10.1038/s41598-020-61386-4

Increasing incidence of macular edema in excessive morning blood pressure surge in patients with retinal vein occlusion
Cited by: 2
Author(s): Hyun-Jin Kim, Yong Un Shin, Yong-Gu Lee, Min Ho Kang, Mincheol Seong, Heeyoon Cho, Ran Heo, Jin Kyu Park, Young‐Hyo Lim, Junho Shin
Software Mentions: 6
Published: over 6 years ago

10.1093/gbe/evu149

Small but Powerful, the Primary Endosymbiont of Moss Bugs, Candidatus Evansia muelleri, Holds a Reduced Genome with Large Biosynthetic Capabilities
Cited by: 33
Author(s): Diego Santos-García, Amparo Latorre, Andrés Moya, George Gibbs, Viktor Hartung, Konrad Dettner, Stefan Martin Kuechler, Francisco J. Silva
Software Mentions: 6
Published: about 12 years ago

10.1002/jrsm.1428

The Kilim plot: A tool for visualizing network meta‐analysis results for multiple outcomes
Cited by: 15
Author(s): Michael Seo, Toshi A Furukawa, Areti Angeliki Veroniki, Toby Pillinger, Anneka Tomlinson, Georgia Salanti, Andrea Cipriani, Orestis Efthimiou
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0179092

Inter-rater reliability of categorical versus continuous scoring of fish vitality: Does it affect the utility of the reflex action mortality predictor (RAMP) approach?
Cited by: 12
Author(s): Pieter Meeremans, Noëlle Yochum, Marc Kochzius, Bart Ampe, Frank Tuyttens, Sven Sebastian Uhlmann
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pntd.0008179

Predicting disease risk areas through co-production of spatial models: The example of Kyasanur Forest Disease in India’s forest landscapes
Cited by: 26
Author(s): Bethan V. Purse, Narayanaswamy Darshan, Gudadappa S. Kasabi, F. Gerard, Abhishek Samrat, Charles George, Abi Tamim Vanak, Meera Anna Oommen, Mujeeb Rahman, Sarah J. Burthe, Juliette Young, Prashanth Nuggehalli Srinivas, Stefanie Schäfer, Peter A. Henrys, Vijay K. Sandhya, Mohammed Mudassar Chanda, Manoj Murhekar, S.L. Hoti, Shivani K. Kiran
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.33953

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins
Cited by: 84
Author(s): Nitzan Koppel, Jordan E. Bisanz, Maria-Eirini Pandelia, Peter J. Turnbaugh, Emily P. Balskus
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0043846

Long-Term Field Data and Climate-Habitat Models Show That Orangutan Persistence Depends on Effective Forest Management and Greenhouse Gas Mitigation
Cited by: 20
Author(s): Stephen D. Gregory, Barry W. Brook, Benoît Goossens, Marc Ancrenaz, Rayner Alfred, Laurentius Ambu, Damien A. Fordham
Software Mentions: 6
Published: almost 14 years ago

10.3390/ani9110973

The Development of a Hoof Conformation Assessment for Use in Dairy Goats
Cited by: 5
Author(s): Laura Deeming, Ngaio J. Beausoleil, Kevin J. Stafford, James R. Webster, Maryann Staincliffe, Gosia Zobel
Software Mentions: 6
Published: over 6 years ago

10.3390/pathogens10091109

Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure
Cited by: 6
Author(s): Priyanka Mehta, Shanmukh Alle, Anusha Chaturvedi, Aparna Swaminathan, Sheeba Saifi, Ranjeet Maurya, Partha Chattopadhyay, Priti Devi, Ruchi Chauhan, Akshay Kanakan, Janani Srinivasa Vasudevan, Ramanathan Sethuraman, Subramanian Chidambaram, Mashrin Srivastava, Avinash Chakravarthi, Johnny Jacob, Madhuri Namagiri, Varma Konala, Sujeet Jha, U. Deva Priyakumar, P. K. Vinod, Rajesh Pandey
Software Mentions: 6
Published: almost 5 years ago

10.1017/cts.2017.310

RRApp, a robust randomization app, for clinical and translational research
Cited by: 9
Author(s): Chengcheng Tu, Emma K. T. Benn
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-020-77878-2

