10.1098/rsfs.2019.0119

Towards blood flow in the virtual human: efficient self-coupling of HemeLB
Cited by: 9
Author(s): J. W. S. McCullough, Robin A. Richardson, Alex Patronis, René Halver, Ryan Marshall, Martin Ruefenacht, Brian J. N. Wylie, Thomas Odaker, Michael Wiedemann, Bryn Lloyd, Esra Neufeld, Godehard Sutmann, Anthony Skjellum, Dieter Kranzlmüller, Peter V. Coveney
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009745

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution
Cited by: 9
Author(s): Matthew H. Van Dam, Analyn Cabras, James Henderson, Andrew J. Rominger, Cynthia Pérez Estrada, Arina D. Omer, Olga Dudchenko, E Aiden, Athena Lam
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSystems.00116-21

Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome
Cited by: 25
Author(s): Celeste Allaband, Amulya Lingaraju, Cameron Martino, Baylee J. Russell, Anupriya Tripathi, Orit Poulsen, Ana Carolina Dantas Machado, Dan Zhou, Jin Xue, Emmanuel O. Elijah, Atul Malhotra, Pieter C. Dorrestein, Rob Knight, Gabriel G. Haddad, Amir Zarrinpar
Software Mentions: 4
Published: about 5 years ago

10.1038/s41597-019-0345-6

Depth-to-bedrock map of China at a spatial resolution of 100 meters
Cited by: 38
Author(s): Fapeng Yan, Wei Shangguan, Jing Zhang, Bifeng Hu
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-020-01214-7

Genome sequence of segmented filamentous bacteria present in the human intestine
Cited by: 20
Author(s): Hans Jonsson, Luisa W. Hugerth, John Sundh, E. Lundin, Anders F. Andersson
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0182056

Dynamics and asymmetry in the dimer of the norovirus major capsid protein
Cited by: 8
Author(s): Thibault Tubiana, Yves Boulard, Stéphane Bressanelli
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-021-02362-7

SpatialDWLS: accurate deconvolution of spatial transcriptomic data
Cited by: 107
Author(s): Rui Dong, Guo‐Cheng Yuan
Software Mentions: 4
Published: about 5 years ago

10.1038/sdata.2016.44

The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments
Cited by: 931
Author(s): Krzysztof J. Gorgolewski, Tibor Auer, Vince D. Calhoun, R. Cameron Craddock, Samir Das, Eugene P. Duff, Guillaume Flandin, Samik Ghosh, Tristan Glatard, Yaroslav O. Halchenko, Daniel A. Handwerker, Michael Hanke, David B. Keator, Xiangrui Li, Zachary Michael, Camille Maumet, B. Nolan Nichols, Thomas E. Nichols, John Pellman, Jean‐Baptiste Poline, Ariel Rokem, Gunnar Schaefer, Vanessa Sochat, William Triplett, Jessica A. Turner, Gaël Varoquaux, Russell A. Poldrack
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0108852

Expression, Purification, and Structural Insights for the Human Uric Acid Transporter, GLUT9, Using the Xenopus laevis Oocytes System
Cited by: 34
Author(s): Benjamin Clémençon, Benjamin P. Lüscher, Michael Fine, Marc Baumann, Daniel Surbek, Olivier Bonny, Matthias A. Hediger
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12935-020-01264-1

Nine glycolysis-related gene signature predicting the survival of patients with endometrial adenocarcinoma
Cited by: 26
Author(s): Jinhui Liu, Siyue Li, Feng Gao, Hua Meng, Song Nie, Rui Sun, Jing Yang, Wenjun Cheng
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0131504

