10.3389/fpls.2019.00511

Activity in the Arbuscular Mycorrhizal Hyphosphere Warning Neighbouring Plants
Cited by: 8
Author(s): Carmina Cabral, Bernd Wollenweber, Carla António, Sabine Ravnskov
Software Mentions: 5
Published: about 7 years ago

10.1093/jxb/eraa289

Measuring Rubisco activity: challenges and opportunities of NADH-linked microtiter plate-based and 14C-based assays
Cited by: 11
Author(s): Cristina Rodrigues Gabriel Sales, Anabela Bernardes da Silva, Elizabete Carmo‐Silva
Software Mentions: 5
Published: about 6 years ago

10.1155/2020/6937475

A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma
Cited by: 18
Author(s): Yingkun Xu, Xiunan Li, Yaling Han, Zilong Wang, Chenglin Han, Ningke Ruan, Jianyi Li, Xiao Yu, Qinghua Xia, Guangzhen Wu
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2164-14-850

Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle
Cited by: 62
Author(s): Erin D. Scully, Kelli Hoover, John E. Carlson, Ming Tien, Scott M. Geib
Software Mentions: 5
Published: over 12 years ago

10.1186/1471-2407-10-351

Characterization of the apoptotic response of human leukemia cells to organosulfur compounds
Cited by: 7
Author(s): Wendy Wei-Lynn Wong, Paul C. Boutros, Amanda R. Wasylishen, Kristal D. Guckert, Erin M. O’Brien, Rebecca E. Griffiths, Anna Martirosyan, Christina Bros, Igor Jurišica, Richard Francis Langler, Linda Z. Penn
Software Mentions: 5
Published: about 16 years ago

10.3390/proteomes6030031

Regional Diversity in the Postsynaptic Proteome of the Mouse Brain
Cited by: 37
Author(s): Marcia Roy, Oksana Sorokina, Colin McLean, Silvia Tapia-González, Javier DeFelipe, J. Douglas Armstrong, Seth G. N. Grant
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-017-08892-0

Development and assessment of a lysophospholipid-based deep learning model to discriminate geographical origins of white rice
Cited by: 14
Author(s): Nguyen Phuoc Long, Dong Kyu Lim, Changyeun Mo, Gi‐Young Kim, Sung Won Kwon
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-019-53975-9

Longitudinal study of the bacterial and fungal microbiota in the human sinuses reveals seasonal and annual changes in diversity
Cited by: 34
Author(s): Brett Wagner Mackenzie, Kevin Chang, Melissa Zoing, Ravi Jain, Michael Hoggard, Kristi Biswas, Richard Douglas, Michael W. Taylor
Software Mentions: 5
Published: over 6 years ago

10.1007/s10456-021-09788-4

The endosomal RIN2/Rab5C machinery prevents VEGFR2 degradation to control gene expression and tip cell identity during angiogenesis
Cited by: 20
Author(s): Lanette Kempers, Yuki Wakayama, Ivo van der Bijl, Charita Furumaya, Iris M. De Cuyper, Aldo Jongejan, Marije Kat, Anne-Marieke D. van Stalborch, Antonius L. van Boxtel, Marvin Hubert, Dirk Geerts, Jaap D. van Buul, Dirk de Korte, Wiebke Herzog, Coert Margadant
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-90145-2

An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia
Cited by: 5
Author(s): Anita Kloss‐Brandstätter, Monika Summerer, David Horst, Basil A. Horst, Gertraud Streiter, Julia Raschenberger, Florian Kronenberg, Torpong Sanguansermsri, Jürgen Horst, Hansi Weißensteiner
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0205804

Risk taking of educated nematodes
Cited by: 15
Author(s): Denis S. Willett, Hans T. Alborn, Lukasz L. Stelinski, David I. Shapiro‐Ilan
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0166283

Relationships between egg-recognition and egg-ejection in a grasp-ejector species
Cited by: 34
Author(s): Manuel Soler, Francisco Ruiz‐Raya, Gianluca Roncalli, Juan Diego Ibáñez‐Álamo
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0241345