Recent land use and management changes decouple the adaptation of livestock diversity to the environment
Cited by: 9
Author(s): Elena Velado‐Alonso, Ignacio Morales‐Castilla, Antonio Gómez‐Sal
Software Mentions: 6
Published: over 5 years ago

10.2196/21855

Health Care Providers’ Performance, Mindset, and Attitudes Toward a Neonatal Resuscitation Computer-Based Simulator: Empirical Study
Cited by: 5
Author(s): Maria Cutumisu, Simran K. Ghoman, Chang Lu, Sachin Patel, Catalina Garcia-Hidalgo, Caroline Fray, Matthew Brown, Russell Greiner, Georg M. Schmölzer
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-020-1942-6

A framework for transcriptome-wide association studies in breast cancer in diverse study populations
Cited by: 60
Author(s): Arjun Bhattacharya, Montserrat García‐Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-016-2718-y

Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin
Cited by: 11
Author(s): Karl G. Kugler, Zeljkica Jandric, Reinhard Beyer, Eva Klopf, Walter Glaser, Marc Lemmens, Mehrdad Shams, Klaus Mayer, Gerhard Adam, Christoph Schüller
Software Mentions: 6
Published: about 10 years ago

10.3390/ijms21228769

Physiological Changes in Barley mlo-11 Powdery Mildew Resistance Conditioned by Tandem Repeat Copy Number
Cited by: 3
Author(s): Cynthia Ge, Paula Moolhuijzen, Lee T. Hickey, Elzette Wentzel, Wei‐Wei Deng, Eric Dinglasan, Simon R. Ellwood
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1009118

SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data
Cited by: 6
Author(s): Jing Qi, Yang Zhou, Zhao Zhang, Shuilin Jin
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.45672

Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination
Cited by: 27
Author(s): Lee Langer, James M. Ward, Trevor Archer
Software Mentions: 6
Published: about 7 years ago

10.7554/eLife.61909

Real-time, low-latency closed-loop feedback using markerless posture tracking
Cited by: 78
Author(s): Gary A Kane, Gonçalo Lopes, Jonny L. Saunders, Alexander Mathis
Software Mentions: 6
Published: over 5 years ago

10.1242/dmm.049012

Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol
Cited by: 16
Author(s): Karen E. Boschen, Travis Ptacek, Matthew E. Berginski, Jeremy M. Simon, Scott E. Parnell
Software Mentions: 6
Published: about 5 years ago

10.1186/s13321-020-0415-y

The C++ programming language in cheminformatics and computational chemistry
Cited by: 13
Author(s): Dmitrii N. Rassokhin
Software Mentions: 6
Published: over 6 years ago

10.3390/microorganisms8081225

Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet
Cited by: 19
Author(s): Tianyi Jiang, Huan Wu, Xin Yang, Yue Li, Ziyi Zhang, Feng Chen, Liping Zhao, Chenhong Zhang
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0025279

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Cited by: 62
Author(s): Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang
Software Mentions: 6
Published: over 14 years ago

10.1128/mSphere.00455-21

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition
Cited by: 9
Author(s): Heather L. Deel, Alexandra L. Emmons, Jennifer Kiely, Franklin E. Damann, David Carter, Aaron M. Lynne, Rob Knight, Zhenjiang Xu, Sibyl R. Bucheli, Jessica L. Metcalf
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13148-015-0097-x

DNA methylation levels are highly correlated between pooled samples and averaged values when analysed using the Infinium HumanMethylation450 BeadChip array
Cited by: 15
Author(s): Cristina Gallego-Fábrega, Caty Carrera, Elena Muiño, Joan Montaner, Jurek Krupinski, Israel Fernández-Cadenas
Software Mentions: 6
Published: almost 11 years ago

10.1038/s41598-021-88440-z

Machine-learning based prediction of Cushing’s syndrome in dogs attending UK primary-care veterinary practice
Cited by: 7
Author(s): Imogen Schofield, David Brodbelt, Noel Kennedy, Stijn Niessen, David Church, Rebecca Geddes, Dan G. O’Neill
Software Mentions: 6
Published: about 5 years ago

10.1093/gigascience/giaa064

Integrative computational epigenomics to build data-driven gene regulation hypotheses
Cited by: 10
Author(s): Tyrone Chen, Sonika Tyagi
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.54655

