10.1186/s12859-020-03652-w

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
Cited by: 22
Author(s): Kellen Garrison Cresswell, John C. Stansfield, Mikhail G. Dozmorov
Software Mentions: 7
Published: almost 6 years ago

10.3390/microorganisms5040068

Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea
Cited by: 16
Author(s): Bernd Wemheuer, Franziska Wemheuer, Dimitri V. Meier, Sara Billerbeck, Helge-Ansgar Giebel, Meinhard Simon, Christoph Scherber, Rolf Daniel
Software Mentions: 7
Published: over 8 years ago

10.3390/cells10092430

Artificial Intelligence-Assisted Identification of Genetic Factors Predisposing High-Risk Individuals to Asymptomatic Heart Failure
Cited by: 7
Author(s): Ning Yang, Chi-Hsiao Yeh, Tsung Hsien Tsai, Yi Ju Chou, Paul Wei Che Hsu, Chun-Hsien Li, Yun Hsuan Chan, Ling Kuo, Chun Tai Mao, Yu-Chiau Shyu, Ming‐Jui Hung, Chao‐Lun Lai, Huey Kang Sytwu, Ting Fen Tsai
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0237419

Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19
Cited by: 106
Author(s): Lara Jehi, Xinge Ji, Alex Milinovich, Serpil C. Erzurum, Amy Merlino, Steve Gordon, James B. Young, Michael W. Kattan
Software Mentions: 7
Published: almost 6 years ago

10.3389/fvets.2019.00499

Developing Diagnostic Frameworks in Veterinary Behavioral Medicine: Disambiguating Separation Related Problems in Dogs
Cited by: 25
Author(s): Luciana Santos de Assis, Raquel Matos, Thomas W. Pike, Ohp Burman, Daniel S. Mills
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0155826

Elevational Distribution of Flightless Ground Beetles in the Tropical Rainforests of North-Eastern Australia
Cited by: 10
Author(s): Kyran M. Staunton, Akihiro Nakamura, Chris J. Burwell, Simon K. A. Robson, Stephen E. Williams
Software Mentions: 7
Published: about 10 years ago

10.3389/fcimb.2021.604129

Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage
Cited by: 6
Author(s): Kathrin Witmer, Farah A. Dahalan, Tom Metcalf, Arthur M. Talman, Virginia M. Howick, Mara K. N. Lawniczak
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.744113

Identification and Validation of Hypoxia-Related lncRNA Signature as a Prognostic Model for Hepatocellular Carcinoma
Cited by: 8
Author(s): Chengke Zhou, Huajun Zhang, Liqing Lu
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41375-018-0302-y

Late treatment-related mortality versus competing causes of death after allogeneic transplantation for myelodysplastic syndromes and secondary acute myeloid leukemia
Cited by: 22
Author(s): Johannes Schetelig, Liesbeth C. de Wreede, Michel van Gelder, Linda Köster, Jürgen Finke, Dietger Niederwieser, Dietrich Beelen, Ghulam J. Mufti, Uwe Platzbecker, Arnold Ganser, Silke Heidenreich, Johan Maertens, Gèrard Socié, Arne Brecht, Matthias Stelljes, Guido Kobbe, Liisa Volin, Arnon Nagler, Antonı́n Vı́tek, Thomas Luft, Per Ljungman, Ibrahim Yakoub‐Agha, Marie Robin, Nicolaus Kröger
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-018-34129-9

SAC3D1: a novel prognostic marker in hepatocellular carcinoma
Cited by: 37
Author(s): Myoung‐Eun Han, Jiyoung Kim, Ga Hyun Kim, Si Young Park, Yun Hak Kim, Sae‐Ock Oh
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-018-37746-6

The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region
Cited by: 22
Author(s): Nora Fernández-Jiménez, Koldo García-Etxebarria, Leticia Plaza-Izurieta, Irati Romero-Garmendia, Amaia Jauregi-Miguel, María Legarda, Szilvia Ecsedi, Ainara Castellanos–Rubio, Vincent Cahais, Cyrille Cuenin, Davide Degli Esposti, Iñaki Irastorza, Héctor Hernández-Vargas, Zdenko Herceg, José Ramón Bilbao
Software Mentions: 7
Published: over 7 years ago