Predicting dive start performance from kinematic variables at water entry in (sub-)elite swimmers
Cited by: 2
Author(s): Marit P. van Dijk, Peter J. Beek, A. J. “Knoek” van Soest
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-86919-3

Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Cited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms21010145

Gene Copy Number and Post-Transductional Mechanisms Regulate TRAP1 Expression in Human Colorectal Carcinomas
Cited by: 3
Author(s): Michele Pietrafesa, Francesca Maddalena, Luciana Possidente, Valentina Condelli, Pietro Zoppoli, Valeria Li Bergolis, Maria Grazia Rodriquenz, Michele Aieta, Giulia Vita, Franca Esposito, Matteo Landriscina
Software Mentions: 5
Published: over 6 years ago

10.1128/mSphere.00005-17

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions
Cited by: 28
Author(s): Jocelyn M. Choo, Tokuwa Kanno, Nur Masirah M. Zain, Lex E. X. Leong, Guy C. J. Abell, Julie Keeble, Kenneth D. Bruce, A. James Mason, Geraint B. Rogers
Software Mentions: 5
Published: over 9 years ago

10.1186/s13059-015-0604-6

DGEclust: differential expression analysis of clustered count data
Cited by: 14
Author(s): Dimitrios V Vavoulis, Margherita Francescatto, Peter Heutink, Julian Gough
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0210030

Knowing is half the battle: Assessments of both student perception and performance are necessary to successfully evaluate curricular transformation
Cited by: 9
Author(s): Tarren J. Shaw, Shih-Ping Yang, Troy R. Nash, Rachel M. Pigg, Jeffrey M. Grim
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-021-07774-0

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
Cited by: 10
Author(s): Aileen R Ferraro, Abigail J Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0243105

Machine learning-based e-commerce platform repurchase customer prediction model
Cited by: 14
Author(s): Cheng-Ju Liu, Tienshou Huang, Ping-Tsan Ho, Jui-Chan Huang, Ching-Tang Hsieh
Software Mentions: 5
Published: over 5 years ago

10.1186/s12888-015-0685-5

Distinguishing bipolar and major depressive disorders by brain structural morphometry: a pilot study
Cited by: 66
Author(s): Gabriel Pui Cheong Fung, Yi Deng, Qing Zhao, Zhi Li, Miao Qu, Li Ke, Yonghu Zeng, Jin Zhou, Yantao Ma, Xin Yu, Zhiren Wang, David Shum, Raymond C.K. Chan
Software Mentions: 5
Published: over 10 years ago

10.3390/nu13041217

Quality and Quantity of Protein Intake Influence Incidence of Type 2 Diabetes Mellitus in Coronary Heart Disease Patients: From the CORDIOPREV Study
Cited by: 7
Author(s): Silvia de la Cruz‐Ares, Francisco M. Gutiérrez-Mariscal, Juan F. Alcalá‐Díaz, Gracia M. Quintana-Navarro, Alicia Podadera-Herreros, Magdalena P. Cardelo, José D. Torres-Peña, Antonio P. Arenas de Larriva, Pablo Pérez-Martı́nez, Javier Delgado-Lista, Elena M. Yubero‐Serrano, José López‐Miranda
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0247374

Top-down and sideways: Herbivory and cross-ecosystem connectivity shape restoration success at the salt marsh-upland ecotone
Cited by: 8
Author(s): Kerstin Wasson, Karen E. Tanner, Andrea Woofolk, Sean McCain, Justin P. Suraci
Software Mentions: 5
Published: over 5 years ago

10.1038/srep46332

Windscapes and olfactory foraging in a large carnivore
Cited by: 40
Author(s): Ron R. Togunov, Andrew E. Derocher, Nicholas J. Lunn
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-021-07924-4

Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)
Cited by: 10
Author(s): Yan He, Hongyan Yu, Hongling Zhao, Hua Zhu, Qingjing Zhang, Anqi Wang, Yubang Shen, Xiaoyan Xu, Jiale Li
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0094047

Factors Influencing Host Plant Choice and Larval Performance in Bactericera cockerelli
Cited by: 27
Author(s): Sean M. Prager, Isaac L. Esquivel, John T. Trumble
Software Mentions: 5
Published: over 12 years ago

