Scientific Papers with Software Mentions

10.1371/journal.pone.0149238

Feeding Ecology of Northeast Atlantic Mackerel, Norwegian Spring-Spawning Herring and Blue Whiting in the Norwegian Sea
Cited by: 66
Author(s): Eneko Bachiller, Georg Skaret, Leif Nøttestad, Aril Slotte
Software Mentions: 4
Published: over 10 years ago

10.3390/microorganisms9010005

Effects of Thermal Stress on the Gut Microbiome of Juvenile Milkfish (Chanos chanos)
Cited by: 24
Author(s): Christiane Hassenrück, Hannes Reinwald, Andreas Kunzmann, Inken Tiedemann, Astrid Gärdes
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.119.400757

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Cited by: 9
Author(s): Pengfei Qiao, Lin Meng, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore, Michael J. Scanlon
Software Mentions: 4
Published: over 6 years ago

10.3389/fendo.2019.00735

Reduced Expression of PLCXD3 Associates With Disruption of Glucose Sensing and Insulin Signaling in Pancreatic β-Cells
Cited by: 18
Author(s): Hayat Aljaibeji, Debasmita Mukhopadhyay, Abdul Khader Mohammed, Sarah Dhaiban, Mahmood Yaseen Hachim, Noha Mousaad Elemam, Nabil Sulaiman, Albert Salehi, Jalal Taneera
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00133-16

SSUnique: Detecting Sequence Novelty in Microbiome Surveys
Cited by: 4
Author(s): Michael D. J. Lynch, Josh D. Neufeld
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-018-31618-9

Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L.
Cited by: 21
Author(s): Mehdi Soltani Howyzeh, Seyed Ahmad Sadat Noori, Vahid Shariati J, Mahboubeh Amiripour
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2020.01363

Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System
Cited by: 47
Author(s): Ali Srour, Hala A. Ammar, Arjun Subedi, Mirian F. Pimentel, Rachel L. Cook, Jason P. Bond, Ahmad M. Fakhoury
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0188640

Epidemiological and genetic characteristics of EV71 in hand, foot, and mouth disease in Guangxi, southern China, from 2010 to 2015
Cited by: 27
Author(s): Minmei Chen, Yu‐Min Ju, Zhiping Xie, Zhou Kai-jiao, Yi Tan, Mo JianJun
Software Mentions: 4
Published: over 8 years ago

10.1093/gbe/evy155

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective
Cited by: 43
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Omid Shams Solari, James Brown, John K. Colbourne, Michael E. Pfrender, Leda Mirbahai
Software Mentions: 4
Published: almost 8 years ago

10.1128/mSystems.00211-17

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese
Cited by: 55
Author(s): Andrea S. Bertuzzi, Aaron M. Walsh, Jeremiah J. Sheehan, Paul D. Cotter, Fiona Crispie, P.L.H. McSweeney, Kieran N. Kilcawley, Mary C. Rea
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0228439

FastEmbed: Predicting vulnerability exploitation possibility based on ensemble machine learning algorithm
Cited by: 39
Author(s): Yong Fang, Yongcheng Liu, Cheng Huang, Liang Liu
Software Mentions: 4
Published: over 6 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40462-019-0188-y

Time and energy costs of different foraging choices in an avian generalist species
Cited by: 13
Author(s): Alejandro Sotillo, Jeroen Baert, Wendt Müller, Eric Stienen, Amadeu M.V.M. Soares, Luc Lens
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.566734

Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging
Cited by: 4
Author(s): Yujuan Gui, Mélanie Thomas, Pierre Garcia, Mona Karout, Rashi Halder, Alessandro Michelucci, Heike Kollmus, Cuiqi Zhou, Shlomo Melmed, Klaus Schughart, Rudi Balling, Michel Mittelbronn, Joseph H. Nadeau, Robert W. Williams, Thomas Sauter, Manuel Buttini, Lasse Sinkkonen
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0083725

