10.1186/s12915-020-00874-5

Automated identification of the mouse brain’s spatial compartments from in situ sequencing data
Cited by: 16
Author(s): Gabriele Partel, Markus M. Hilscher, Milli Giorgia, Leslie Solorzano, Anna H. Klemm, Mats Nilsson, Carolina Wählby
Software Mentions: 4
Published: almost 6 years ago

10.1186/1476-072X-9-14

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping
Cited by: 46
Author(s): Maged N. Kamel Boulos, Jeffrey Warren, Jianya Gong, Peng Yue
Software Mentions: 4
Published: over 16 years ago

10.1186/s12939-020-01371-5

Exploring country-wide equitable government health care facility access in Uganda
Cited by: 21
Author(s): Nicholas Dowhaniuk
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.3000153

Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm
Cited by: 17
Author(s): Alessandro Magli, June Baik, Lauren J. Mills, Il-Youp Kwak, Bridget S. Dillon, Ricardo Mondragón-González, David Stafford, Scott Swanson, Ron Stewart, James A. Thomson, Daniel J. Garry, Brian David Dynlacht, Rita C.R. Perlingeiro
Software Mentions: 4
Published: over 7 years ago

10.1186/s40168-021-01145-3

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling
Cited by: 19
Author(s): Hwee Sze Tee, David W. Waite, Gavin Lear, Kim M. Handley
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.62438

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
Cited by: 52
Author(s): Philip P. Adams, Gabriele Baniulyte, Caroline Esnault, Kavya Chegireddy, Navjot Singh, Molly Monge, Ryan Dale, Gisela Storz, Joseph T. Wade
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008358

Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior
Cited by: 34
Author(s): R. Zuzanna Misiewicz, Stella Iurato, Natalia Kulesskaya, Laura Salminen, Luís Filipe Rodrigues, Giuseppina Maccarrone, Jade Martins, Darina Czamara, Mikaela Laine, Ewa Sokołowska, Kalevi Trontti, Christiane Rewerts, Božidar Novak, Naama Volk, Dong Ik Park, Eija Jokitalo, Lars Paulín, Petri Auvinen, Vootele Võikar, Alon Chen, Angelika Erhardt, Christoph W. Turck, Iiris Hovatta
Software Mentions: 4
Published: almost 7 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

10.1371/journal.pone.0048375

NetView: A High-Definition Network-Visualization Approach to Detect Fine-Scale Population Structures from Genome-Wide Patterns of Variation
Cited by: 99
Author(s): Markus Neuditschko, Mehar S. Khatkar, Herman W. Raadsma
Software Mentions: 4
Published: almost 14 years ago

10.1038/s42003-021-02112-2

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
Cited by: 82
Author(s): Silvia G. Acinas, Pablo Sánchez, Guillem Salazar, Francisco M. Cornejo‐Castillo, Marta Sebastián, Ramiro Logares, Marta Royo-Llonch, Lucas Paoli, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima‐Mendez, Simon Roux, José M. González, Jesús M. Arrieta, Intikhab Álam, Allan Kamau, Chris Bowler, Jeroen Raes, Stéphane Pesant, Peer Bork, Susana Agustı́, Takashi Gojobori, Dolors Vaqué, Matthew B. Sullivan, Carlos Pedrós‐Alió, Ramón Massana, Carlos M. Duarte, Josep M. Gasol
Software Mentions: 4
Published: about 5 years ago

10.1093/gigascience/giz029

An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
Cited by: 34
Author(s): Jan Axtner, Alex Crampton‐Platt, Lisa Hörig, Azlan Mohamed, Charles C.Y. Xu, Douglas W. Yu, Andreas Wilting
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.00873

Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability
Cited by: 7
Author(s): Wenjing Liu, Emily B. Graham, Linghao Zhong, Jianwei Zhang, Shijie Li, Xiangui Lin, Youzhi Feng
Software Mentions: 4
Published: about 6 years ago

10.3390/ani10101764

The Effect of Coconut Oil Addition to Feed of Pigs on Rectal Microbial Diversity and Bacterial Abundance
Cited by: 12
Author(s): Michal Rolinec, Juraj Medo, Michal Gábor, Martina Miluchová, D. Bíro, Milan Šimko, Miroslav Juráček, Ondrej Hanušovský, Zuzana Schubertová, Branislav Gálik
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-8-456

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
Cited by: 33
Author(s): J. Christopher Bare, Paul Shannon, Amy K. Schmid, Nitin S. Baliga
Software Mentions: 4
Published: over 18 years ago

10.1371/journal.pone.0155461

SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data
Cited by: 69
Author(s): José Manuel Abuín, Juan C. Pichel, Tomás F. Pena, Jorge Amigo
Software Mentions: 4
Published: about 10 years ago