10.3758/s13414-019-01674-y

Goal-directed unequal attention allocation during multiple object tracking
Cited by: 12
Author(s): Emily M. Crowe, Christina J. Howard, Angela Attwood, Christopher Kent
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.64977

Unique integrated stress response sensors regulate cancer cell susceptibility when Hsp70 activity is compromised
Cited by: 11
Author(s): Sara Sannino, Megan E. Yates, Mark E. Schurdak, Steffi Oesterreich, Adrian V. Lee, Peter Wipf, Jeffrey L. Brodsky
Software Mentions: 5
Published: about 5 years ago

10.1002/ece3.5887

Phenotypic plasticity, but not adaptive tracking, underlies seasonal variation in post‐cold hardening freeze tolerance of<i>Drosophila melanogaster</i>
Cited by: 9
Author(s): Helen M. Stone, Priscilla A. Erickson, Alan O. Bergland
Software Mentions: 5
Published: over 6 years ago

10.1098/rsos.190279

Pollen from multiple sunflower cultivars and species reduces a common bumblebee gut pathogen
Cited by: 39
Author(s): George LoCascio, Luis Alejandro Aguirre, Rebecca E. Irwin, Lynn S. Adler
Software Mentions: 5
Published: over 7 years ago

10.1080/21642850.2018.1521283

Network analysis: a brief overview and tutorial
Cited by: 271
Author(s): David Hevey
Software Mentions: 5
Published: over 8 years ago

10.1167/tvst.8.5.4

A Method to Calibrate the Carbon Dioxide (Chemical) Stimuli of Pneumatic Esthesiometer Externally
Cited by: 1
Author(s): Varadharajan Jayakumar, Trefford Simpson
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13643-019-1032-6

Individual participant data (IPD)-level meta-analysis of randomised controlled trials among dark-skinned populations to estimate the dietary requirement for vitamin D
Cited by: 3
Author(s): Kevin D. Cashman, Christian Ritz
Software Mentions: 5
Published: about 7 years ago

10.16910/jemr.13.1.2

Looking (for) patterns: Similarities and differences between infant and adult free scene-viewing patterns
Cited by: 0
Author(s): Daan R. van Renswoude, Maartje E. J. Raijmakers, Ingmar Visser
Software Mentions: 5
Published: over 6 years ago

10.3389/fpsyt.2021.739776

Lifestyle and Symptom Management Needs: A Network Analysis of Family Caregiver Needs of Cancer Patients
Cited by: 1
Author(s): Winson Fu Zun Yang, Yiong Huak Chan, Konstadina Griva, Sangita Kuparasundram, Rathi Mahendran
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-66806-z

CD96, a new immune checkpoint, correlates with immune profile and clinical outcome of glioma
Cited by: 26
Author(s): Fangkun Liu, Jing Huang, Fengjiao He, Xiaodong Ma, Fan Fan, Ming Meng, Zhuo Yang, Jintao Zhang
Software Mentions: 5
Published: about 6 years ago

10.1111/acel.12925

Conservation of physiological dysregulation signatures of aging across primates
Cited by: 24
Author(s): Gabriel Dansereau, Tina W. Wey, Véronique Legault, Marie-Christine Brunet, Joseph W. Kemnitz, Luigi Ferrucci, Alan A. Cohen
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.ppat.1009349

PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity
Cited by: 15
Author(s): Helen Parry, Alexander C. Dowell, Jianmin Zuo, Kriti Verma, Francesca Kinsella, Jusnara Begum, Wayne Croft, Archana Sharma-Oates, Guy Pratt, Paul Moss
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.00973

A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains
Cited by: 15
Author(s): Xiangchen Li, Wenjun Tong, Lina Wang, Siddiq Ur Rahman, Gehong Wei, Shiheng Tao
Software Mentions: 5
Published: about 8 years ago

10.1186/1471-213X-12-33

Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst
Cited by: 82
Author(s): Manabu Ozawa, Miki Sakatani, Jiqiang Yao, Savita Shanker, Fahong Yu, Rui Yamashita, Shokichi Wakabayashi, Kenta Nakai, Kyle B. Dobbs, Mateus José Sudano, William G. Farmerie, Peter J. Hansen
Software Mentions: 5
Published: over 13 years ago