A Lower Level of Forced Expiratory Volume in 1 Second Is a Risk Factor for All-Cause and Cardiovascular Mortality in a Japanese Population: The Takahata Study
Cited by: 34
Author(s): Yoko Shibata, Sumito Inoue, Akira Igarashi, Keiko Yamauchi, Shuichi Abe, Yasuko Aida, Keiko Nunomiya, Masamichi Sato, Hiroshi Nakano, Kento Sato, Takako Nemoto, Tomomi Kimura, Tetsu Watanabe, Tsuneo Konta, Makoto Daimon, Yoshiyuki Ueno, Takeshi Kato, Takamasa Kayama, Isao Kubota
Software Mentions: 4
Published: over 12 years ago

10.3389/fpls.2020.567249

Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon
Cited by: 7
Author(s): Kanae Masuda, Naoko Fujita, Ho Wen Yang, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Takashi Akagi
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-019-1671-x

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
Cited by: 101
Author(s): Daniel Alpern, Vincent Gardeux, Julie Russeil, Bastien Mangeat, Antonio C. A. Meireles-Filho, Romane Breysse, David L. Hacker, Bart Deplancke
Software Mentions: 4
Published: over 7 years ago

10.1186/s40425-019-0609-x

Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Cited by: 22
Author(s): Sehhoon Park, Je‐Gun Joung, Min Ye, Jae‐Yong Nam, Daeun Ryu, Dongryul Oh, Woong-Yang Park, Sehoon Lee, Yoon La Choi, Jin Seok Ahn, Myung‐Ju Ahn, Keunchil Park, Jong‐Mu Sun
Software Mentions: 4
Published: about 7 years ago

10.1097/MD.0000000000010153

Comorbid risks of psychological disorders and gastroesophageal reflux disorder using the national health insurance service—National Sample Cohort
Cited by: 11
Author(s): Ye-Seul Lee, Bo‐Hyoung Jang, Seong‐Gyu Ko, Younbyoung Chae
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-016-1276-2

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Cited by: 87
Author(s): Sergi Sayols, Denise Scherzinger, H. Klein
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijerph18136934

A Latent Class Analysis of Health Lifestyles in Relation to Suicidality among Adolescents in Mauritius
Cited by: 6
Author(s): Fanny Hoogstoel, Sékou Samadoulougou, Vincent Lorant, Fati Kirakoya‐Samadoulougou
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2020.577718

Augmenting E Protein Activity Impairs cDC2 Differentiation at the Pre-cDC Stage
Cited by: 0
Author(s): Sandra Bajaña, Kevin L. Thomas, Constantin Georgescu, Ying Zhao, Jonathan D. Wren, Susan Kovats, Xiaohong Sun
Software Mentions: 4
Published: over 5 years ago

10.3389/fsurg.2021.717084

Identification of a Novel Signature Predicting Overall Survival in Head and Neck Squamous Cell Carcinoma
Cited by: 4
Author(s): Haige Zheng, Huixian Liu, Yumin Lu, Li Hengguo
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0226057

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Cited by: 16
Author(s): Surendra Chaurasiya, Scott Widmann, Cindy Botero, Chin-Yo Lin, Jan‐Åke Gustafsson, Anders Ström
Software Mentions: 4
Published: about 6 years ago

10.1007/s00401-021-02327-x

Targeting fibroblast growth factor receptors to combat aggressive ependymoma
Cited by: 9
Author(s): Daniela Lötsch, Dominik Kirchhofer, Bernhard Englinger, Li Jiang, Konstantin Okonechnikov, Daniel Senfter, Anna Laemmerer, Lisa Gabler, Christine Pirker, Andrew M. Donson, Peter Bannauer, Pia Korbel, Carola Jaunecker, Jens-Martin Hübner, Lisa Mayr, Sibylle Madlener, Maria Theresa Schmook, Gerda Ricken, Kendra K. Maaß, Michael Grusch, Klaus Holzmann, Bettina Grasl‐Kraupp, Sabine Spiegl-Kreinecker, Jennifer L. Hsu, Christian Dorfer, Karl Rössler, Amedeo A. Azizi, Nicholas Foreman, Andreas Peyrl, Christine Haberler, Thomas Czech, Irene Slavc, Mariella G. Filbin, Kristian W. Pajtler, Marcel Kool, Walter Berger, Johannes Gojo
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.45374