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
Cited by: 58
Author(s): Ira Alexandra Iosub, Rob W. van Nues, Stuart McKellar, Karen Jule Nieken, Marta Marchioretto, Brandon Sy, Jai J. Tree, Gabriella Viero, Sander Granneman
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.66797

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers
Cited by: 6
Author(s): Kai He, Triston Eastman, Hannah Czolacz, Shuhao Li, Akio Shinohara, Shin-ichiro Kawada, Mark S. Springer, Michael Berenbrink, Kevin L. Campbell
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0086536

Dual Targeting of MEK and PI3K Pathways Attenuates Established and Progressive Pulmonary Fibrosis
Cited by: 22
Author(s): Satish K. Madala, Ramakrishna Edukulla, Mukta Phatak, Stephanie Schmidt, Cynthia Davidson, Thomas H. Acciani, Thomas R. Korfhagen, Mario Medvedovic, Timothy D. Le Cras, Kimberly Wagner, William D. Hardie
Software Mentions: 6
Published: over 12 years ago

10.1016/j.cels.2018.08.001

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts
Cited by: 77
Author(s): Aleksej Zelezniak, Jakob Vowinckel, Floriana Capuano, Christoph B. Messner, Vadim Demichev, Nicole Polowsky, Michael Mülleder, Stephan Kamrad, Bernd Klaus, Markus A. Keller, Markus Ralser
Software Mentions: 6
Published: almost 8 years ago

10.1098/rsob.160183

Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach
Cited by: 10
Author(s): Ashley J. Waardenberg, Homan Bernou, Mohamed Salim, Richard P. Harvey, Romaric Bouveret
Software Mentions: 6
Published: almost 10 years ago

10.3389/fgene.2021.612011

TGFβ1: An Indicator for Tumor Immune Microenvironment of Colon Cancer From a Comprehensive Analysis of TCGA
Cited by: 3
Author(s): Jinyan Wang, Jinqiu Wang, Quan Gu, Yan Yang, Yajun Ma, Quan’an Zhang
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0106397

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
Cited by: 138
Author(s): Mehmet K. Samur
Software Mentions: 6
Published: almost 12 years ago

10.1371/journal.pone.0234805

Erythrocyte sedimentation rate and hemoglobin-binding protein in free-living box turtles (Terrapene spp.)
Cited by: 6
Author(s): Laura Adamovicz, Sarah J. Baker, Ethan J. Kessler, Marta Kelly, Samantha Johnson, Janet Winter, Christopher A. Phillips, Matthew C. Allender
Software Mentions: 6
Published: about 6 years ago

10.1523/JNEUROSCI.1675-19.2019

Midkine-a Is Required for Cell Cycle Progression of Müller Glia during Neuronal Regeneration in the Vertebrate Retina
Cited by: 28
Author(s): Mikiko Nagashima, Travis S. D’Cruz, Antoinette Eyram Danku, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.618277

Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
Cited by: 7
Author(s): Mateusz Garbulowski, Karolina Smolińska, Klev Diamanti, Gang Pan, Khurram Maqbool, Lars Feuk, Jan Komorowski
Software Mentions: 6
Published: over 5 years ago

10.1016/j.cell.2016.09.007

Functional Metabolomics Describes the Yeast Biosynthetic Regulome
Cited by: 129
Author(s): Michael Mülleder, Enrica Calvani, Mohammad Tauqeer Alam, Richard Kangda Wang, Florian Eckerstorfer, Aleksej Zelezniak, Markus Ralser
Software Mentions: 6
Published: almost 10 years ago

10.1155/2020/1686480

miRNA-Based Feature Classifier Is Associated with Tumor Mutational Burden in Head and Neck Squamous Cell Carcinoma
Cited by: 7
Author(s): Yu Xia, Qi Wang, Xiaolin Huang, Xinhai Yin, Jukun Song, Ke Zhao, Xiaofeng Duan
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-021-02435-7

DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
Cited by: 15
Author(s): Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2018.00792

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations
Cited by: 25
Author(s): Jessica Chopyk, Sarah Allard, Daniel J. Nasko, Anthony Bui, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 6
Published: about 8 years ago