10.1186/s12859-018-2057-x

lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals
Cited by: 111
Author(s): Andrey Ziyatdinov, Miquel Vázquez-Santiago, Héléna Brunel, Ángel Martinez-Perez, Hugues Aschard, José Manuel Nieto Soria
Software Mentions: 5
Published: over 8 years ago

10.3390/ijms20020296

High-Throughput Omics and Statistical Learning Integration for the Discovery and Validation of Novel Diagnostic Signatures in Colorectal Cancer
Cited by: 30
Author(s): Nguyen Phuoc Long, Seongoh Park, Nguyễn Hoàng Anh, Tran Diem Nghi, Sang Jun Yoon, Jeong Hill Park, Jong-Tae Lim, Sung Won Kwon
Software Mentions: 5
Published: over 7 years ago

10.1002/ece3.1373

Outbreeding effects in an inbreeding insect,<i><scp>C</scp>imex lectularius</i>
Cited by: 11
Author(s): Toby Fountain, Roger K. Butlin, Klaus Reinhardt, Oliver Otti
Software Mentions: 5
Published: over 11 years ago

10.3390/insects11100698

Ameliorative Effects of Phytochemical Ingestion on Viral Infection in Honey Bees
Cited by: 9
Author(s): Edward M. Hsieh, May R. Berenbaum, Adam Doležal
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-017-1302-3

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Cited by: 127
Author(s): Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey, James Whelan
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2105-11-221

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
Cited by: 77
Author(s): Alberto Risueño, Celia Fontanillo, Marcel E. Dinger, Javier De Las Rivas
Software Mentions: 5
Published: about 16 years ago

10.1107/S2052252518000519

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
Cited by: 23
Author(s): Michael E. Wall
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pcbi.1009345

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network
Cited by: 11
Author(s): Zhengqiao Zhao, Stephen Woloszynek, Felix Agbavor, Joshua Chang Mell, Bahrad A. Sokhansanj, Gail Rosen
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.63274

Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
Cited by: 68
Author(s): Steven Henikoff, Hatice S Kaya-Okur, Kami Ahmad
Software Mentions: 5
Published: over 5 years ago

10.1107/S0907444911049791

Conventions and workflows for using <i>Situs</i>
Cited by: 157
Author(s): Willy Wriggers
Software Mentions: 5
Published: over 14 years ago

10.1038/s41598-021-88939-5

GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds
Cited by: 6
Author(s): Marawan Ahmed, Horia Jalily Hasani, Subha Kalyaanamoorthy, Khaled Barakat
Software Mentions: 5
Published: about 5 years ago

10.1186/s13017-021-00389-6

Team dynamics in emergency surgery teams: results from a first international survey
Cited by: 18
Author(s): Lorenzo Cobianchi, Francesca Dal Mas, Maurizio Massaro, Paola Fugazzola, Federico Coccolini, Yoram Kluger, Ari Leppäniemi, Ernest E. Moore, Massimo Sartelli, Peter Angelos, Luca Ansaloni
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pmed.1003741

Utility of ctDNA in predicting response to neoadjuvant chemoradiotherapy and prognosis assessment in locally advanced rectal cancer: A prospective cohort study
Cited by: 55
Author(s): Yaqi Wang, Lifeng Yang, Hua Bao, Xiaojun Fan, Xuesen Fan, Juefeng Wan, Lijun Shen, Yun Guan, Hairong Bao, Xue Wu, Xu Yang, Yang Shao, Yueming Sun, Tong Tong, Xinxiang Li, Ye Xu, Sanjun Cai, Ji Zhu, Zhen Zhang
Software Mentions: 5
Published: almost 5 years ago

10.3389/fninf.2014.00076

Limits to high-speed simulations of spiking neural networks using general-purpose computers
Cited by: 50
Author(s): Friedemann Zenke, Wulfram Gerstner
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12859-020-03725-w

Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent
Cited by: 15
Author(s): Jan Klosa, Noah Simon, Pål O. Westermark, Volkmar Liebscher, Dörte Wittenburg
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.707970