Gender variations in citation distributions in medicine are very small and due to self-citation and journal prestige
Cited by: 43
Author(s): Jens Peter Andersen, Jesper W. Schneider, Reshma Jagsi, Mathias Wullum Nielsen
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-75259-3

Decrease in social cohesion in a colonial seabird under a perturbation regime
Cited by: 6
Author(s): Meritxell Genovart, Olivier Giménez, Albert Bertolero, Rémi Choquet, Daniel Oró, Roger Pradel
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-13-42

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies
Cited by: 17
Author(s): Michiel E. Adriaens, Magali Jaillard, Lars Eijssen, Claus Mayer, Chris T. Evelo
Software Mentions: 4
Published: over 14 years ago

10.1098/rsos.171571

Testing social learning of anti-predator responses in juvenile jackdaws: the importance of accounting for levels of agitation
Cited by: 17
Author(s): Guillam E. McIvor, Victoria E. Lee, Alex Thornton
Software Mentions: 4
Published: over 8 years ago

10.18632/aging.203122

Do eye diseases increase the risk of arthritis in the elderly population?
Cited by: 7
Author(s): Wenyi Jin, Qian Yao, Zilin Liu, Weipeng Cao, Yubiao Zhang, Zhifei Che, Hao Peng
Software Mentions: 4
Published: about 5 years ago

10.3389/fmed.2021.654635

Multi-Omics Integrative Analysis Uncovers Molecular Subtypes and mRNAs as Therapeutic Targets for Liver Cancer
Cited by: 4
Author(s): Yi Shen, Wei Xiong, Qi Gu, Qin Zhang, Yue Jia, Changsong Liu, Duan Wang
Software Mentions: 4
Published: about 5 years ago

10.1093/database/bax103

Baseline and extensions approach to information retrieval of complex medical data: Poznan's approach to the bioCADDIE 2016
Cited by: 5
Author(s): Artur Cieślewicz, Jakub Dutkiewicz, Czesław Jędrzejek
Software Mentions: 4
Published: over 8 years ago

10.3389/fncel.2021.629279

Validation of Induced Microglia-Like Cells (iMG Cells) for Future Studies of Brain Diseases
Cited by: 24
Author(s): Atoshi Banerjee, Yujie Lu, Kenny Do, Travis Mize, Xiaogang Wu, Xiangning Chen, Jingchun Chen
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2016.00603

TGF-β Affects the Differentiation of Human GM-CSF+ CD4+ T Cells in an Activation- and Sodium-Dependent Manner
Cited by: 5
Author(s): Szabolcs Éliás, Angelika Schmidt, Venkateshan Kannan, John Andersson, Jesper Tegnér
Software Mentions: 4
Published: over 9 years ago

10.1038/s42003-020-01413-2

A haplotype-led approach to increase the precision of wheat breeding
Cited by: 62
Author(s): Jemima Brinton, Ricardo H. Ramírez-González, James Simmonds, Luzie U. Wingen, Simon Orford, Simon Griffiths, Wheat Genome, Georg Haberer, Manuel Spannagl, Sean Walkowiak, Curtis Pozniak, Cristóbal Uauy
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2021.736573

Development and Validation of a Clinical Prognostic Nomogram for Esophageal Adenocarcinoma Patients
Cited by: 11
Author(s): Chengchen Shao, Yue Yu, Qi-fan Li, Xiaolong Liu, Haiyan Song, Yi Shen, Jun Yi
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0251502