10.3390/cells10050973

Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing
Cited by: 5
Author(s): Shaojian Gao, Zhijie Wu, Jeerthi Kannan, Liza Mathews, Xingmin Feng, Sachiko Kajigaya, Neal S. Young
Software Mentions: 7
Published: about 5 years ago

10.3389/fonc.2020.608334

Nomogram for Predicting Lymph Node Involvement in Triple-Negative Breast Cancer
Cited by: 18
Author(s): Xiang Cui, Hongxia Zhu, Jiefu Huang
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2020.00685

Hybridization Between Yuccas From Baja California: Genomic and Environmental Patterns
Cited by: 9
Author(s): María Clara Arteaga, Rafael Bello-Bedoy, Jaime Gasca-Pineda
Software Mentions: 7
Published: about 6 years ago

10.1186/s12935-019-1079-4

Prognostic nomograms for predicting cause-specific survival and overall survival of stage I–III colon cancer patients: a large population-based study
Cited by: 26
Author(s): Zheng Zhou, Shaobo Mo, Weixing Dai, Wenqiang Xiang, Lingyu Han, Qingguo Li, Renjie Wang, Lu Liu, Long Zhang, Sanjun Cai, Guoxiang Cai
Software Mentions: 7
Published: over 6 years ago

10.1093/gigascience/giaa022

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
Cited by: 28
Author(s): Haris Zafeiropoulos, Ha Quoc Viet, Katerina Vasileiadou, Antonis Potirakis, Christos Arvanitidis, Pantelis Topalis, Christina Pavloudi, Evangelos Pafilis
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0255012

Hierarchical modelling of immunoglobulin coated bacteria in dogs with chronic enteropathy shows reduction in coating with disease remission but marked inter-individual and treatment-response variability
Cited by: 0
Author(s): Lina María Martínez-López, Alexis Perez‐Gonzalez, Elizabeth A. Washington, Andrew Woodward, Alexandra J. Roth‐Schulze, Julien Dandrieux, Thurid Johnstone, Nathalee Prakash, Aaron R. Jex, Caroline Mansfield
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41419-021-04067-y

Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4
Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pntd.0008333

Spatial epidemiology of Japanese encephalitis virus and other infections of the central nervous system infections in Lao PDR (2003–2011): A retrospective analysis
Cited by: 2
Author(s): Sayaphet Rattanavong, Audrey Dubot‐Pérès, Mayfong Mayxay, Manivanh Vongsouvath, Sue J. Lee, Julien Cappelle, Paul N. Newton, Daniel M. Parker
Software Mentions: 7
Published: about 6 years ago

10.1186/s13075-016-1120-0

A discrete cluster of urinary biomarkers discriminates between active systemic lupus erythematosus patients with and without glomerulonephritis
Cited by: 25
Author(s): Carolina Landolt-Marticorena, Stephenie D. Prokopec, Stacey Morrison, Babak Noamani, Dennisse Bonilla, Heather N. Reich, James W. Scholey, Carmen Ávila-Casado, Paul R. Fortin, Paul C. Boutros, Joan E. Wither
Software Mentions: 7
Published: over 9 years ago

10.1186/s13059-019-1868-z

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
Cited by: 9
Author(s): Minji Kim, Meizhen Zheng, Simon Zhongyuan Tian, Byoungkoo Lee, Jeffrey H. Chuang, Yijun Ruan
Software Mentions: 7
Published: over 6 years ago

10.3390/biom11060796

Lower Gene Expression of Angiotensin Converting Enzyme 2 Receptor in Lung Tissues of Smokers With COVID-19Pneumonia
Cited by: 2
Author(s): Francesca Lunardi, Francesco Fortarezza, Luca Vedovelli, Federica Pezzuto, Annalisa Boscolo, Marco Rossato, Roberto Vettor, Anna María Cattelan, Claudia Del Vecchio, Andrea Crisanti, Paolo Navalesi, Darío Gregori, Fiorella Calabrese
Software Mentions: 7
Published: about 5 years ago

10.3389/fgene.2018.00250

GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data
Cited by: 15
Author(s): Mayur Divate, Edwin Cheung
Software Mentions: 7
Published: almost 8 years ago

