22
Author(s): Aarón Millán-Oropeza, Céline Henry, Clara Lejeune, Michelle David, Marie‐Joëlle Virolle
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-021-91205-3

Diurnal preference and depressive symptomatology: a meta-analysis
Cited by: 22
Author(s): Ray Norbury
Software Mentions: 9
Published: over 4 years ago

10.7717/peerj.9017

Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon
Cited by: 10
Author(s): Jake Ivan P. Baquiran, Michael Angelou L. Nada, Niño Posadas, Dana P. Manogan, Patrick C. Cabaitan, Cecilia Conaco
Software Mentions: 9
Published: almost 6 years ago

10.3389/fpsyg.2020.533593

Students’ Motivation and Affection Profiles and Their Relation to Mathematics Achievement, Persistence, and Behaviors
Cited by: 7
Author(s): Feiya Xiao, Li Sun
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0229887

Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets
Cited by: 4
Author(s): Jueeli D. Vaidya, S. van Gastelen, Hauke Smidt, Caroline M. Plugge, Joan E. Edwards
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-020-59292-w

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering
Cited by: 5
Author(s): Johanne Ahrenfeldt, Madina Waisi, Isabella Charlotte Loft, Philip Thomas Lanken Conradsen Clausen, Rosa Lundbye Allesøe, Judit Szarvas, René S. Hendriksen, Frank Møller Aarestrup, Ole Lund
Software Mentions: 9
Published: almost 6 years ago

10.1186/1471-2288-14-91

Comparing classification methods for diffuse reflectance spectra to improve tissue specific laser surgery
Cited by: 8
Author(s): Alexander Engelhardt, Rajesh Kanawade, Christian Knipfer, Matthias Schmid, Florian Stelzle, Werner Adler
Software Mentions: 9
Published: over 11 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-020-59516-z

Variability in estimated gene expression among commonly used RNA-seq pipelines
Cited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: almost 6 years ago

10.3389/fgene.2020.00192

Integrated Analysis Identifies a Nine-microRNA Signature Biomarker for Diagnosis and Prognosis in Colorectal Cancer
Cited by: 31
Author(s): Ziyang Di, Maojun Di, Weihua Fu, Qiang Tang, Yanwei Liu, Peijie Lei, Xinsheng Gu, Tong Liu, Min Sun
Software Mentions: 9
Published: almost 6 years ago

10.1371/journal.pone.0241025

Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species
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Author(s): Brenda Gabriela Diaz, Maria Imaculada Zucchi, Alessandro Alves‐Pereira, Caléo Panhoca de Almeida, Aline Costa Lima Moraes, Suelen Alves Vianna, Joaquim Adelino de Azevedo-Filho, Carlos Augusto Colombo
Software Mentions: 9
Published: over 4 years ago

10.3389/fgene.2021.691465

ARG2, MAP4K5 and TSTA3 as Diagnostic Markers of Steroid-Induced Osteonecrosis of the Femoral Head and Their Correlation With Immune Infiltration
Cited by: 10
Author(s): Rongguo Yu, Jiayu Zhang, Youguang Zhuo, Hong Xu, Jie Ye, Susu Tang, Nannan Liu, Yiyuan Zhang
Software Mentions: 9
Published: over 4 years ago

10.7717/peerj.5217

Avian community characteristics and demographics reveal how conservation value of regenerating tropical dry forest changes with forest age
Cited by: 8
Author(s): Steven C. Latta, Nathan L. Brouwer, Danilo Mejía, María M. Paulino
Software Mentions: 9
Published: over 7 years ago

10.1186/s13062-021-00293-8

Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers
Cited by: 7
Author(s): Sergio Romera-Giner, Zoraida Andreu Martínez, Francisco García‐García, Marta R. Hidalgo
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-017-14576-6

Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Cited by: 37
Author(s): Meiser Anjuli, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
Software Mentions: 9
Published: over 8 years ago

10.7717/peerj.6746

Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau
Cited by: 19
Author(s): Pengyu Zhao, Jiabing Bao, Xue Wang, Yi Liu, Cui Li, Bo Chai
Software Mentions: 9
Published: almost 7 years ago

10.1186/s40478-019-0851-y

Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas
Cited by: 12
Author(s): Ruslan Al‐Ali, Katharina Bauer, Jong‐Whi Park, Ruba Al-Abdulla, Valentina Fermi, Andreas von Deimling, Christel Herold‐Mende, Jan‐Philipp Mallm, Carl Herrmann, Wolfgang Wick, Şevin Turcan
Software Mentions: 9
Published: about 6 years ago

10.3389/fgene.2021.661988

Identification of Aging-Related Genes Associated With Clinical and Prognostic Features of Hepatocellular Carcinoma
Cited by: 12
Author(s): Xingte Chen, Lei Wang, Liang Hong, Zhiying Su, Xiaohong Zhong, Han Zhou, Xueqing Zhang, Junxin Wang, Lingdong Shao
Software Mentions: 9
Published: over 4 years ago

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