“Know your epidemic, know your response”: Epidemiological assessment of the substance use disorder crisis in the United States
Cited by: 8
Author(s): Andrés Hernández, Minxuan Lan, Neil J. MacKinnon, Adam J. Branscum, Diego F. Cuadros
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-021-02304-3

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression
Cited by: 54
Author(s): Pan Gao, Qing Lyu, Amr R. Ghanam, Cícera R. Lazzarotto, Gregory A. Newby, Wei Zhang, Mi-Hyun Choi, Orazio J. Slivano, Kevin Holden, John Walker, Anastasia P. Kadina, Rob J. Munroe, Christian Abratte, John C. Schimenti, David R. Liu, Shengdar Q. Tsai, Xiaochun Long, Joseph M. Miano
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.517637

The Landscape of Immune Cells Infiltrating in Prostate Cancer
Cited by: 54
Author(s): Zhicong Wu, Hua Chen, Wenyang Luo, Hanyun Zhang, Guihuan Li, Fanning Zeng, Fan Deng
Software Mentions: 4
Published: over 5 years ago

10.3390/pathogens9050380

Inhibition of Asaia in Adult Mosquitoes Causes Male-Specific Mortality and Diverse Transcriptome Changes
Cited by: 12
Author(s): Maria Vittoria Mancini, Claudia Damiani, Sarah M. Short, Alessia Cappelli, Ulisse Ulissi, Aida Capone, Aurelio Serrao, Paolo Rossi, Augusto Amici, Cristina Kalogris, George Dimopoulos, Irene Ricci, Guido Favia
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0188264

Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts
Cited by: 25
Author(s): Aimy Sebastian, Nicholas R. Hum, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Gabriela G. Loots
Software Mentions: 4
Published: over 8 years ago

10.1093/gbe/evaa094

piRNA and Transposon Dynamics in Drosophila: A Female Story
Cited by: 17
Author(s): Bastien Saint-Leandre, Pierre Capy, Aurélie Hua-Van, Jonathan Filée
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pbio.1002307

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets
Cited by: 51
Author(s): Gregory J. Hogan, Patrick O. Brown, Daniel Herschlag
Software Mentions: 4
Published: over 10 years ago

10.1534/g3.119.400998

A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
Cited by: 20
Author(s): Tohru Kanno, Peter Venhuizen, Ming‐Tsung Wu, Phebe Chiou, Chia-Liang Chang, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: about 6 years ago

10.1128/mSystems.00334-20

Human Milk Oligosaccharides Modulate the Risk for Preterm Birth in a Microbiome-Dependent and -Independent Manner
Cited by: 9
Author(s): Manuela-Raluca Pausan, V Kolovetsiou-Kreiner, Gesa Richter, Tobias Madl, Elisabeth Giselbrecht, Barbara Obermayer‐Pietsch, Eva-Christine Weiss, Evelyn Jantscher-Krenn, Christine Moissl-Eichinger
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-11-294

Consistent annotation of gene expression arrays
Cited by: 28
Author(s): Benoît Ballester, Nathan Johnson, G Proctor, Paul Flicek
Software Mentions: 4
Published: about 16 years ago

10.3389/fgene.2021.628136

Breast Cancer Case Identification Based on Deep Learning and Bioinformatics Analysis
Cited by: 8
Author(s): Dongfang Jia, Cheng Chen, Fangfang Chen, Ningrui Zhang, Ziwei Yan
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00834-20

Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States
Cited by: 16
Author(s): Melissa B. Manus, Sahana Kuthyar, Ana Gabriela Perroni‐Marañón, Alejandra Núñez‐de la Mora, Katherine R. Amato
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12123639

Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer
Cited by: 13
Author(s): Sen Peng, Lora L. Hebert, Jennifer Eschbacher, Suwon Kim
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1009373

Genetic dissection of complex traits using hierarchical biological knowledge
Cited by: 1
Author(s): Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker
Software Mentions: 4
Published: almost 5 years ago