A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: about 11 years ago

10.1038/s41597-020-00752-3

Soil bacterial community structures in relation to different oil palm management practices
Cited by: 11
Author(s): Dirk Hölscher, Dominik Schneider, Nina Hennings, Anja Meryandini, Rolf Daniel
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1006828

p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate
Cited by: 34
Author(s): Rose Richardson, Karen S. Mitchell, Nigel L. Hammond, Maria Rosaria Mollo, Evelyn N. Kouwenhoven, Niki Wyatt, Ian J. Donaldson, Leo Zeef, Tim Burgis, Rognvald Blance, Simon J. van Heeringen, Hendrik G. Stunnenberg, Huiqing Zhou, Caterina Missero, Rose Anne Romano, Satrajit Sinha, Michael J. Dixon, Jill Dixon
Software Mentions: 4
Published: about 9 years ago

10.1002/2211-5463.13032

Delivery of a mitochondria‐targeted antioxidant from biocompatible, polymeric nanofibrous scaffolds
Cited by: 7
Author(s): Yasaman Hamedani, Rayane Brinck Teixeira, Catherine Karbasiafshar, Peter Wipf, Sankha Bhowmick, M. Ruhul Abid
Software Mentions: 4
Published: over 5 years ago

10.1186/s13068-018-1193-x

Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production
Cited by: 91
Author(s): Matthew Scarborough, Griffin Lynch, Mitch Dickson, Mick McGee, Timothy J. Donohue, Daniel R. Noguera
Software Mentions: 4
Published: about 8 years ago

10.3233/JAD-200445

Cognitive, Genetic, Brain Volume, and Diffusion Tensor Imaging Markers as Early Indicators of Dementia
Cited by: 4
Author(s): Theresa Müller, Nicola Maria Payton, Grégoria Kalpouzos, Frank Jessen, Giulia Grande, Lars Bäckman, Erika J. Laukka
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1008256

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)
Cited by: 13
Author(s): Shuonan Chen, Jackson Loper, Xiaoyin Chen, Alex Vaughan, Anthony M. Zador, Liam Paninski
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-6-169

The EH1 motif in metazoan transcription factors
Cited by: 67
Author(s): Richard R. Copley
Software Mentions: 4
Published: over 20 years ago

10.3390/metabo7030034

Natural Product Discovery Using Planes of Principal Component Analysis in R (PoPCAR)
Cited by: 22
Author(s): Shaurya Chanana, Chris S. Thomas, D. C. Braun, Yunfei Hou, Thomas P. Wyche, Tim S. Bugni
Software Mentions: 4
Published: about 9 years ago

10.18632/oncotarget.24044

CD30 expression and survival in extranodal NK/T-cell lymphoma: a systematic review and meta-analysis
Cited by: 15
Author(s): Zihang Chen, Pujun Guan, Shan Tong, Yunxia Ye, Limin Gao, Zhi Wang, Sha Zhao, Wenyan Zhang, Li Zhang, Ling Pan, Weiping Liu
Software Mentions: 4
Published: over 8 years ago

10.1038/srep33446

Maternal Genetic Ancestry and Legacy of 10th Century AD Hungarians
Cited by: 28
Author(s): Aranka Csősz, Anna Szécsényi-Nagy, Veronika Csákyová, Péter Langó, Viktória Bódis, Kitti Köhler, Gyöngyvér Tömöry, Milan Nagy, Balázs Gusztáv Mende
Software Mentions: 4
Published: almost 10 years ago

10.3390/nu12082414

Impacts of Habitual Diets Intake on Gut Microbial Counts in Healthy Japanese Adults
Cited by: 6
Author(s): T. Sugimoto, Tatsuichiro Shima, Ryuta Amamoto, Chiaki Kaga, Yukiko Kado, Osamu Watanabe, Junko Shiinoki, Kaoru Iwazaki, Hiroko Shigemura, Hirokazu Tsuji, Satoshi Matsumoto
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13326-017-0118-0

BioFed: federated query processing over life sciences linked open data
Cited by: 43
Author(s): Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude N. Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz‐Schuhmann
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2019.00826

Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing
Cited by: 27
Author(s): Stephen R. Doyle, Geetha Sankaranarayanan, Fiona Allan, Duncan Berger, Pablo David Jimenez Castro, James B. Collins, Thomas Crellen, María A. Duque-Correa, Peter Ellis, Tegegn G. Jaleta, Roz Laing, Kirsty Maitland, Catherine McCarthy, Tchonfienet Moundai, Ben Softley, Elizabeth A. Thiele, Philippe Tchindebet Ouakou, John Vianney Tushabe, Joanne P. Webster, Adam Weiss, James B. Lok, Eileen Devaney, Ray M. Kaplan, James A. Cotton, Matthew Berriman, Nancy Holroyd
Software Mentions: 4
Published: almost 7 years ago

10.4056/sigs.5279417

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
Cited by: 21
Author(s): Dagmar Waltemath, Frank Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolás Rodríguez, Falk Schreiber, Lucian P. Smith, Fengkai Zhang, Eric Bonnet
Software Mentions: 4
Published: over 12 years ago

10.1186/s40168-018-0550-0

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Cited by: 67
Author(s): Johannes Alneberg, Christofer M. G. Karlsson, Anna-Maria Divne, Claudia Bergin, Félix Homa, Markus V. Lindh, Luisa W. Hugerth, Thijs J. G. Ettema, Stefan Bertilsson, Anders F. Andersson, Jarone Pinhassi
Software Mentions: 4
Published: almost 8 years ago

10.1002/2211-5463.12521

In silico identification and biochemical characterization of the human dicarboxylate clamp TPR protein interaction network
Cited by: 4
Author(s): Alexandra Bernadotte, Rajnish Kumar, Bengt Winblad, Pavel F. Pavlov
Software Mentions: 4
Published: almost 8 years ago

10.1002/ece3.5463

Impact of demography on linked selection in two outcrossing Brassicaceae species
Cited by: 9
Author(s): Tiina M. Mattila, Benjamin Laenen, Róbert Horváth, Tuomas Hämälä, Outi Savolainen, Tanja Slotte
Software Mentions: 4
Published: almost 7 years ago

10.3389/fendo.2019.00941

The Association of Gut Microbiota With Idiopathic Central Precocious Puberty in Girls
Cited by: 20
Author(s): Guoqing Dong, Jiyong Zhang, Zhenyu Yang, Xin Feng, Jianxu Li, Dongfang Li, Miao Hao, Yinhu Li, Minghui Qiu, Xiyan Lu, Peihui Liu, Yanwu Zeng, Ximing Xu, Xiaoping Luo, Wenkui Dai, Sitang Gong
Software Mentions: 4
Published: over 6 years ago

10.26508/lsa.202000944

In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood
Cited by: 6
Author(s): Louis Legoff, Shereen Cynthia D’Cruz, Katia Bouchekhchoukha, Christine Monfort, Christian Jaulin, Luc Multigner, Fátima Smagulova
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-015-0795-6

TOGGLE: toolbox for generic NGS analyses
Cited by: 20
Author(s): Cécile Monat, Christine Tranchant‐Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela, Marilyne Summo, François Sabot
Software Mentions: 4
Published: over 10 years ago

10.1186/s12859-020-3495-9

YSMR: a video tracking and analysis program for bacterial motility
Cited by: 3
Author(s): Julian Schwanbeck, Ines Oehmig, Jerôme Dretzke, Andreas E. Zautner, Uwe Groß, Wolfgang Bohne
Software Mentions: 4
Published: over 6 years ago

10.1111/eva.13079

Host plants and <i>Wolbachia</i> shape the population genetics of sympatric herbivore populations
Cited by: 11
Author(s): Zhen F. Fu, Amanda R. Meier, Brendan Epstein, Alan O. Bergland, Carmen I. Castillo Carrillo, William C. Cooper, Regina K. Cruzado, David Horton, Andrew S. Jensen, Joanna L. Kelley, Arash Rashed, Stuart R. Reitz, Silvia I. Rondon, Jenita Thinakaran, Erik J. Wenninger, Carrie H. Wohleb, David W. Crowder, William E. Snyder
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpsyg.2020.584231