C1GALT1, Negatively Regulated by miR-181d-5p, Promotes Tumor Progression via Upregulating RAC1 in Lung Adenocarcinoma
Cited by: 7
Author(s): Dong Xiao, Yongyu Liu, Xinzhou Deng, Jun Shao, Shuangyue Tian, Shuang Chen, Ronald Huang, Ziao Lin, Chunli Chen, Li Shen
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.38795

Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin
Cited by: 20
Author(s): Angela M Phillips, Michael B. Doud, Luna O Gonzalez, Vincent Butty, Yu‐Shan Lin, Jesse D. Bloom, Matthew D. Shoulders
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-018-26131-y

Precipitation and ectoparasitism reduce reproductive success in an arctic-nesting top-predator
Cited by: 15
Author(s): Vincent Lamarre, Pierre Legagneux, Alastair Franke, Nicolas Casajus, Douglas C. Currie, Dominique Berteaux, Joël Bêty
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2019.02075

Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis
Cited by: 14
Author(s): Gi Yoon Shin, Jeffrey K. Schachterle, Divine Yufetar Shyntum, Lucy N. Moleleki, Teresa A. Coutinho, George W. Sundin
Software Mentions: 5
Published: almost 7 years ago

10.1128/AEM.03074-15

Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an <i>In Vivo</i> Competition Assay
Cited by: 13
Author(s): Zhao Jin, Sara C. Di Rienzi, Anders Janzon, Jeff J. Werner, Largus T. Angenent, Jeffrey L. Dangl, Douglas M. Fowler, Ruth E. Ley
Software Mentions: 5
Published: over 10 years ago

10.1038/srep45651

Patterns in the skin microbiota differ in children and teenagers between rural and urban environments
Cited by: 85
Author(s): Jenni Lehtimäki, Antti Karkman, Tiina Laatikainen, Laura Paalanen, Leena von Hertzen, Tari Haahtela, Ilkka Hanski, Lasse Ruokolainen
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.69068

Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology
Cited by: 26
Author(s): Joshua H. Siegle, Peter Ledochowitsch, Xiaoxuan Jia, Daniel Millman, Gabriel Koch Ocker, Shiella Caldejon, Linzy Casal, Andy Cho, Daniel J. Denman, Séverine Durand, Peter A. Groblewski, Gregg Heller, India Kato, Sara Kivikas, Jérôme Lecoq, Chelsea Nayan, Kiet Ngo, Philip R. Nicovich, Kat North, Tamina K Ramirez, Jackie Swapp, Xana Waughman, Ali Williford, Shawn R. Olsen, Christof Koch, Michael A. Buice, Saskia E. J. de Vries
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2018.01035

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean
Cited by: 45
Author(s): Josephine Z. Rapp, Mar Fernández‐Méndez, Christina Bienhold, Antje Boetius
Software Mentions: 5
Published: about 8 years ago

10.1093/database/bax080

Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse
Cited by: 0
Author(s): Jonas Hausen, Björn Scholz-Starke, Ulrich Burkhardt, Stephan Lesch, Sebastian Rick, David J. Russell, Martina Roß-Nickoll, Andreas Schäffer
Software Mentions: 5
Published: over 9 years ago

10.1038/sdata.2015.55

A multi-source dataset of urban life in the city of Milan and the Province of Trentino
Cited by: 203
Author(s): Gianni Barlacchi, Marco De Nadai, R. Larcher, Antonio Casella, Cristiana Chitic, Giovanni Luca Torrisi, Fabrizio Antonelli, Alessandro Vespignani, Alex Pentland, Bruno Lepri
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0183057

Data-driven coarse graining of large biomolecular structures
Cited by: 11
Author(s): Yi‐Ling Chen, Michael Habeck
Software Mentions: 5
Published: almost 9 years ago

10.1099/mgen.0.000500

Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance
Cited by: 7
Author(s): Kara K. Tsang, Finlay Maguire, Haley L. Zubyk, Sommer Chou, Arman Edalatmand, Gerard D. Wright, Robert G. Beiko, Andrew G. McArthur
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2288-13-65