10.1098/rsos.160900

Prediction limits of mobile phone activity modelling
Cited by: 4
Author(s): Dániel Kondor, Sébastian Grauwin, Zsófia Kallus, István Gódor, Stanislav Sobolevsky, Carlo Ratti
Software Mentions: 4
Published: over 9 years ago

10.1186/2049-2618-2-1

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
Cited by: 314
Author(s): Brandon Brooks, Brian Firek, Christopher S. Miller, Itai Sharon, Brian C. Thomas, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 4
Published: over 12 years ago

10.1128/mSystems.00786-20

Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community
Cited by: 26
Author(s): Dimitri V. Meier, Stefanie Imminger, Osnat Gillor, Dagmar Woebken
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.11777

Inter- and intraspecific variation in the Artibeus species complex demonstrates size and shape partitioning among species
Cited by: 10
Author(s): Brandon P Hedrick
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.8744

Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
Cited by: 8
Author(s): Neil Brocklehurst, Gemma Louise Benevento
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0248320

Plant structural diversity alters sediment retention on and underneath herbaceous vegetation in a flume experiment
Cited by: 6
Author(s): Lena Kretz, Katinka Koll, Carolin Seele‐Dilbat, Fons van der Plas, Alexandra Weigelt, Christian Wirth
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0164766

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2018.00251

Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics
Cited by: 27
Author(s): Rafael R. C. Cuadrat, Danny Ionescu, Alberto M. R. Dávila, Hans‐Peter Grossart
Software Mentions: 4
Published: over 8 years ago

10.1186/s13287-019-1245-6

DNA methylation dynamic of bone marrow hematopoietic stem cells after allogeneic transplantation
Cited by: 13
Author(s): Stefania Trino, Pietro Zoppoli, Angelo Michele Carella, Ilaria Laurenzana, Alessandro Weisz, Domenico Memoli, Giovanni Calice, Francesco La Rocca, Vittorio Simeon, Lucia Savino, Luigi Del Vecchio, Pellegrino Musto, Antonella Caivano, Luciana De Luca
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-59549-4

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii
Cited by: 7
Author(s): Katrine Højholt Iversen, Louise Rasmussen, Kosai Al-Nakeeb, José Juan Almagro Armenteros, Christian Salgård Jensen, Rimtas Dargis, Oksana Lukjancenko, Ulrik Stenz Justesen, Claus Moser, Flemming Schønning Rosenvinge, Xiaohui Chen Nielsen, Jens Jørgen Christensen, Simon Rasmussen
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-021-02637-6

DEVOLUTION—A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data
Cited by: 6
Author(s): Natalie Andersson, Subhayan Chattopadhyay, Anders Valind, Jenny Karlsson, David Gisselsson
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12918-019-0694-y

GNE: a deep learning framework for gene network inference by aggregating biological information
Cited by: 29
Author(s): Kishan Kc, Rui Li, Feng Cui, Qi Yu, Anne R. Haake
Software Mentions: 4
Published: over 7 years ago

10.1534/g3.113.009431

gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images
Cited by: 99
Author(s): Omar Wagih, Leopold Parts
Software Mentions: 4
Published: over 12 years ago

10.3389/fgene.2021.634554

Molecular Mapping of Water-Stress Responsive Genomic Loci in Lettuce (Lactuca spp.) Using Kinetics Chlorophyll Fluorescence, Hyperspectral Imaging and Machine Learning
Cited by: 9
Author(s): Pawan Kumar, Renée L. Eriksen, Ivan Šimko, Beiquan Mou
Software Mentions: 4
Published: over 5 years ago

10.3389/fpsyg.2015.01782

Thinking Outside the Box: Developing Dynamic Data Visualizations for Psychology with Shiny
Cited by: 31
Author(s): David Ellis, Hannah Lena Merdian
Software Mentions: 4
Published: over 10 years ago