10.1128/mBio.01408-18

Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses
Cited by: 23
Author(s): Min Zhao, Kefang Liu, Jiejian Luo, Shuguang Tan, Chuansong Quan, Shuijun Zhang, Yan Chai, Jianxun Qi, Yan Li, Yang Bi, Haixia Xiao, Gary Wong, Jianfang Zhou, Taijiao Jiang, Wenjun Liu, Hongjie Yu, Jinghua Yan, Yingxia Liu, Yuelong Shu, Guizhen Wu, Aiping Wu, George F. Gao, William J. Liu
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.4705

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
Cited by: 149
Author(s): Owen S. Wangensteen, Creu Palacín, Magdalena Guardiola, Xavier Turon
Software Mentions: 4
Published: over 8 years ago

10.18632/oncotarget.9535

Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer
Cited by: 35
Author(s): Jingwen Zhao, Yu Zhao, Liguo Wang, Jun Zhang, Jeffrey Karnes, Manish Kohli, Guixia Wang, Haojie Huang
Software Mentions: 4
Published: about 10 years ago

10.1107/S139900471400087X

Anomalies in the refinement of isoleucine
Cited by: 3
Author(s): Karen R. M. Berntsen, Gert Vriend
Software Mentions: 4
Published: over 12 years ago

10.3390/s20113166

A Distributed Stream Processing Middleware Framework for Real-Time Analysis of Heterogeneous Data on Big Data Platform: Case of Environmental Monitoring
Cited by: 15
Author(s): Adeyinka K. Akanbi, Muthoni Masinde
Software Mentions: 4
Published: about 6 years ago

10.1186/s12862-019-1432-1

The multifactorial nature of beak and skull shape evolution in parrots and cockatoos (Psittaciformes)
Cited by: 35
Author(s): Jen A. Bright, Jesús Marugán‐Lobón, Emily J. Rayfield, Samuel N. Cobb
Software Mentions: 4
Published: about 7 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

10.1016/j.celrep.2013.08.012

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency
Cited by: 95
Author(s): George E. Gentsch, Nick Owens, Stephen R. Martin, Paul Piccinelli, Tiago Faial, Matthew Trotter, Michael J. Gilchrist, James C. Smith
Software Mentions: 4
Published: almost 13 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/srep13364

Chimeric peptide constructs comprising linear B-cell epitopes: application to the serodiagnosis of infectious diseases
Cited by: 26
Author(s): Yao Lu, Zhong Li, Huan Teng, Hongke Xu, Songnan Qi, Jianan He, Dayong Gu, Qijun Chen, Hongwei Ma
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-019-5605-5

Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens
Cited by: 20
Author(s): Andrei A. Kudinov, Natalia V. Dementieva, О.В. Митрофанова, Olga I. Stanishevskaya, Е.С. Федорова, Tatiana A. Larkina, Arina I Mishina, Kirill Plemyashov, Darren K. Griffin, Michael N Romanov
Software Mentions: 4
Published: over 7 years ago

10.1002/1878-0261.12364

A drug‐repositioning screen for primary pancreatic ductal adenocarcinoma cells identifies 6‐thioguanine as an effective therapeutic agent for TPMT‐low cancer cells
Cited by: 15
Author(s): Inki Kim, Yong-Sung Choi, Jae Yen Song, Eun A Choi, Sojung Park, Eun Ji Lee, Je-Keun Rhee, Song Cheol Kim, Suhwan Chang
Software Mentions: 4
Published: almost 8 years ago

10.1107/S2059798320015879

<i>CERES</i>: a cryo-EM re-refinement system for continuous improvement of deposited models
Cited by: 11
Author(s): Dorothée Liebschner, Pavel V. Afonine, Nigel W. Moriarty, Billy K. Poon, Vincent B. Chen, Paul D. Adams
Software Mentions: 4
Published: over 5 years ago

10.1186/s12974-021-02206-y

Acute pre-operative ibuprofen improves cognition in a rat model for postoperative cognitive dysfunction
Cited by: 14
Author(s): Klaske Oberman, Iris B. Hovens, Jacco J. de Haan, Joana Falcao-Salles, Barbara L. van Leeuwen, Regien G. Schoemaker
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.10947

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
Cited by: 34
Author(s): James A. Fellows Yates, Thiseas Christos Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime Garcia, Judith Neukamm, Alexander Peltzer
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.19406

Modeling susceptibility to drug-induced long QT with a panel of subject-specific induced pluripotent stem cells
Cited by: 79
Author(s): Francesca Stillitano, Jens Hansen, Chi-Wing Kong, Ioannis Karakikes, Christian Funck‐Brentano, Lin Geng, Stuart A. Scott, Stephan Reynier, Wu Ma, Yannick Valogne, Carole Desseaux, Joe‐Elie Salem, Dorota Jeziorowska, Noël Zahr, Ronald Li, Ravi Iyengar, Roger J. Hajjar, Jean‐Sébastien Hulot
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-020-67666-3