10.1093/gbe/evaa071

Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat
Cited by: 30
Author(s): Benjamin Schwessinger, Yan Jun Chen, Richard Tien, Josef Korbinian Vogt, Jana Sperschneider, Ramawatar Nagar, Mark McMullan, Thomas Sicheritz-Pontén, Chris K. Sørensen, Mogens S. Hovmøller, John P. Rathjen, Annemarie Fejer Justesen
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-020-73083-3

Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs
Cited by: 12
Author(s): Hiu Wai Lee, Borja Esteve‐Altava, Arhat Abzhanov
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12864-016-2849-1

Deciphering transcriptome profiles of peripheral blood mononuclear cells in response to PRRSV vaccination in pigs
Cited by: 26
Author(s): M. S. Islam, Christine Große‐Brinkhaus, Maren Pröll, Muhammad Jasim Uddin, Sharmin Aqter Rony, Dawit Tesfaye, Ernst Tholen, Michael Hölker, K. Schellander, Christiane Neuhoff
Software Mentions: 6
Published: almost 10 years ago

10.1016/j.tube.2019.101859

Distinct serum biosignatures are associated with different tuberculosis treatment outcomes
Cited by: 22
Author(s): Katharina Ronacher, Novel N. Chegou, Léanie Kleynhans, Joel Fleury Djoba Siawaya, Nelita du Plessis, André G. Loxton, Elizna Maasdorp, Gerard Tromp, Martin Kidd, Kim Stanley, Magdalena Kriel, Ângela Menezes, Andrea Gutschmidt, Gian D. van der Spuy, Robin M. Warren, Reynaldo Dietze, Alphonse Okwera, Bonnie Thiel, John T. Belisle, Jacqueline M. Cliff, W. Henry Boom, John L. Johnson, Paul D. van Helden, Hazel M. Dockrell, Gerhard Walzl
Software Mentions: 6
Published: almost 7 years ago

10.7717/peerj.10050

Are giant clams (<i>Tridacna maxima</i>) distractible? A multi-modal study
Cited by: 6
Author(s): Ryan Doyle, Jonathan Kim, Angelika Pe, Daniel T. Blumstein
Software Mentions: 6
Published: over 5 years ago

10.1186/s13071-020-04098-y

Rats as potential reservoirs for neglected zoonotic Bartonella species in Flanders, Belgium
Cited by: 7
Author(s): Maria Krügel, Martin Pfeffer, Nina Król, Christian Imholt, Kristof Baert, Rainer G. Ulrich, Anna Obiegala
Software Mentions: 6
Published: about 6 years ago

10.1016/j.cell.2013.11.043

The Architecture of Parent-of-Origin Effects in Mice
Cited by: 79
Author(s): Richard Mott, Yuan Wei, Pamela J. Kaisaki, Xiangchao Gan, James Cleak, Andrew Edwards, Amelie Baud, Jonathan Flint
Software Mentions: 6
Published: over 12 years ago

10.3389/fonc.2021.630706

The Immune-Related Gene HCST as a Novel Biomarker for the Diagnosis and Prognosis of Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Yongying Zhou, Xiao Wang, Weibing Zhang, Huiyong Liu, Daoquan Liu, Ping Chen, Dongmei Xu, Jianmin Liu, Yan Li, Guang Zeng, Mingzhou Li, Zhonghua Wu, Yingao Zhang, Xinghuan Wang, Michael E. DiSanto, Xinhua Zhang
Software Mentions: 6
Published: about 5 years ago

10.1002/ana.26009

The Effect of <scp> <i>SMN</i> </scp> Gene Dosage on <scp>ALS</scp> Risk and Disease Severity
Cited by: 9
Author(s): Matthieu Moisse, Ramona A J Zwamborn, Joke J.F.A. van Vugt, Rick A. A. van der Spek, Wouter van Rheenen, Brendan Kenna, Kristel van Eijk, Kevin P. Kenna, Philippe Corcia, Philippe Couratier, Patrick Vourc’h, Orla Hardiman, Russell L. McLaughlin, Marc Guillaume, Vivian E. Drory, Nicola Ticozzi, Vincenzo Silani, Mamede de Carvalho, Jesús Mora, Mónica Povedano, Michael Benatar, Markus Weber, A. Nazlı Başak, Xiao Chen, Michael A. Eberle, Ammar Al‐Chalabi, Christopher E. Shaw, Pamela J. Shaw, Karen Morrison, John E. Landers, Jonathan D. Glass, Wim Robberecht, Michael A. van Es, Leonard H. van den Berg, Jan H. Veldink, Philip Van Damme
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-020-3434-9