10.3390/metabo9090171

WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data
Cited by: 18
Author(s): Nico Borgsmüller, Yoann Gloaguen, Tobias Opialla, Eric Blanc, Emilie Sicard, Anne-Lise Royer, Bruno Le Bizec, Stéphanie Durand, Carole Migné, Mélanie Petera, Estelle Pujos‐Guillot, Franck Giacomoni, Yann Guitton, Dieter Beule, Jennifer Kirwan
Software Mentions: 4
Published: almost 7 years ago

10.1098/rspb.2021.0094

Drought-driven wildfire impacts on structure and dynamics in a wet Central Amazonian forest
Cited by: 20
Author(s): Aline Pontes‐Lopes, Camila V. J. Silva, Jos Barlow, Lorena M. Rincón, Wesley Augusto Campanharo, Cássio Alencar Nunes, Catherine Torres de Almeida, Celso Henrique Leite Silva Júnior, Henrique Luís Godinho Cassol, Ricardo Dalagnol, Scott C. Stark, Paulo Maurı́cio Lima de Alencastro Graça, Luiz E. O. C. Aragão
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0095875

The DNA Methylome and Transcriptome of Different Brain Regions in Schizophrenia and Bipolar Disorder
Cited by: 70
Author(s): Yun Xiao, Cynthia Camarillo, Yanyan Ping, Tania Bedard Arana, Hongying Zhao, Peter M. Thompson, Chaohan Xu, Bai-Horng Su, Huihui Fan, Javier Ordoñez, Li Wang, Chunxiang Mao, Yunpeng Zhang, Dianne A. Cruz, Michael Escamilla, Xia Li, Xu Chun
Software Mentions: 4
Published: about 12 years ago

10.1186/s12859-017-1897-0

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: over 8 years ago

10.1186/s13073-021-00929-4

Haplotype-resolved germline and somatic alterations in renal medullary carcinomas
Cited by: 4
Author(s): Kar Tong Tan, Hyunji Kim, Jian Carrot‐Zhang, Yuxiang Zhang, Won Jun Kim, Guillaume Kugener, Jeremiah A. Wala, Thomas P. Howard, Yueh Yun, Rameen Beroukhim, Heng Li, Gavin Ha, Seth L. Alper, Elizabeth J. Perlman, Elizabeth Mullen, William C. Hahn, Matthew Meyerson, Andrew L. Hong
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-015-2277-7

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome
Cited by: 42
Author(s): Erik A. Visser, Jill L. Wegrzyn, Emma T. Steenkmap, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 4
Published: over 10 years ago

10.3389/fphys.2021.698463

Integrating External and Internal Load for Monitoring Fitness and Fatigue Status in Standard Microcycles in Elite Rink Hockey
Cited by: 3
Author(s): Daniel Fernández, David Moya Malapeira, Joan A. Cadefau, Gerard Carmona
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0163348

On the Morphological Description of Tracheal and Esophageal Displacement and Its Phylogenetic Distribution in Avialae
Cited by: 5
Author(s): Jeremy Klingler
Software Mentions: 4
Published: almost 10 years ago

10.3390/jcm8050639

The Role of MicroRNAs in the Regulation of Gastric Cancer Stem Cells: A Meta-Analysis of the Current Status
Cited by: 22
Author(s): Vitalba Ruggieri, Sabino Russi, Pietro Zoppoli, Francesco La Rocca, Tiziana Angrisano, Geppino Falco, Giovanni Calice, Simona Laurino
Software Mentions: 4
Published: about 7 years ago

10.1002/ece3.5652

The evolution of climate tolerance in conifer‐feeding aphids in relation to their host's climatic niche
Cited by: 8
Author(s): Pierre Arnal, Armelle Coeur d’Acier, Colin Favret, Gottfried Martin, Ge‐Xia Qiao, Emmanuelle Jousselin, Andrea S. Meseguer
Software Mentions: 4
Published: almost 7 years ago