Effects of Scale on Multimodal Deixis: Evidence From Quiahije Chatino
Cited by: 4
Author(s): Kate Mesh, Emiliana Cruz, Joost van de Weijer, Niclas Burenhult, Marianne Gullberg
Software Mentions: 4
Published: over 5 years ago

10.1200/CCI.19.00127

CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase
Cited by: 10
Author(s): Alex H. Wagner, Susanna Kiwala, Adam Coffman, Joshua F. McMichael, Kelsy C. Cotto, T. Brian Mooney, Erica K. Barnell, Kilannin Krysiak, Arpad Danos, Jason Walker, Obi L. Griffith
Software Mentions: 4
Published: over 5 years ago

10.1007/s10577-020-09643-0

CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites
Cited by: 4
Author(s): Michi Miura, Honglin Chen
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0124671

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Cited by: 158
Author(s): Dáithí C. Murray, Megan L. Coghlan, Michael Bunce
Software Mentions: 4
Published: over 11 years ago

10.3390/toxins12100659

Gradual and Discrete Ontogenetic Shifts in Rattlesnake Venom Composition and Assessment of Hormonal and Ecological Correlates
Cited by: 4
Author(s): Richard B Schonour, Emma M. Huff, Matthew L. Holding, Natalie M. Claunch, Schyler A. Ellsworth, Michael Hogan, Kenneth P. Wray, James J. McGivern, Mark J. Margres, Timothy J. Colston, Darin R. Rokyta
Software Mentions: 4
Published: almost 6 years ago

10.1002/ajpa.23763

The efficacy of whole human genome capture on ancient dental calculus and dentin
Cited by: 21
Author(s): Kirsten A. Ziesemer, Jazmín Ramos‐Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno L. P. Hoogland, Courtney A. Hofman, Domingo C. Salazar‐García, Bruno Fröhlich, George R. Milner, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner, Hannes Schroeder
Software Mentions: 4
Published: over 7 years ago

10.1038/srep27257

Evaluating the responses of a territorial solitary carnivore to potential mates and competitors
Cited by: 28
Author(s): Maximilian L. Allen, Veronica Yovovich, Christopher C. Wilmers
Software Mentions: 4
Published: about 10 years ago

10.3390/s20133645

OpCode-Level Function Call Graph Based Android Malware Classification Using Deep Learning
Cited by: 24
Author(s): Weina Niu, Rong Cao, Xiaosong Zhang, Kangyi Ding, Kaimeng Zhang, Ting Li
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-019-6225-9

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance
Cited by: 44
Author(s): Xiaoling Yu, Wen Zhang, Zhiping Zhao, Chengsong Ye, Shao-Lai Zhou, Shaogui Wu, Lijing Han, Zhaofang Han, Hanhui Ye
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-018-2257-4

MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data
Cited by: 8
Author(s): Hitoshi Iuchi, Masahiro Sugimoto, Masaru Tomita
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-018-4671-4

Indel detection from DNA and RNA sequencing data with transIndel
Cited by: 23
Author(s): Rendong Yang, Jamie L. Van Etten, Scott M. Dehm
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-20200-y

Cultural effects on computational metrics of spatial and temporal context
Cited by: 3
Author(s): Nicholas D. Wright, Jan Grohn, Chen Song, Geraint Rees, Rebecca Lawson
Software Mentions: 4
Published: over 8 years ago

10.1093/database/baw071

A knowledge-poor approach to chemical-disease relation extraction
Cited by: 21
Author(s): Firoj Alam, Anna Corazza, Alberto Lavelli, Roberto Zanoli
Software Mentions: 4
Published: over 10 years ago

10.1172/jci.insight.143289

LncRNA DRAIR is downregulated in diabetic monocytes and modulates inflammatory phenotype via epigenetic mechanisms
Cited by: 15
Author(s): Marpadga A. Reddy, Vishnu Amaram, Sadhan Das, Vinay Singh Tanwar, Rituparna Ganguly, Mei Wang, Linda Lanting, Lingxiao Zhang, Maryam Abdollahi, Zhuo Chen, Xiwei Wu, Sridevi Devaraj, Rama Natarajan
Software Mentions: 4
Published: about 5 years ago