10.1007/s00125-017-4437-6

Assessment of glucose regulation in pregnancy after gastric bypass surgery
Cited by: 25
Author(s): Christian Göbl, Latife Bozkurt, Andrea Tura, Michael Leutner, Laura Andrei, Lukas Fahr, Peter Husslein, Wolfgang Eppel, Alexandra Kautzky–Willer
Software Mentions: 7
Published: almost 9 years ago

10.1371/journal.pgen.1008984

Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model
Cited by: 16
Author(s): Huimin Na, Stefan Zdraljevic, Robyn E. Tanny, Albertha J.M. Walhout, Erik C. Andersen
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13059-020-1945-3

Protein velocity and acceleration from single-cell multiomics experiments
Cited by: 43
Author(s): Gennady Gorin, Valentine Svensson, Lior Pachter
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-020-69082-z

Immune expression signatures as candidate prognostic biomarkers of age and gender survival differences in cutaneous melanoma
Cited by: 6
Author(s): Yi Jun Kim, Kyubo Kim, Kye Hwa Lee, Jiyoung Kim, Wonguen Jung
Software Mentions: 7
Published: almost 6 years ago

10.1111/pbi.13205

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Cited by: 45
Author(s): Linkai Huang, Guangyan Feng, Haidong Yan, Zhongren Zhang, B. Shaun Bushman, Jianping Wang, Aureliano Bombarely, Mingzhou Li, Zhongfu Yang, Gang Nie, Wengang Xie, Lei Xu, Peilin Chen, Xinxin Zhao, Wenkai Jiang, Xinquan Zhang
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0152578

Role of Cattle Movements in Bovine Tuberculosis Spread in France between 2005 and 2014
Cited by: 44
Author(s): Aurore Palisson, Aurélie Courcoul, Benoı̂t Durand
Software Mentions: 7
Published: over 10 years ago

10.3389/fonc.2021.626961

Identification of Stemness Characteristics Associated With the Immune Microenvironment and Prognosis in Gastric Cancer
Cited by: 15
Author(s): Deli Mao, Zhijun Zhou, Shenglei Song, Dongsheng Li, Yulong He, Zhewei Wei, Changhua Zhang
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2020.01900

Biomarkers of the Response to Immune Checkpoint Inhibitors in Metastatic Urothelial Carcinoma
Cited by: 5
Author(s): Siteng Chen, Ning Zhang, Tao Wang, Encheng Zhang, Xiang Wang, Junhua Zheng
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12859-016-0970-4

MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics
Cited by: 22
Author(s): Youzhong Liu, Kirill S. Smirnov, Marianna Lucio, Régis D. Gougeon, Hervé Alexandre, Philippe Schmitt‐Kopplin
Software Mentions: 7
Published: over 10 years ago

10.7554/eLife.51413

Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation
Cited by: 190
Author(s): Ankit Jambusaria, Zhigang Hong, Lianghui Zhang, Shubhi Srivastava, Arundhati Jana, Péter T. Tóth, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 7
Published: over 6 years ago

10.1093/gigascience/giaa135

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology
Cited by: 33
Author(s): Christina Weißbecker, Beatrix Schnabel, Anna Heintz‐Buschart
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.678780

Identification of a Four-Gene Signature With Prognostic Significance in Endometrial Cancer Using Weighted-Gene Correlation Network Analysis
Cited by: 7
Author(s): Shijin Huang, Lihong Pang, Changqiang Wei
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pcbi.1006158

Comment on "A comprehensive overview and evaluation of circular RNA detection tools"
Cited by: 14
Author(s): Chia-Ying Chen, Trees‐Juen Chuang
Software Mentions: 7
Published: about 7 years ago

10.1186/s12864-016-3300-3

Assessing characteristics of RNA amplification methods for single cell RNA sequencing
Cited by: 32
Author(s): Hannah Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian–Bing Fan, Stephen Fisher, Jennifer Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin, Rui Li, William J. Mack, Sean McGroty, Joseph Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher Walker, Jinhui Wang, Kai Wang, Wei Wang, André Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim
Software Mentions: 7
Published: over 9 years ago

10.15252/msb.20167507

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation
Cited by: 43
Author(s): Margaux Michel, Carina Demel, Benedikt Zacher, Björn Schwalb, Stefan Krebs, Helmut Blum, Julien Gagneur, Patrick Cramer
Software Mentions: 7
Published: over 9 years ago