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Cited by: 7
Author(s): Martin Lewinski, Yannik Bramkamp, Tino Köster, Dorothee Staiger
Software Mentions: 6
Published: over 6 years ago

10.1186/s40246-021-00323-6

An ensemble of the iCluster method to analyze longitudinal lncRNA expression data for psoriasis patients
Cited by: 2
Author(s): Suyan Tian, Chi Wang
Software Mentions: 6
Published: about 5 years ago

10.3390/cancers13010143

Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies
Cited by: 17
Author(s): Irene Pérez-Díez, Marta R. Hidalgo, Pablo Malmierca-Merlo, Zoraida Andreu, Sergio Romera-Giner, Rosa Farràs, María de la Iglesia-Vayá, Mariano Provencio, Atocha Romero, Francisco García‐García
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-017-08235-z

Discrimination of plant root zone water status in greenhouse production based on phenotyping and machine learning techniques
Cited by: 21
Author(s): Doudou Guo, J.A. de Juan, Liu Chang, Zhang Jing-jin, Dan Huang
Software Mentions: 6
Published: almost 9 years ago

10.1093/gigascience/giaa137

Long-read assembly of the <i>Brassica napus</i> reference genome Darmor-bzh
Cited by: 50
Author(s): Mathieu Rousseau‐Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Régine Delourme, Gwenaëlle Deniot, Stéfan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, Anne‐Marie Chèvre, Jean‐Marc Aury
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-016-0282-3

Identification of key regulators of pancreatic cancer progression through multidimensional systems-level analysis
Cited by: 45
Author(s): Deepa Rajamani, Manoj Bhasin
Software Mentions: 6
Published: about 10 years ago

10.1186/s12859-019-3121-x

A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons
Cited by: 2
Author(s): Stanislav Listopad, Trina M. Norden-Krichmar
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0240538

Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate
Cited by: 5
Author(s): Jana Bürger, Andrey V. Malyshev, Nathalie Colbach
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.3000534

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response
Cited by: 112
Author(s): Omri M. Finkel, Isai Salas-González, Gabriel Castrillo, Stijn Spaepen, Theresa F. Law, Paulo José Pereira Lima Teixeira, Corbin D. Jones, Jeffery L. Dangl
Software Mentions: 6
Published: over 6 years ago

10.3390/plants8090354

Population Genomic Approaches for Weed Science
Cited by: 14
Author(s): Sara L. Martin, Jean-Sébastien Parent, Martin Laforest, Eric R. Page, Julia M. Kreiner, Tracey James
Software Mentions: 6
Published: almost 7 years ago

10.1186/s13073-017-0511-4

Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells
Cited by: 6
Author(s): Snehangshu Kundu, Muhammad Akhtar-Ali, Niklas Handin, Narendra Padhan, Jimmy Larsson, Maria Karoutsou, Kenneth Ban, Jacek R. Wiśniewski, Per Artursson, Liqun He, Mats Hellström, Tobias Sjöblom
Software Mentions: 6
Published: over 8 years ago

10.1038/s42003-020-01439-6

Predicting clinical resistance prevalence using sewage metagenomic data
Cited by: 28
Author(s): Antti Karkman, Fanny Berglund, Carl-Fredrik Flach, Erik Kristiansson, D. G. Joakim Larsson
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pmed.1001944

Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data
Cited by: 60
Author(s): Olga Tosas Auguet, Jason R. Betley, Richard A. Stabler, Amita Patel, Avgousta Ioannou, Helene Marbach, Pasco Hearn, Anna Aryee, Simon Goldenberg, Jonathan A. Otter, Nergish Desai, Tacim Karadag, Chris Grundy, Michael W. Gaunt, Ben S. Cooper, Jonathan D Edgeworth, Theodore Kypraios
Software Mentions: 6
Published: over 10 years ago