10.1038/s42003-021-02361-1

Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer
Cited by: 21
Author(s): Aalok Patwa, Rikiya Yamashita, Long Jin, Tyler Risom, Michael Angelo, Leeat Keren, Daniel L. Rubin
Software Mentions: 4
Published: about 5 years ago

10.1186/s13643-017-0558-8

Hepatitis C infection epidemiology in Mongolia: protocol of a systematic review and meta-analysis
Cited by: 1
Author(s): Karima Chaabna, Laith J. Abu‐Raddad
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Cited by: 25
Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: almost 7 years ago

10.1523/ENEURO.0211-20.2020

Regulatory Elements Inserted into AAVs Confer Preferential Activity in Cortical Interneurons
Cited by: 11
Author(s): Anna Noren Rubin, Ruchi Malik, Kathleen K.A. Cho, Kenneth J. Lim, Susan Lindtner, Sarah E. Robinson Schwartz, Daniel Vogt, Vikaas S. Sohal, John L.R. Rubenstein
Software Mentions: 4
Published: over 5 years ago

10.1186/s13643-020-01360-3

The impact of vitamin D food fortification and health outcomes in children: a systematic review and meta-regression
Cited by: 19
Author(s): Reem Al Khalifah, Rawan Alsheikh, Yossef Alnasser, Rana Alsheikh, Nora Alhelali, Ammar Naji, Nouf Al Backer
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0206531

The music that helps people sleep and the reasons they believe it works: A mixed methods analysis of online survey reports
Cited by: 42
Author(s): Tabitha Trahan, Simon J. Durrant, Daniel Müllensiefen, Victoria J. Williamson
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0210859

Synthetic lethality guiding selection of drug combinations in ovarian cancer
Cited by: 16
Author(s): Andreas Heinzel, Maximilian Marhold, Paul M. Mayer, Michael Schwarz, Erwin Tomasich, Arno Lukas, Michael Krainer, Paul Perco
Software Mentions: 4
Published: over 7 years ago

10.1093/gigascience/gix107

HOMINID: a framework for identifying associations between host genetic variation and microbiome composition
Cited by: 8
Author(s): Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.8047

Evolution of winter molting strategies in European and North American migratory passerines
Cited by: 5
Author(s): Claudie Pageau, Jared Sonnleitner, Christopher M. Tonra, Mateen Shaikh, Matthew W. Reudink
Software Mentions: 4
Published: almost 5 years ago

10.3390/nu11122865

Parenteral Nutrition in Patients with Inflammatory Bowel Disease Systematic Review, Meta-Analysis and Meta-Regression
Cited by: 13
Author(s): Jose Miguel Comeche, Iris Comino, Cesare Altavilla, José Tuells, Ana Gutiérrez-Hervás, Pablo Caballero
Software Mentions: 4
Published: over 6 years ago

10.1186/s12920-020-00820-y

Mutational profiling of micro-dissected pre-malignant lesions from archived specimens
Cited by: 4
Author(s): Daniela Nachmanson, J. S. Steward, Huazhen Yao, Adam Officer, Eliza Jeong, Thomas J. O’Keefe, Farnaz Hasteh, Kristen Jepsen, Gillian L. Hirst, Laura J. Esserman, Alexander D. Borowsky, Olivier Harismendy
Software Mentions: 4
Published: over 5 years ago

10.3390/s21051879

Westdrive X LoopAR: An Open-Access Virtual Reality Project in Unity for Evaluating User Interaction Methods during Takeover Requests
Cited by: 6
Author(s): Farbod Nosrat Nezami, Maximilian Alexander Wächter, Nora Maleki, Philipp Spaniol, Lea M. Kühne, Anke Haas, Johannes M. Pingel, Linus Tiemann, Frederik Nienhaus, Lynn Keller, Sabine U. König, Peter König, Gordon Pipa
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0085777

powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions
Cited by: 663
Author(s): Jeff Alstott, Edward T. Bullmore, Dietmar Plenz
Software Mentions: 4
Published: over 12 years ago