10.1038/s41598-020-77578-x

Empty mesoporous silica particles significantly delay disease progression and extend survival in a mouse model of ALS
Cited by: 7
Author(s): Marcel F. Leyton-Jaimes, Patrik Ivert, Jan Hoeber, Yilin Han, Adam Feiler, Chunfang Zhou, Stanislava Pankratova, Varda Shoshan‐Barmatz, Adrian Israelson, Elena N. Kozlova
Software Mentions: 7
Published: over 5 years ago

10.3390/brainsci10020109

Chronic Chemogenetic Stimulation of the Nucleus Accumbens Produces Lasting Reductions in Binge Drinking and Ameliorates Alcohol-Related Morphological and Transcriptional Changes
Cited by: 27
Author(s): Dar'ya Pozhidayeva, Sean P. Farris, Calla M Goeke, Evan Firsick, Kayla G. Townsley, Marina Guizzetti, Angela R. Ozburn
Software Mentions: 7
Published: over 6 years ago

10.1111/jcmm.15472

Transcriptomic landscape profiling of metformin‐treated healthy mice: Implication for potential hypertension risk when prophylactically used
Cited by: 4
Author(s): Yuhuan Meng, Rui Xiang, Han Yan, Yiran Zhou, Yuntao Hu, Jichun Yang, Yuan Zhou, Qinghua Cui
Software Mentions: 7
Published: about 6 years ago

10.1038/s41598-020-76536-x

Disparity of time-contrast curves generated by various types of power injectors used in magnetic resonance imaging
Cited by: 0
Author(s): Marcus Doppler, Ewald Moser, Uros Klickovic, Christian Našel
Software Mentions: 7
Published: over 5 years ago

10.15252/msb.20198831

The impact of the genetic background on gene deletion phenotypes in <i>Saccharomyces cerevisiae</i>
Cited by: 40
Author(s): Marco Galardini, Bede P. Busby, Cristina Viéitez, Alistair S. Dunham, Athanasios Typas, Pedro Beltrão
Software Mentions: 7
Published: over 6 years ago

10.1186/s40793-020-00365-8

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond
Cited by: 14
Author(s): Jessica Chopyk, Daniel J. Nasko, Sarah Allard, Anthony Bui, Mihai Pop, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 7
Published: over 5 years ago

10.1038/srep30794

Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry
Cited by: 33
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 7
Published: almost 10 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: over 10 years ago

10.1038/s41598-021-98926-5

Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey
Cited by: 22
Author(s): Masaaki Sato, Nariaki Inoue, Ryogen Nambu, Naoki Furuichi, Tsutomu Imaizumi, Masayuki Ushio
Software Mentions: 7
Published: almost 5 years ago

10.1128/mBio.02723-20

Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development
Cited by: 17
Author(s): Kathleen Beilsmith, Matthew Perisin, Joy Bergelson
Software Mentions: 7
Published: over 5 years ago

10.1186/s13321-019-0342-y

KMR: knowledge-oriented medicine representation learning for drug–drug interaction and similarity computation
Cited by: 16
Author(s): Ying Shen, Kun Yuan, Min Yang, Buzhou Tang, Yaliang Li, Nan Du, Kai Lei
Software Mentions: 7
Published: over 7 years ago

10.1186/s40635-021-00410-x

Validation of a novel system to assess end-expiratory lung volume and alveolar recruitment in an ARDS model
Cited by: 0
Author(s): Laurent Bitker, Nakédia M. F. Carvalho, Sascha Reidt, Christoph Schranz, Dominik Novotni, Maciej Orkisz, Eduardo Davila Serrano, Jean-Pierre Revelly, Jean-Christophe Richard
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12918-016-0337-5

Quantifying differences in cell line population dynamics using CellPD
Cited by: 22
Author(s): Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond Jonckheere, David B. Agus, Shannon M. Mumenthaler, Paul Macklin
Software Mentions: 7
Published: almost 10 years ago

10.1186/s13148-018-0510-3

Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception
Cited by: 25
Author(s): Davide Gentilini, Edgardo Somigliana, Luca Pagliardini, Elisa Rabellotti, Paolo Garagnani, Luisa Bernardinelli, Enrico Papaleo, Massimo Candiani, Anna Maria Di Blasio, Paola Viganò
Software Mentions: 7
Published: about 8 years ago