An R package for analyzing and modeling ranking data
Cited by: 26
Author(s): Paul H. Lee, Philip L. H. Yu
Software Mentions: 5
Published: about 13 years ago

10.1128/mSystems.00913-20

Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms
Cited by: 23
Author(s): Nicole Pearcy, Yue Hu, Michelle Baker, Alexandre Maciel-Guerra, Ning Xue, Wei Wang, Jasmeet Kaler, Zong–Gen Peng, Fengqin Li, Tania Dottorini
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0235218

Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities
Cited by: 17
Author(s): Yan Li, Meimei Wang, Qiufeng Li, Yanxia Gao, Qian Li, Jianguo Li, Yong Cao
Software Mentions: 5
Published: about 6 years ago

10.1093/gigascience/giaa046

Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples
Cited by: 49
Author(s): Rafael R. C. Cuadrat, Maria Sorokina, Bruno de Bezerril Andrade, Tobias Goris, Alberto M. R. Dávila
Software Mentions: 5
Published: about 6 years ago

10.3390/v13081647

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner
Cited by: 25
Author(s): Devon A. Gregory, Chris G. Wieberg, Jeff Wenzel, Chung‐Ho Lin, Marc C. Johnson
Software Mentions: 5
Published: almost 5 years ago

10.1016/j.clon.2019.08.008

Time to Surgery Following Short-Course Radiotherapy in Rectal Cancer and its Impact on Postoperative Outcomes. A Population-Based Study Across the English National Health Service, 2009–2014
Cited by: 7
Author(s): Bethany Levick, Alexandra Gilbert, Katie Spencer, Amy Downing, John Taylor, P. J. Finan, David Sebag‐Montefiore, Eva Morris
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-019-1860-7

CRUP: a comprehensive framework to predict condition-specific regulatory units
Cited by: 26
Author(s): Anna Ramisch, Verena Heinrich, Laura V. Glaser, Alisa Fuchs, Xinyi Yang, Philipp Benner, Robert Schöpflin, Na Li, Sarah Kinkley, Anja Römer-Hillmann, John Longinotto, Steffen Heyne, Beate Czepukojc, Sonja M. Kessler, Alexandra K. Kiemer, Cristina Cadenas, Laura Arrigoni, Nina Gasparoni, Thomas Manke, Thomas Pap, J. Andrew Pospisilik, Jan G. Hengstler, Jörn Walter, Sebastiaan H. Meijsing, Ho‐Ryun Chung, Martin Vingron
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2018.00671

UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes
Cited by: 20
Author(s): Santiago Radío, Rafael Sebastián Fort, Beatríz Garat, José Sotelo‐Silveira, Pablo Smircich
Software Mentions: 5
Published: over 7 years ago

10.1038/s41597-019-0341-x

The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies
Cited by: 50
Author(s): Christoph Rzymski, Tiago Tresoldi, Simon J. Greenhill, Mei-Shin Wu, Nathanael E. Schweikhard, Maria Koptjevskaja‐Tamm, Volker Gast, Timotheus Adrianus Bodt, Abbie Hantgan, Gereon A. Kaiping, S. Chang, Yunfan Lai, Natalia Morozova, Heini Arjava, Nataliia Hübler, Ezequiel Koile, Steve Pepper, Mariann Proos, Briana Van Epps, Ingrid Blanco, Carolin Hundt, Sergei Monakhov, Kristina Pianykh, Sallona Ramesh, Russell D. Gray, Robert Forkel, Johann‐Mattis List
Software Mentions: 5
Published: over 6 years ago

10.12688/f1000research.17456.1

pdb-tools: a swiss army knife for molecular structures
Cited by: 81
Author(s): João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
Software Mentions: 5
Published: over 7 years ago

10.1002/1878-0261.12706

Ribonucleotide reductase small subunit M2 is a master driver of aggressive prostate cancer
Cited by: 17
Author(s): Ying Z. Mazzu, Joshua Armenia, Subhiksha Nandakumar, Goutam Chakraborty, Yuki Yoshikawa, Lina Jehane, Gwo‐Shu Mary Lee, Mohammad Atiq, Nabeela Khan, Nikolaus Schultz, Philip W. Kantoff
Software Mentions: 5
Published: about 6 years ago