10.3389/fgene.2020.00158

TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains
Cited by: 32
Author(s): Kellen Garrison Cresswell, Mikhail G. Dozmorov
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pntd.0006344

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome
Cited by: 31
Author(s): Laura-Isobel McCall, Anupriya Tripathi, Fernando Vargas, Rob Knight, Pieter C. Dorrestein, Jair L. Siqueira-Neto
Software Mentions: 4
Published: over 8 years ago

10.1186/s13195-021-00871-y

Short leukocyte telomeres predict 25-year Alzheimer's disease incidence in non-APOE ε4-carriers
Cited by: 17
Author(s): Fernanda Schäfer Hackenhaar, Maria Josefsson, Annelie Nordin Adolfsson, Mattias Landfors, Karolina Kauppi, Magnus Hultdin, Rolf Adolfsson, Sofie Degerman, Sara Pudas
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0242520

On the agreement between bibliometrics and peer review: Evidence from the Italian research assessment exercises
Cited by: 5
Author(s): Alberto Baccini, Lucio Barabesi, Giuseppe De Nicolao
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1004755

FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks
Cited by: 55
Author(s): Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Zhe Sun, Matthew L. MacDonald, Robert A. Sweet, Jieru Wang, Wei Chen
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1009229

3D genome evolution and reorganization in the Drosophila melanogaster species group
Cited by: 24
Author(s): Nicole S. Torosin, Aparna Anand, Tirupathi Rao Golla, Weihuan Cao, Chris Ellison
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0238546

MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: almost 6 years ago

10.1007/s00277-020-04068-5

Long-term survival and polyclonal immunoglobulin reconstitution after allogeneic stem cell transplantation in multiple myeloma
Cited by: 3
Author(s): Christine Eisfeld, Eva Eßeling, Ramona Wullenkord, Cyrus Khandanpour, Julia Reusch, Jan‐Henrik Mikesch, Christian Reicherts, Andrea Kerkhoff, Christoph Schliemann, Torsten Keßler, Rolf M. Mesters, Wolfgang E. Berdel, Georg Lenz, Matthias Stelljes
Software Mentions: 4
Published: about 6 years ago

10.1515/med-2021-0242

Surgical myocardial revascularization outcomes in Kawasaki disease: systematic review and meta-analysis
Cited by: 2
Author(s): Antonio Salsano, Jingda Liao, Ambra Miette, Massimo Capoccia, Giovanni Mariscalco, Francesco Santini, Antonio F. Corno
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-93528-7

Preoperative nomogram for microvascular invasion prediction based on clinical database in hepatocellular carcinoma
Cited by: 6
Author(s): Shuqi Mao, Xi Yu, Yong Yang, Yuying Shan, Joseph Mugaanyi, Shengping Wu, Caide Lu
Software Mentions: 4
Published: about 5 years ago

10.1042/BSR20194459

<i>GPNMB</i> contributes to a vicious circle for chronic obstructive pulmonary disease
Cited by: 1
Author(s): Xijuan Zhang, Zhong‐hua Cui, Yan Dong, Xiuwen Liang, Yanxin Zhao, Ancha Baranova, Hongbao Cao, Ling Wang
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-64570-8

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects
Cited by: 16
Author(s): My Hanh Le, Daryi Wang
Software Mentions: 4
Published: about 6 years ago

10.1093/jhered/esaa057

Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (<i>Felis catus</i>) and Asian Leopard Cat (<i>Prionailurus bengalensis</i>)
Cited by: 22
Author(s): Kevin R. Bredemeyer, Andrew Harris, Gang Li, Li-Jun Zhao, Nicole M. Foley, Melody Roelke‐Parker, Stephen J. O’Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2021.648026

Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae)
Cited by: 10
Author(s): Chen Shen, Chujie Zhang, Jie Chen, Yanping Guo
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-59016-0