10.1371/journal.pone.0187742

Increased sediment load during a large-scale dam removal changes nearshore subtidal communities
Cited by: 26
Author(s): Stephen P. Rubin, Ian Miller, Melissa M. Foley, Helen Berry, Jeffrey J. Duda, Benjamin Hudson, Nancy Elder, Matthew M. Beirne, Jonathan A. Warrick, Michael L. McHenry, Andrew W. Stevens, Emily Eidam, A. S. Ogston, Guy Gelfenbaum, Rob Pedersen
Software Mentions: 7
Published: over 8 years ago

10.7717/peerj.7038

Decoupled recovery of ecological communities after reclamation
Cited by: 3
Author(s): Zachary A. Sylvain, David H. Branson, Tatyana A. Rand, Natalie M. West, Erin K. Espeland
Software Mentions: 7
Published: about 7 years ago

10.3390/mps3020034

OCTAVVS: A Graphical Toolbox for High-Throughput Preprocessing and Analysis of Vibrational Spectroscopy Imaging Data
Cited by: 7
Author(s): Carl Troein, Syahril Siregar, Michiel Op De Beeck, Carsten Peterson, Anders Tunlid, Per Persson
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0253411

PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
Cited by: 12
Author(s): Bulat Faezov, Roland L. Dunbrack
Software Mentions: 7
Published: almost 5 years ago

10.3389/fvets.2020.00214

Cultural “Blind Spots,” Social Influence and the Welfare of Working Donkeys in Brick Kilns in Northern India
Cited by: 16
Author(s): Tamlin Watson, Laura M Kubasiewicz, Natasha Chamberlain, Caroline Nye, Zoe Raw, Faith Burden
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0239381

Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses
Cited by: 8
Author(s): Nafis Ul Alam, Umar Faruq Chowdhury
Software Mentions: 7
Published: almost 6 years ago

10.3389/fvets.2018.00269

The Use of Kernel Density Estimation With a Bio-Physical Model Provides a Method to Quantify Connectivity Among Salmon Farms: Spatial Planning and Management With Epidemiological Relevance
Cited by: 27
Author(s): Danielle L. Cantrell, Erin E. Rees, Raphaël Vanderstichel, Jon E. Grant, Ramón Filgueira, Crawford W. Revie
Software Mentions: 7
Published: over 7 years ago

10.1186/s40168-020-00993-9

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data
Cited by: 61
Author(s): Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz‐Buschart, Cédric Christian Laczny, Patrick May, Paul Wilmes
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1009382

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Cited by: 3
Author(s): Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro
Software Mentions: 7
Published: almost 5 years ago

10.1002/bit.27209

Comparative genome‐scale analysis of <i>Pichia pastoris</i> variants informs selection of an optimal base strain
Cited by: 31
Author(s): Joseph Brady, Charles A. Whittaker, Melody C. Tan, D. Lee Kristensen, Duanduan Ma, Neil C. Dalvie, Kerry R. Love, J. Christopher Love
Software Mentions: 7
Published: over 6 years ago

10.1186/gb-2012-13-4-r29

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.
Cited by: 84
Author(s): Mauro A. A. Castro, Xin Wang, Michael Fletcher, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 7
Published: over 14 years ago

10.1186/s12888-021-03501-x

Validation of case definitions of depression derived from administrative data against the CIDI-SF as reference standard: results from the PROspective Québec (PROQ) study
Cited by: 3
Author(s): Ana Paula Bruno Pena-Gralle, Denis Talbot, Xavier Trudel, Karine Aubé, Alain Lesage, Sophie Lauzier, Alain Milot, Chantal Brisson
Software Mentions: 7
Published: over 4 years ago

10.3389/fphys.2021.609770

Construction of Prognostic Risk Prediction Model of Oral Squamous Cell Carcinoma Based on Nine Survival-Associated Metabolic Genes
Cited by: 10
Author(s): Zhun Huang, Yangyang Yao, Ting‐Yu Chen, Yifan Zhao, Chao Zhang, Yu‐Ming Niu
Software Mentions: 7
Published: over 5 years ago