10.3390/cancers12092466

Expression Profiling of Extracellular Matrix Genes Reveals Global and Entity-Specific Characteristics in Adenoid Cystic, Mucoepidermoid and Salivary Duct Carcinomas
Cited by: 16
Author(s): Christoph Arolt, Moritz Meyer, Franziska Hoffmann, Svenja Wagener‐Ryczek, David Schwarz, Lisa Nachtsheim, Dirk Beutner, Margarete Odenthal, Orlando Guntinas‐Lichius, Reinhard Buettner, Ferdinand von Eggeling, Jens Peter Klußmann, Alexander Quaas
Software Mentions: 4
Published: almost 6 years ago

10.3390/cancers12020381

NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models
Cited by: 16
Author(s): J. Tyson McDonald, R. Stainforth, Jack Miller, Thomas J. Cahill, Willian A. da Silveira, Komal S. Rathi, Gary Hardiman, Deanne Taylor, Sylvain V. Costes, Vinita Chauhan, Robert Meller, Afshin Beheshti
Software Mentions: 4
Published: over 6 years ago

10.1200/JCO.19.00577

Germline GPR161 Mutations Predispose to Pediatric Medulloblastoma
Cited by: 44
Author(s): Matthias Begemann, Sebastian M. Waszak, Giles Robinson, Natalie Jäger, Tanvi Sharma, Cordula Knopp, Florian Kraft, Olga Moser, Martin Mynarek, Léa Guerrini-Rousseau, Laurence Brugières, Pascale Varlet, Torsten Pietsch, Daniel C. Bowers, Murali Chintagumpala, Felix Sahm, Jan O. Korbel, Stefan Rutkowski, Thomas Eggermann, Amar Gajjar, Paul A. Northcott, Miriam Elbracht, Stefan M. Pfister, Udo Kontny, Ingo Kurth
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers12040892

Integrated Analysis of RNA-Binding Proteins in Glioma
Cited by: 43
Author(s): Zhixing Wang, Wanjun Tang, Jing Yuan, Boqin Qiang, Wei Han, Xiaozhong Peng
Software Mentions: 4
Published: over 6 years ago

10.1186/s12917-018-1406-3

Dynamic network measures reveal the impact of cattle markets and alpine summering on the risk of epidemic outbreaks in the Swiss cattle population
Cited by: 21
Author(s): Beatriz Vidondo, Bernhard Voelkl
Software Mentions: 4
Published: over 8 years ago

10.1155/2018/2906292

A Simple Guideline to Assess the Characteristics of RNA-Seq Data
Cited by: 21
Author(s): Keun Hong Son, Sungryul Yu, Wonseok Shin, Kyudong Han, Keunsoo Kang
Software Mentions: 4
Published: over 7 years ago

10.1186/s12935-019-0953-4

Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes
Cited by: 22
Author(s): Guo Wei, Hui Yu, Lu Zhang, Xiuwei Chen, Yunduo Liu, Yaoxian Wang, Yunyan Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-81269-6

Chronic BDNF simultaneously inhibits and unmasks superficial dorsal horn neuronal activity
Cited by: 4
Author(s): Sascha R.A. Alles, Max A. Odem, Van B. Lu, Ryan M. Cassidy, Peter A. Smith
Software Mentions: 4
Published: over 5 years ago

10.3390/plants9111492

Anachronic Fruit Traits and Natural History Suggest Extinct Megafauna Herbivores as the Dispersers of an Endangered Tree
Cited by: 0
Author(s): Diego Muñoz‐Concha, Karla Muñoz, Andrea P. Loayza
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-6018-1

Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation
Cited by: 19
Author(s): Izabela Coimbra Ibraim, Mariana Teixeira Dornelles Parise, Doglas Parise, Michelle Zibetti Tadra Sfeir, Thiago Luiz de Paula Castro, Alice R. Wattam, Preetam Ghosh, Debmalya Barh, Emannuel Maltempi Souza, Aristóteles Goés-Neto, Anne Cybelle Pinto Gomide, Vasco Azevedo
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijerph18168602