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study
Cited by: 71
Author(s): Zachary M. Burcham, Nicole L. Garneau, Sarah S. Comstock, Robin M. Tucker, Rob Knight, Jessica L. Metcalf
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-56631-4

Helicobacter pylori infection associates with fecal microbiota composition and diversity
Cited by: 41
Author(s): Fabian Frost, Tim Kacprowski, Malte Rühlemann, Corinna Bang, André Franke, Kathrin Zimmermann, Matthias Nauck, Uwe Völker, Henry Völzke, Reiner Biffar, Christian Schulz, Julia Mayerle, Frank Ulrich Weiss, Georg Homuth, Markus M. Lerch
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.67577

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
Cited by: 57
Author(s): Heather E. Machado, Alan O. Bergland, Ryan W. Taylor, Susanne Tilk, Emily L. Behrman, Kelly A. Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Bernard Kim, Iryna Kozeretska, Brian P. Lazzaro, Thomas J. S. Merritt, John E. Pool, Katherine R. O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul S. Schmidt, Dmitri A. Petrov
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-24040-8

Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China
Cited by: 80
Author(s): Baihui Ren, Yuanman Hu, Baodong Chen, Ying Zhang, Jan Thiele, Ronghua Shi, Miao Liu, Rencang Bu
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.20983

A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: over 9 years ago

10.1186/s13099-014-0039-8

Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs
Cited by: 44
Author(s): Husen Zhang, Haifeng Wang, Megan Shepherd, Ke Wen, Guohua Li, Xing-Dong Yang, Jacob Kocher, Ernawati Arifin Giri-Rachman, Allan W. Dickerman, Robert E. Settlage, Lijuan Yuan
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pgen.1007376

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
Cited by: 59
Author(s): Michael B. Burns, Emmanuel Montassier, Juan E. Abrahante, Sambhawa Priya, David Niccum, Alexander Khoruts, Timothy K. Starr, Dan Knights, Ran Blekhman
Software Mentions: 4
Published: about 8 years ago

10.1002/ece3.3042

Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora
Cited by: 9
Author(s): Áki J. Láruson
Software Mentions: 4
Published: about 9 years ago

10.3390/e21101023

Teaching Ordinal Patterns to a Computer: Efficient Encoding Algorithms Based on the Lehmer Code
Cited by: 10
Author(s): Sebastian Berger, Andrii Kravtsiv, Gerhard Schneider, Denis Jordan
Software Mentions: 4
Published: almost 7 years ago

10.3389/fimmu.2020.01192

Behçet's Disease Under Microbiotic Surveillance? A Combined Analysis of Two Cohorts of Behçet's Disease Patients
Cited by: 21
Author(s): Tim B. van der Houwen, Jan A. M. van Laar, Jasper H Kappen, P. Martin van Hagen, Marcel R. de Zoete, Guus H. van Muijlwijk, Roos-Marijn Berbers, Ad C. Fluit, Malbert R. C. Rogers, James Groot, C. Marijn Hazelbag, Clarissa Consolandi, Marco Severgnini, Clelia Peano, Mario Milco D’Elios, Giacomo Emmi, Helen L. Leavis
Software Mentions: 4
Published: about 6 years ago

10.1098/rstb.2017.0382

OpenWorm: overview and recent advances in integrative biological simulation of <i>Caenorhabditis elegans</i>
Cited by: 68
Author(s): Gopal P. Sarma, Chee Wai Lee, Tom Portegys, Vahid Ghayoomie, Travis W Jacobs, Bradly Alicea, Matteo Carandini, Michael Currie, Richard C. Gerkin, Shane Gingell, Padraig Gleeson, Richard Gordon, Ramin Hasani, Giovanni Idili, Sergey Khayrulin, David Lung, Andrey Palyanov, Mark D Watts, Stephen Larson
Software Mentions: 4
Published: almost 8 years ago

10.1002/ece3.5718

Responses of zooplankton body size and community trophic structure to temperature change in a subtropical reservoir
Cited by: 29
Author(s): Xiaofei Gao, Huihuang Chen, Lynn Govaert, Wenping Wang, Jun Yang
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0089456