10.1186/s13000-021-01118-y

Identification of immune-infiltrating cell-related biomarkers in hepatocellular carcinoma based on gene co-expression network analysis
Cited by: 6
Author(s): Yinghui Hou, Guizhi Zhang
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0250783

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores
Cited by: 12
Author(s): John K. Pearman, Georgia Thomson‐Laing, Jamie Howarth, Marcus J. Vandergoes, L. M. Thompson, Andrew Rees, Susanna A. Wood
Software Mentions: 7
Published: about 5 years ago

10.3762/bjnano.6.165

The eNanoMapper database for nanomaterial safety information
Cited by: 82
Author(s): Nina Jeliazkova, Charalampos Chomenidis, Philip Doganis, Bengt Fadeel, Roland C. Grafström, Barry Hardy, Janna Hastings, Markus Hegi, Vedrin Jeliazkov, Nikolay Kochev, Pekka Kohonen, Cristian R. Munteanu, Haralambos Sarimveis, Bart Smeets, Pantelis Sopasakis, Georgia Tsiliki, David Vorgrimmler, Egon Willighagen
Software Mentions: 7
Published: almost 11 years ago

10.1186/1471-2105-14-S1-S1

Visualization of protein interaction networks: problems and solutions
Cited by: 70
Author(s): Giuseppe Agapito, Pietro Hiram Guzzi, Mario Cannataro
Software Mentions: 7
Published: over 13 years ago

10.1038/srep29042

Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Cited by: 35
Author(s): Frédéric Bouché, Maria D’Aloia, Pierre Tocquin, Guillaume Lobet, Nathalie Detry, Claire Périlleux
Software Mentions: 7
Published: about 10 years ago

10.1371/journal.pone.0106150

Towards Monitoring Biodiversity in Amazonian Forests: How Regular Samples Capture Meso-Scale Altitudinal Variation in 25 km2 Plots
Cited by: 9
Author(s): D. Ryan Norris, Marie‐Josée Fortin, William E. Magnusson
Software Mentions: 7
Published: almost 12 years ago

10.1186/s12859-017-1711-z

GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles
Cited by: 8
Author(s): Michael Klein, David F. Stern, Hongyu Zhao
Software Mentions: 7
Published: about 9 years ago

10.3390/ijerph18020565

Does Last Year’s Cost Predict the Present Cost? An Application of Machine Leaning for the Japanese Area-Basis Public Health Insurance Database
Cited by: 4
Author(s): Yasuo Nomura, Yoshimasa Ishii, Yota Chiba, Shunsuke Suzuki, Akira Suzuki, Senichi Suzuki, Kenji Morita, Joji Tanabe, Koji Yamakawa, Yasuo Ishiwata, Misao Ishikawa, Kaoru Sogabe, Erika Kakuta, Ayako Okada, Ryoko Otsuka, Nobuhiro Hanada
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1009385

Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive
Cited by: 19
Author(s): Georg Oberhofer, Tobin Ivy, Bruce A. Hay
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-019-2611-1

sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs
Cited by: 18
Author(s): Apostolos Dimitromanolakis, Jingxiong Xu, Agnieszka Król, Laurent Briollais
Software Mentions: 7
Published: over 7 years ago

10.3390/cancers13092102

Integration of Urinary EN2 Protein &amp; Cell-Free RNA Data in the Development of a Multivariable Risk Model for the Detection of Prostate Cancer Prior to Biopsy
Cited by: 4
Author(s): Shea P. Connell, Robert Mills, Hardev Pandha, Richard Morgan, Christopher S. Cooper, Jeremy Clark, Daniel Brewer
Software Mentions: 7
Published: about 5 years ago

10.7717/peerj.8206

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Cited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.51529

Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Cited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0211692

The impact of bipedal mechanical loading history on longitudinal long bone growth
Cited by: 7
Author(s): A. D. Foster
Software Mentions: 7
Published: over 7 years ago