10.1128/mBio.01037-19

Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection
Cited by: 24
Author(s): Leonardo Silva de Araujo, Marcelo Ribeiro-Alves, Thyago Leal-Calvo, Janaina Aparecida Medeiros Leung, Verónica Durán, Mohamed Samir, Steven R. Talbot, Aravind Tallam, Fernanda Carvalho de Queiroz Mello, Robert Geffers, Maria Helena Féres Saad, Frank Peßler
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0210101

Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species
Cited by: 13
Author(s): Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Mirko Di Febbraro, Antonio Profico, Giorgia Girardi, Pasquale Raia
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0251653

Minimally invasive brain injections for viral-mediated transgenesis: New tools for behavioral genetics in sticklebacks
Cited by: 2
Author(s): Noelle James, Alison M. Bell
Software Mentions: 6
Published: about 5 years ago

10.3390/cancers13051136

Nanopore Sequencing Reveals Global Transcriptome Signatures of Mitochondrial and Ribosomal Gene Expressions in Various Human Cancer Stem-like Cell Populations
Cited by: 13
Author(s): Kaya E. Witte, Oliver Hertel, Beatrice A. Windmöller, Laureen P. Helweg, Anna L. Höving, Cornelius Knabbe, Tobias Busche, Johannes F. W. Greiner, Jörn Kalinowski, Thomas Noll, F. Mertzlufft, Morris Beshay, Jesco Pfitzenmaier, Barbara Kaltschmidt, Christian Kaltschmidt, Constanze Banz‐Jansen, Matthias Simon
Software Mentions: 6
Published: over 5 years ago

10.1007/s00239-021-10012-6

Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires
Cited by: 8
Author(s): Thomas D. Lewin, Amy H. Royall, Peter W.H. Holland
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.9975

Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer
Cited by: 11
Author(s): Xiuming Zhai, Zhaowei Yang, Xiji Liu, Z P Dong, Dandan Zhou
Software Mentions: 6
Published: almost 6 years ago

10.1038/sdata.2016.25

Extensive sequencing of seven human genomes to characterize benchmark reference materials
Cited by: 535
Author(s): Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay K. Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E. Mason, Noah Alexander, Elizabeth Hénaff, Alexa B. R. McIntyre, Dhruva Chandramohan, Feng Chen, Erich B. Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Y. Liang, Michael Saghbini, Željko Džakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric E. Schadt, Robert Sebra, Ali Kashif Bashir, Rebecca Truty, Christopher Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T. Sherry, Alexander Wait Zaranek, Madeleine Ball, Jason Bobe, Preston W. Estep, George M. Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace Zheng, Michael Schnall-Levin, Heather Ordonez, Patrice A Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit
Software Mentions: 6
Published: about 10 years ago

10.3389/fimmu.2020.00851

Gene Expression Profiling of PDGFRA Mutant GIST Reveals Immune Signatures as a Specific Fingerprint of D842V Exon 18 Mutation
Cited by: 10
Author(s): Valentina Indio, Gloria Ravegnini, Annalisa Astolfi, Milena Urbini, Maristella Saponara, Antonio De Leo, Elisa Gruppioni, Giuseppe Tarantino, Sabrina Angelini, Andrea Pession, Maria Abbondanza Pantaleo, Margherita Nannini
Software Mentions: 6
Published: about 6 years ago

10.12688/f1000research.28608.2

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Cited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: about 5 years ago

10.1038/s42003-018-0119-2

Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach
Cited by: 26
Author(s): Francesca Leasi, Joseph L. Sevigny, Eric M. Laflamme, Tom Artois, Marco Curini‐Galletti, Alberto de Jesús Navarrete, Maikon Di Domênico, Freya Goetz, Jeffrey A. Hall, Rick Hochberg, Katharina M. Jörger, Ulf Jondelius, Mary Antonio Donatello Todaro, Herman H. Wirshing, Jon L. Norenburg, W. Kelley Thomas
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41598-019-40697-1

Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control
Cited by: 3
Author(s): Petar Petrov, Alexey V Sarapulov, Lél Eöry, Cristina Scielzo, Lydia Scarfò, Jacqueline Smith, David W. Burt, Pieta K. Mattila
Software Mentions: 6
Published: over 7 years ago

10.7150/ijms.61309

Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis
Cited by: 6
Author(s): Ke Zhu, Aiqun Xu, Wanli Xia, Pulin Li, Rui Han, Enze Wang, Sijing Zhou, Ran Wang
Software Mentions: 6
Published: over 5 years ago