10.1186/s12859-017-1934-z

ImageJ2: ImageJ for the next generation of scientific image data
Cited by: 4,051
Author(s): Curtis Rueden, Johannes Schindelin, Mark Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri
Software Mentions: 5
Published: over 8 years ago

10.1093/gbe/evaa187

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)
Cited by: 29
Author(s): Bonnie A. Fraser, James R. Whiting, Josephine R. Paris, Cameron J. Weadick, Paul J. Parsons, Deborah Charlesworth, Roberta Bergero, Felix Bemm, Maria Hoffmann, Verena A. Kottler, Chang Liu, Christine Dreyer, Detlef Weigel
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41421-020-00236-z

Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss
Cited by: 74
Author(s): Chuang Guo, Pengfei Cai, Lina Jin, Qing Sha, Qiaoni Yu, Wen Zhang, Chen Jiang, Qian Liu, Dandan Zong, Kun Li, Jingwen Fang, Fangting Lu, Yanshi Wang, Daojing Li, Jun Lin, Lü Li, Zhutian Zeng, Xianhong Tong, Haiming Wei, Kun Qu
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.50601

Cell-type-specific control of basolateral amygdala neuronal circuits via entorhinal cortex-driven feedforward inhibition
Cited by: 15
Author(s): Eartha Mae Guthman, Joshua D. Garcia, Ming Ma, Philip Chu, Serapio M. Baca, Katharine R. Smith, Diego Restrepo, Molly M. Huntsman
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0143128

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize
Cited by: 30
Author(s): Liu Ya, Miaoyi Zhou, Zhaoxu Gao, Wen Ren, Fan Yang, Hang He, Jiuran Zhao
Software Mentions: 5
Published: over 10 years ago

10.1186/s12862-017-0939-6

Fitness costs of symbiont switching using entomopathogenic nematodes as a model
Cited by: 23
Author(s): Jeffery S. McMullen, Brittany F. Peterson, Steven Forst, Heidi Goodrich-Blair, S. Patricia Stock
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pcbi.1008806

VolPy: Automated and scalable analysis pipelines for voltage imaging datasets
Cited by: 17
Author(s): Changjia Cai, Johannes Friedrich, Amrita Singh, M. Hossein Eybposh, Eftychios A. Pnevmatikakis, Kaspar Podgorski, Andrea Giovannucci
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.55132

Conformational distributions of isolated myosin motor domains encode their mechanochemical properties
Cited by: 26
Author(s): Justin R. Porter, Artur Meller, Maxwell I. Zimmerman, Michael J. Greenberg, Gregory R. Bowman
Software Mentions: 5
Published: about 6 years ago

10.3390/cells9102283

Gut Microbiome Changes in Patients with Active Left-Sided Ulcerative Colitis after Fecal Microbiome Transplantation and Topical 5-aminosalicylic Acid Therapy
Cited by: 34
Author(s): Dagmar Schierová, Jan Březina, Jakub Mrázek, K. Fliegerová, Simona Kvasnová, Lukáš Bajer, Pavel Drastich
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.37184

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
Cited by: 68
Author(s): Ji Li, Peter S. Choi, Christine L. Chaffer, Katherine Labella, Justin Hwang, Andrew O. Giacomelli, Jong Wook Kim, Nina Ilić, John G. Doench, Seav Huong Ly, Chao Dai, Kimberly R. Hagel, Andrew L. Hong, Ole Gjoerup, Shom Goel, Jennifer Y Ge, David E. Root, Jean J. Zhao, Angela N. Brooks, Robert A. Weinberg, William C. Hahn
Software Mentions: 5
Published: almost 8 years ago

10.3758/s13428-017-0907-5

PyMICE: APython library for analysis of IntelliCage data
Cited by: 5
Author(s): Jakub M. Dzik, Alicja Puścian, Zofia Mijakowska, Kasia Radwańska, Szymon Łȩski
Software Mentions: 5
Published: about 9 years ago