10.1038/s41375-020-0791-3

Validation of nomogram-revised risk index and comparison with other models for extranodal nasal-type NK/T-cell lymphoma in the modern chemotherapy era: indication for prognostication and clinical decision-making
Cited by: 66
Author(s): Si Ye Chen, Yong Yang, S. Qi, Ying Wang, Chen Hu, Xia He, L. Zhang, Gang Wu, Baolin Qu, Qian Li, Xuwei Hou, Fu Quan Zhang, X.Y. Qiao, Hua Wang, Gao Feng Li, Yu Jing Zhang, Yuan Zhu, Jian Cao, Sheng Hui Lan, Jun Wu, Tao Wu, Shijun Zhu, Mei Shi, Li Xu, Zhi Yong Yuan, Joachim Yahalom, Richard W. Tsang, Yinggai Song, Jun Zhu, Hang Su, Ye Xiong Li
Software Mentions: 7
Published: over 6 years ago

10.1186/s12983-019-0309-x

Mining morphometrics and age from past survey photographs
Cited by: 3
Author(s): Caitlin Black, Hannah S. Mumby, Michelle Henley
Software Mentions: 7
Published: about 7 years ago

10.3389/fnagi.2019.00203

Revisiting the MotionWatch8©: Calibrating Cut-Points for Measuring Physical Activity and Sedentary Behavior Among Adults With Stroke
Cited by: 6
Author(s): Ryan S. Falck, John R. Best, Michael C. R. Li, Janice J. Eng, Teresa Liu-Ambrose
Software Mentions: 7
Published: almost 7 years ago

10.21203/rs.3.rs-380803/v1

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19
Cited by: 9
Author(s): Alexandra Tsitsiklis, Beth Shoshana Zha, Ashley Byrne, Catherine DeVoe, Sophia Levan, Elze Rackaityte, Sara Sunshine, Eran Mick, Rajani Ghale, Alejandra Jauregui, Norma Neff, Aartik Sarma, Paula Hayakawa Serpa, Thomas Deiss, Amy Kistler, Sidney Carrillo, K. Mark Ansel, Aleksandra Leligdowicz, S. Christenson, Nicola L. Jones, Benjamin Wu, Spyros Darmanis, Michael A. Matthay, Susan V. Lynch, Joseph L. DeRisi, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Matthew F. Krummel, Prescott G. Woodruff, David J. Erle, O. A. Rosenberg, Carolyn S. Calfee, Charles Langelier
Software Mentions: 7
Published: about 5 years ago

10.1016/j.heliyon.2021.e06160

Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin
Cited by: 4
Author(s): Artem Nedoluzhko, Fedor Sharko, Svetlana Tsygankova, Eugenia Boulygina, Amina S. Ibragimova, Anton Teslyuk, Jorge Galindo-Villegas, С. М. Расторгуев
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0048365

Molecular and Immunological Characterization of Gluten Proteins Isolated from Oat Cultivars That Differ in Toxicity for Celiac Disease
Cited by: 67
Author(s): Ana Real, Isabel Comino, Laura de Lorenzo, Francisco Merchán, Javier Gil-Humanes, María J. Giménez, Miguel Ángel López-Casado, Ma Isabel Torres, Ángel Cebolla, Carolina Sousa, Francisco Barro, Fernando Pistón
Software Mentions: 7
Published: over 13 years ago

10.1186/1471-2180-14-171

Colony-live — a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli
Cited by: 38
Author(s): Rikiya Takeuchi, Takeyuki Tamura, Toru Nakayashiki, Yuzo Tanaka, Ai Muto, Barry L. Wanner, Hirotada Mori
Software Mentions: 7
Published: about 12 years ago

10.1186/s40168-018-0595-0

Skin and gut microbiomes of a wild mammal respond to different environmental cues
Cited by: 38
Author(s): Anton Lavrinienko, Eugene Tukalenko, Tapio Mappes, Phillip C. Watts
Software Mentions: 7
Published: over 7 years ago

10.12688/f1000research.11290.1

Gene length and detection bias in single cell RNA sequencing protocols
Cited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: about 9 years ago

10.1002/ece3.5617

Meta‐analyzing the likely cross‐species responses to climate change
Cited by: 10
Author(s): Jean C. G. Ortega, Nathalia Ingrid Gomes Machado, José Alexandre Felizola Diniz‐Filho, Thiago F. Rangel, Miguel B. Araújo, Rafael Loyola, Luis Maurício Bini
Software Mentions: 7
Published: almost 7 years ago