10.1186/s13148-018-0582-0

Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
Cited by: 20
Author(s): Adeline Divoux, Katalin Sandor, Dóra Bojcsuk, Amlan Talukder, Xiaoman Li, Bálint László Bálint, Timothy F. Osborne, Steven R. Smith
Software Mentions: 6
Published: over 7 years ago

10.1016/j.celrep.2020.108629

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide
Cited by: 10
Author(s): Kathrin Leppek, Gun Woo Byeon, Kotaro Fujii, Maria Barna
Software Mentions: 6
Published: over 5 years ago

10.3389/fimmu.2021.729217

Timing of Transcriptomic Peripheral Blood Mononuclear Cell Responses of Sheep to Fasciola hepatica Infection Differs From Those of Cattle, Reflecting Different Disease Phenotypes
Cited by: 4
Author(s): Dagmara A. Niedziela, Amalia Naranjo‐Lucena, Verónica Molina-Hernández, John A. Browne, Á. Martínez-Moreno, J. Pérez, David E. MacHugh, Grace Mulcahy
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41396-018-0264-0

Strong succession in arbuscular mycorrhizal fungal communities
Cited by: 78
Author(s): Cheng Gao, Liliam Montoya, Limei Xu, Mary Madera, Joy Hollingsworth, Elizabeth Purdom, Robert B. Hutmacher, Jeff Dahlberg, Devin Coleman‐Derr, Peggy G. Lemaux, John W. Taylor
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pcbi.1005694

PCSF: An R-package for network-based interpretation of high-throughput data
Cited by: 34
Author(s): Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0245087

Anthropogenic landscape decreases mosquito biodiversity and drives malaria vector proliferation in the Amazon rainforest
Cited by: 16
Author(s): Leonardo Suveges Moreira Chaves, Eduardo Sterlino Bergo, Jan E. Conn, Gabriel Zorello Laporta, Paula Ribeiro Prist, Maria Anice Mureb Sallum
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.8192

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Cited by: 21
Author(s): Gökhan Karakülah, Nazmiye Arslan, Cihangir Yandım, Aslı Süner
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-018-32229-0

Soil resources and element stocks in drylands to face global issues
Cited by: 98
Author(s): César Plaza, Claudio Zaccone, Kasia Sawicka, Ana Méndez, Ana M. Tarquis, Gabriel Gascó, G.B.M. Heuvelink, Edward A. G. Schuur, Fernando T. Maestre
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41598-019-51452-x

NADH dehydrogenases Nuo and Nqr1 contribute to extracellular electron transfer by Shewanella oneidensis MR-1 in bioelectrochemical systems
Cited by: 15
Author(s): Cody S. Madsen, Michaela A. TerAvest
Software Mentions: 6
Published: over 6 years ago

10.1186/s40104-020-00465-y

Effects of supplementation of green tea extract on the milk performance of peripartal dairy cows and the expression of stress response genes in the liver
Cited by: 6
Author(s): Denise K. Geßner, Corinna Brock, Lena M. Hof, Erika Most, Christian Koch, Klaus Eder
Software Mentions: 6
Published: about 6 years ago

10.1016/j.devcel.2021.02.007

Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization
Cited by: 15
Author(s): Fabio M D'Orazio, Piotr J. Balwierz, Ada Jimenez González, Yixuan Guo, Benjamín Hernández-Rodríguez, Lucy Wheatley, Aleksandra Jasiulewicz, Yavor Hadzhiev, Juan M. Vaquerizas, Bradley R. Cairns, Boris Lenhard, Ferenc Müller
Software Mentions: 6
Published: over 5 years ago

10.1186/1471-2105-7-3

Gene selection and classification of microarray data using random forest
Cited by: 2,230
Author(s): Ramón Dı́az-Uriarte, Sara Álvarez de Andrés
Software Mentions: 6
Published: over 20 years ago

10.1038/s41598-018-23913-2

Analysis of HIV-1 envelope evolution suggests antibody-mediated selection of common epitopes among Chinese former plasma donors from a narrow-source outbreak
Cited by: 3
Author(s): Sophie Andrews, Yonghong Zhang, Tao Dong, Sarah Rowland‐Jones, Sunetra Gupta, Joakim Esbjörnsson
Software Mentions: 6
Published: about 8 years ago