Using Latent Class Analysis to Identify Health Lifestyle Profiles and Their Association with Suicidality among Adolescents in Benin
Cited by: 2
Author(s): Fanny Hoogstoel, Lucresse Corine Fassinou, Sékou Samadoulougou, Céline Mahieu, Yves Coppieters, Fati Kirakoya‐Samadoulougou
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-017-16520-0

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Cited by: 130
Author(s): Thomas P. Quinn, Mark F. Richardson, David Lovell, Tamsyn M. Crowley
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2021.605015

RNA-Seq Profiling of Circular RNAs During Development of Hindgut in Rat Embryos With Ethylenethiourea-Induced Anorectal Malformations
Cited by: 5
Author(s): Si Ying Li, Chen Yi Wang, Yun Xiao, Xiao Tang, Zheng Wei Yuan, Yu Bai
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/6057948

Identification and Verification of a 17 Immune-Related Gene Pair Prognostic Signature for Colon Cancer
Cited by: 3
Author(s): Qianshi Zhang, Zhen Feng, Yongnian Zhang, Shasha Shi, Yu Zhang, Shuo Ren
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00547-19

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
Cited by: 31
Author(s): Quinten R Ducarmon, Bastian Hornung, A. R. Geelen, E. Kuijper, Romy D. Zwittink
Software Mentions: 4
Published: over 6 years ago

10.3389/fpsyt.2021.617997

Multisite Comparison of MRI Defacing Software Across Multiple Cohorts
Cited by: 25
Author(s): Athena Theyers, Mojdeh Zamyadi, Mark F. O’Reilly, Robert Bartha, Sean Symons, Glenda MacQueen, Stefanie Hassel, Jason P. Lerch, Evdokia Anagnostou, Raymond W. Lam, Benício N. Frey, Roumen Milev, Daniel J. Müller, Sidney H. Kennedy, Christopher J. Scott, Stephen C. Strother, Stephen R. Arnott
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-018-0460-1

Flexible metagenome analysis using the MGX framework
Cited by: 18
Author(s): Sebastian Jaenicke, Stefan P. Albaum, Patrick Blumenkamp, Burkhard Linke, Jens Stoye, Alexander Goesmann
Software Mentions: 4
Published: over 8 years ago

10.1038/s12276-021-00583-1

High prevalence of TP53 loss and whole-genome doubling in early-onset colorectal cancer
Cited by: 11
Author(s): Jeong Eun Kim, Jaeyong Choi, Chang Ohk Sung, Yong Sang Hong, Sun Young Kim, Hyunjung Lee, Tae Won Kim, Jong‐Il Kim
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.593232

Simulation of Microbial Response to Accidental Diesel Spills in Basins Containing Brackish Sea Water and Sediment
Cited by: 4
Author(s): Lijuan Yan, Nan Hui, Suvi Simpanen, Laura Tudeer, Martin Romantschuk
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.8085

Adaptation, phylogeny, and covariance in milk macronutrient composition
Cited by: 0
Author(s): Gregory E. Blomquist
Software Mentions: 4
Published: over 6 years ago

10.15252/embj.2020105784

ALK ligand ALKAL2 potentiates MYCN‐driven neuroblastoma in the absence of ALK mutation
Cited by: 30
Author(s): Marcus Borenäs, Ganesh Umapathy, Wei-Yun Lai, Dan E. Lind, Barbara Witek, Jikui Guan, Patricia Mendoza-García, Tafheem Masudi, A. Claeys, Tzu-Po Chuang, Abeer El Wakil, Badrul Arefin, Susanne Fransson, Jan Koster, Mathias Johansson, Jennie Gaarder, Jimmy Van den Eynden, Bengt Hållberg, Ruth Palmer
Software Mentions: 4
Published: over 5 years ago