10.7554/eLife.62800

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum
Cited by: 18
Author(s): Kathryn H. Milne, Alasdair Ivens, Adam J. Reid, Magda E. Lotkowska, Áine O’Toole, Geetha Sankaranarayanan, Diana Muñoz Sandoval, Wiebke Nahrendorf, Clément Regnault, Nick J. Edwards, Sarah E. Silk, Ruth Payne, Angela M. Minassian, Navin Venkatraman, Mandy Sanders, Adrian V. S. Hill, Michael P. Barrett, Matthew Berriman, Simon J. Draper, J. Alexandra Rowe, Philip J. Spence
Software Mentions: 7
Published: over 5 years ago

10.12688/f1000research.17916.1

Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
Cited by: 19
Author(s): Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch
Software Mentions: 7
Published: over 7 years ago

10.1186/s12862-019-1510-4

Geographic isolation and climatic variability contribute to genetic differentiation in fragmented populations of the long-lived subalpine conifer Pinus cembra L. in the western Alps
Cited by: 26
Author(s): Endre György Tóth, Francine Tremblay, Johann M. Housset, Yves Bergeron, Christopher Carcaillet
Software Mentions: 7
Published: over 6 years ago

10.1038/s41388-021-01876-5

The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct and separable from its DNA-binding function in Ewing sarcoma
Cited by: 12
Author(s): Megann A. Boone, Cenny Taslim, Julie Crow, Julia Selich‐Anderson, Andrea K. Byrum, Iftekhar A. Showpnil, Benjamin D. Sunkel, Meng Wang, Benjamin Z. Stanton, Emily R. Theisen, Stephen L. Lessnick
Software Mentions: 7
Published: about 5 years ago

10.1186/s13059-020-1948-0

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility
Cited by: 42
Author(s): Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z. Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang, Stephen L. Johnson
Software Mentions: 7
Published: over 6 years ago

10.3389/fimmu.2021.645320

Effects of Hypoxia in Intestinal Tumors on Immune Cell Behavior in the Tumor Microenvironment
Cited by: 14
Author(s): Luping Zhang, Shaokun Wang, Yachen Wang, Wenjie Zhao, Yingli Zhang, Nan Zhang, Hong Xu
Software Mentions: 7
Published: over 5 years ago

10.1093/gigascience/gix129

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags
Cited by: 15
Author(s): Xianfeng Chen, Stephen Johnson, Patricio Jeraldo, Junwen Wang, Nicholas Chia, Jean Pierre A. Kocher, Jun Chen
Software Mentions: 7
Published: over 8 years ago

10.3389/fnmol.2021.680280

Impaired SNF2L Chromatin Remodeling Prolongs Accessibility at Promoters Enriched for Fos/Jun Binding Sites and Delays Granule Neuron Differentiation
Cited by: 1
Author(s): Laura Rose Goodwin, Gerardo Zapata, Sara Timpano, Jacob Marenger, David J. Picketts
Software Mentions: 7
Published: almost 5 years ago

10.1016/j.ebiom.2021.103390

AI-guided discovery of the invariant host response to viral pandemics
Cited by: 31
Author(s): Debashis Sahoo, Gajanan D. Katkar, Soni Khandelwal, Mahdi Behroozikhah, Amanraj Claire, Vanessa Castillo, Courtney Tindle, MacKenzie Fuller, Sahar Taheri, Thomas F. Rogers, Nathan Beutler, Sydney I. Ramirez, Stephen A. Rawlings, Victor Pretorius, Davey M Smith, Dennis R. Burton, Laura E. Crotty Alexander, Jason Duran, Shane Crotty, Jennifer M. Dan, Soumita Das, Pradipta Ghosh
Software Mentions: 7
Published: about 5 years ago

10.1186/s40168-017-0302-6

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study
Cited by: 27
Author(s): Moana Mika, Josua Maurer, Insa Korten, Aurélie Allemann, Suzanne Aebi, Silvio D. Brugger, Weihong Qi, Urs Frey, Philipp Latzin, Markus Hilty
Software Mentions: 7
Published: almost 9 years ago

10.1534/g3.120.401325

Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
Cited by: 17
Author(s): Alexander F. Gileta, Jianjun Gao, Apurva S. Chitre, Hannah Bimschleger, Celine L. St. Pierre, Shyam Gopalakrishnan, Abraham A. Palmer
Software Mentions: 7
Published: almost 6 years ago