10.1186/s12918-018-0620-8

Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
Cited by: 11
Author(s): Theresia Conrad, Olaf Kniemeyer, Sebastian Henkel, Thomas Krüger, Derek J. Mattern, Vito Valiante, Reinhard Guthke, Ilse D. Jacobsen, Axel A. Brakhage, Sebastian Vlaic, Jörg Linde
Software Mentions: 6
Published: over 7 years ago

10.3390/insects12020135

Joint Impacts of Drought and Habitat Fragmentation on Native Bee Assemblages in a California Biodiversity Hotspot
Cited by: 9
Author(s): Keng‐Lou James Hung, Sara Sandoval, John S. Ascher, David A. Holway
Software Mentions: 6
Published: over 5 years ago

10.3390/biom10071041

Untargeted LC-MS Metabolomics Differentiates Between Virulent and Avirulent Clinical Strains of Pseudomonas aeruginosa
Cited by: 18
Author(s): Tobias Depke, Janne G. Thöming, Adrian Kordes, Susanne Häußler, Mark Brönstrup
Software Mentions: 6
Published: almost 6 years ago

10.1111/tpj.14184

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes
Cited by: 91
Author(s): Genevieve M. Hoopes, John Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart, C. Robin Buell
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-021-85829-8

Nitrogen has a greater influence than phosphorus on the diazotrophic community in two successive crop seasons in Northeast China
Cited by: 4
Author(s): Jing Zhou, Mingchao Ma, Dawei Guan, Xin Jiang, Nianxin Zhang, Fengyue Shu, Yong Kong, Jun Li
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2019.00618

Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation
Cited by: 32
Author(s): Jin-Ming Cui, Guoqin Mai, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma, Chenli Liu
Software Mentions: 6
Published: over 7 years ago

10.3390/ijerph17062067

Analysis of the Components of a Cognitive-Behavioral Intervention for the prevention of Depression Administered via Conference Call to Nonprofessional Caregivers: A Randomized Controlled Trial
Cited by: 7
Author(s): Fernando Vázquez, Lara López, Ángela Torres, Patricia Otero, Vanessa Blanco, Olga Dı́az, Mario Páramo
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-018-4980-7

Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes
Cited by: 3
Author(s): Katja R Kasimatis, Megan Moerdyk-Schauwecker, Nadine Timmermeyer, Patrick C. Phillips
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0241704

Evaluating the effectiveness of a group-based resilience intervention versus psychoeducation for emergency responders in England: A randomised controlled trial
Cited by: 19
Author(s): Jennifer Wild, Shama El-Salahi, Michelle Degli Esposti, Graham R. Thew
Software Mentions: 6
Published: over 5 years ago

10.26508/lsa.202000707

Robust production of uniform human cerebral organoids from pluripotent stem cells
Cited by: 44
Author(s): Adam Sivitilli, Jessica Gosio, Bibaswan Ghoshal, Alesya Evstratova, Daniel Trcka, Parisa Ghiasi, J. Javier Hernández, Jean Martin Beaulieu, Jeffrey L. Wrana, Liliana Attisano
Software Mentions: 6
Published: about 6 years ago

10.3390/metabo11060361

Opposing Effects of Ceanothus velutinus Phytochemistry on Herbivore Communities at Multiple Scales
Cited by: 2
Author(s): Casey S. Philbin, M. J. Paulsen, Lora A. Richards
Software Mentions: 6
Published: about 5 years ago

10.7150/jca.55570

Upregulating <i>KTN1</i> promotes Hepatocellular Carcinoma progression
Cited by: 1
Author(s): Jian Pan, Naixia Chao, Yao‐Yao Zhang, Tianyi Huang, Chengxiao Chen, Qiuhong Qin, Jinhong Guo, Rongshi Huang, Guopei Luo
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0207051

A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles
Cited by: 4
Author(s): Leonardo Abdala Elias, Denise Brentan Silva, Ricardo Silva, Yan‐Qiong Peng, Da‐Rong Yang, Norberto P. Lopes, Rodrigo Augusto Santinelo Pereira
Software Mentions: 6
Published: over 7 years ago