A Semi-Automated Pipeline for the Segmentation of Rhesus Macaque Hippocampus: Validation across a Wide Age Range
Cited by: 8
Author(s): Michael R. Hunsaker, David G. Amaral
Software Mentions: 4
Published: over 12 years ago

10.1002/ece3.6952

Different landscape effects on the genetic structure of two broadly distributed woody legumes,<i>Acacia salicina</i>and<i>A. stenophylla</i>(Fabaceae)
Cited by: 2
Author(s): Francisco Encinas‐Viso, Christiana McDonald‐Spicer, Nunzio Knerr, Peter H. Thrall, Linda Broadhurst
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.4814

Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments
Cited by: 62
Author(s): Lara Macheriotou, Katja Guilini, Tânia Campinas Bezerra, Bjorn Tytgat, Dinh Tu Nguyen, Thi Van Nguyen, Febe Noppe, Maickel Armenteros, Fehmi Boufahja, Annelien Rigaux, Ann Vanreusel, Sofie Derycke
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.7894

Improving the application of quantitative fatty acid signature analysis in soil food webs: The effects of diet fat content
Cited by: 2
Author(s): Jakob Kühn, Vanessa Henning, Liliane Rueß
Software Mentions: 4
Published: about 5 years ago

10.1016/j.cmet.2020.02.016

Sugar-Induced Obesity and Insulin Resistance Are Uncoupled from Shortened Survival in Drosophila
Cited by: 62
Author(s): Esther van Dam, Lucie A.G. van Leeuwen, Eliano Dos Santos, Joanna L. James, Lena Best, Claudia Lennicke, Alec Vincent, Γεώργιος Μαρίνος, A. Reghan Foley, Marcela Buricova, João Benhur Mokochinski, Holger Kramer, Wolfgang Lieb, Matthias Laudes, André Franke, Christoph Kaleta, Helena M. Cochemé
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.65282

Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake
Cited by: 31
Author(s): Marc A. Schureck, Joseph E. Darling, Alan Merk, Jinfeng Shao, Geervani Daggupati, Prakash Srinivasan, Paul Dominic B. Olinares, Michael P. Rout, Brian T. Chait, Kurt Wollenberg, Sriram Subramaniam, Sanjay A. Desai
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2017.01279

Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture
Cited by: 23
Author(s): Luca Mercenaro, G. Nieddu, Andrea Porceddu, Mario Pezzotti, Salvatore Camiolo
Software Mentions: 4
Published: about 9 years ago

10.1039/d1sc01185e

Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution
Cited by: 12
Author(s): Marcus Wieder, Josh Fass, John D. Chodera
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.7237

Occurrence data uncover patterns of allopatric divergence and interspecies interactions in the evolutionary history of <i>Sceloporus</i> lizards
Cited by: 6
Author(s): Julio A. Rivera, Heather N. Rich, A. Michelle Lawing, Michael S. Rosenberg, Emilı́a P. Martins
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008390

Ten simple rules for writing a paper about scientific software
Cited by: 1
Author(s): Joseph D. Romano, Jason H. Moore
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giaa158

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
Cited by: 4
Author(s): Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning, Rolf Backofen
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.29391

Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites
Cited by: 25
Author(s): Fabien Sindikubwabo, Shibin Ding, Tahir Hussain, Philippe Ortet, Mohamed Barakat, Sebastian Baumgarten, Dominique Cannella, Andrés Palencia, Alexandre Bougdour, Lucid Belmudes, Yohann Couté, Isabelle Tardieux, Cyrille Y. Botté, Artur Scherf, Mohamed-Ali Hakimi
Software Mentions: 4
Published: over 8 years ago

10.1186/s13072-017-0153-1

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state
Cited by: 25
Author(s): Rebekka Mauser, Goran Kungulovski, Corinna Keup, Richard Reinhardt, Albert Jeltsch
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: over 7 years ago