10.1186/s42523-020-00038-4

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution
Cited by: 23
Author(s): Yuliaxis Ramayo-Caldas, Francesc X. Prenafeta-Boldú, Laura M. Zingaretti, Olga González‐Rodríguez, Antoni Dalmau, Raquel Quintanilla, María Ballester
Software Mentions: 5
Published: about 6 years ago

10.1186/s13321-017-0232-0

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set
Cited by: 207
Author(s): Eelke B. Lenselink, Niels ten Dijke, Brandon J. Bongers, George Papadatos, Herman van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, Gerard J. P. van Westen
Software Mentions: 5
Published: almost 9 years ago

10.1534/genetics.120.303038

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean
Cited by: 22
Author(s): Alice MacQueen, Jeffrey W. White, Rian Lee, Juan M. Osorno, Jeremy Schmutz, Phillip N. Miklas, James R. Myers, Phillip E. McClean, Thomas E. Juenger
Software Mentions: 5
Published: about 6 years ago

10.1016/j.celrep.2018.04.004

mRNA Cap Methyltransferase, RNMT-RAM, Promotes RNA Pol II-Dependent Transcription
Cited by: 32
Author(s): Dhaval Varshney, Olivia Lombardi, Gabriele Schweikert, Sianadh Dunn, Olga Suska, Victoria H. Cowling
Software Mentions: 5
Published: about 8 years ago

10.3389/fendo.2021.697437

Quotient of Waist Circumference and Body Mass Index: A Valuable Indicator for the High-Risk Phenotype of Obesity
Cited by: 9
Author(s): Xiao-cong Liu, Yu Huang, Kenneth Lo, Yu-Qing Huang, Jiyan Chen, Yingqing Feng
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2013.00252

Inferring HIV Escape Rates from Multi-Locus Genotype Data
Cited by: 33
Author(s): Taylor A. Kessinger, Alan S. Perelson, Richard A. Neher
Software Mentions: 5
Published: over 13 years ago

10.1021/acs.chemrev.0c01266

Performance-Based Screening of Porous Materials for Carbon Capture
Cited by: 99
Author(s): Amir Hajiahmadi Farmahini, Shreenath Krishnamurthy, Daniel Friedrich, Stefano Brandani, Lev Sarkisov
Software Mentions: 5
Published: almost 5 years ago

10.3390/s20236712

PADL: A Modeling and Deployment Language for Advanced Analytical Services
Cited by: 6
Author(s): Josu Díaz-de-Arcaya, Raúl Miñón, Ana I. Torre-Bastida, Javier Del Ser, Aitor Almeida
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2021.04.039

Microbial exposure during early human development primes fetal immune cells
Cited by: 124
Author(s): A. N. Mishra, Ghee Chuan Lai, Jing Yao Leong, Thet Tun Aung, Noam Shental, Aviva Rotter-Maskowitz, Edwin Shepherdson, Gurmit Singh Naranjan Singh, Rhea Pai, Adhika Shanti, Richard L. Wong, Andrea Lee, Costerwell Khyriem, Charles Antoine Dutertre, Svetoslav Chakarov, Kandhadayar G. Srinivasan, Nurhidaya Binte Shadan, Xiao Meng Zhang, Shabnam Khalilnezhad, Fabien Cottier, Alrina Shin Min Tan, Gillian Low, Phyllis Chen, Yiping Fan, Pei Xiang Hor, Avery Khoo May Lee, Mahesh Choolani, David Vermijlen, Ankur Sharma, Garold Fuks, Ravid Straussman, Norman Pavelka, Benoît Malleret, Naomi McGovern, Salvatore Albani, Jerry Kok Yen Chan, Florent Ginhoux
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj.11230

Ectomycorrhizal fungal communities associated with <i>Larix gemelinii</i> Rupr. in the Great Khingan Mountains, China
Cited by: 2
Author(s): Yong-Long Wang, Ye Zhao, Ying Xu, MA Jian-jun, Busayo Joshua Babalola, Yida Fan
Software Mentions: 5
Published: about 5 years ago

10.14814/phy2.14423

Cardiac surgery does not lead to loss of oscillatory components in circulatory signals
Cited by: 2
Author(s): Kathrine Knai, Petter Aadahl, Nils Kristian Skjærvold
Software Mentions: 5
Published: about 6 years ago