Finding hotspots: development of an adaptive spatial sampling approach
Cited by: 18
Author(s): Ricardo Andrade‐Pacheco, Francois Rerolle, Jean Frantz Lemoine, Leda Hernandez, Aboulaye Meïté, Lazarus Juziwelo, Aurélien F. Bibaut, Mark J. van der Laan, Benjamin F. Arnold, Hugh J. W. Sturrock
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2021.628437

Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System
Cited by: 8
Author(s): Darren Heenan-Daly, Simone Coughlan, Eileen Dillane, Barbara Doyle Prestwich
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2018.00569

Stair-Step Pattern of Soil Bacterial Diversity Mainly Driven by pH and Vegetation Types Along the Elevational Gradients of Gongga Mountain, China
Cited by: 70
Author(s): Jiabao Li, Zehao Shen, Chaonan Li, Yongping Kou, Yansu Wang, Bo Tu, Shiheng Zhang, Xiangzhen Li
Software Mentions: 4
Published: over 8 years ago

10.1080/21505594.2021.1948252

Suppressed inflammation in obese children induced by a high-fiber diet is associated with the attenuation of gut microbial virulence factor genes
Cited by: 5
Author(s): Hui Li, Guojun Wu, Liping Zhao, Menghui Zhang
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-017-02110-7

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: about 9 years ago

10.3389/fcell.2021.649168

Pan-Cancer Genome-Wide DNA Methylation Analyses Revealed That Hypermethylation Influences 3D Architecture and Gene Expression Dysregulation in HOXA Locus During Carcinogenesis of Cancers
Cited by: 3
Author(s): Gang Liu, Zhenhao Liu, Xiaomeng Sun, Xiaoqiong Xia, Yunhe Liu, Lei Liu
Software Mentions: 4
Published: over 5 years ago

10.12688/wellcomeopenres.15058.1

The Virtual Electrode Recording Tool for EXtracellular Potentials (VERTEX) Version 2.0: Modelling in vitro electrical stimulation of brain tissue
Cited by: 1
Author(s): Christopher Thornton, Frances Hutchings, Marcus Kaiser
Software Mentions: 4
Published: over 7 years ago

10.1038/sdata.2017.127

Machine-learned and codified synthesis parameters of oxide materials
Cited by: 118
Author(s): Edward Kim, Kevin Huang, Alex Tomala, Sara Matthews, Emma Strubell, Adam Saunders, Andrew McCallum, Elsa Olivetti
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.59780

On the objectivity, reliability, and validity of deep learning enabled bioimage analyses
Cited by: 25
Author(s): Dennis Segebarth, Matthias Griebel, Nikolai Stein, Cora R. von Collenberg, Corinna Martin, Dominik Fiedler, Lucas B. Comeras, Anupam Sah, Victoria Schoeffler, Teresa M. Lüffe, Alexander Dürr, Rohini Gupta, Manju Sasi, Christina Lillesaar, Maren D. Lange, Ramon Tasan, Nicolas Singewald, Hans‐Christian Pape, Christoph M. Flath, Robert Blum
Software Mentions: 4
Published: almost 6 years ago

10.1107/S1600576717016600

CAPOW: a standalone program for the calculation of optimal weighting parameters for least-squares crystallographic refinements
Cited by: 0
Author(s): Natalie T. Johnson, Holger Ott, Michael R. Probert
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.05224

Social networks predict gut microbiome composition in wild baboons
Cited by: 384
Author(s): Jenny Tung, Luis B. Barreiro, Michael B. Burns, Jean Grenier, Joshua Lynch, Laura Grieneisen, Jeanne Altmann, Susan C. Alberts, Ran Blekhman, Elizabeth A. Archie
Software Mentions: 4
Published: over 11 years ago

10.1038/srep20369

Multidisciplinary investigation links backward-speech trait and working memory through genetic mutation
Cited by: 5
Author(s): Stefan Prekovic, Dušica Filipović Đurđević, Gábor Csifcsák, Olivera Šveljo, Oliver Stojković, Milica M. Janković, Katarina Koprivšek, Laura Covill, Miloš Lučić, Thomas Van den Broeck, Christine Helsen, Fabiola Ceroni, Frank Claessens, Dianne F. Newbury
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0216366

Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia
Cited by: 11
Author(s): Daniel Fernandes, Kendra Sirak, Olivia Cheronet, Rachel Howcroft, Mislav Čavka, Dženi Los, Josip Burmaz, Ron Pinhasi, Mario Novak
Software Mentions: 4
Published: almost 7 years ago

10.3389/fninf.2014.00006

Equation-oriented specification of neural models for simulations
Cited by: 120
Author(s): Marcel Stimberg, Dan F. M. Goodman, Victor Benichoux, Romain Brette
Software Mentions: 4
Published: over 12 years ago

10.1093/database/baz083

Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals
Cited by: 19
Author(s): Kristine K. Dennis, Karan Uppal, Ken H. Liu, Chunyu Ma, Bill Liang, Young‐Mi Go, Dean P. Jones
Software Mentions: 4
Published: over 7 years ago

10.1093/database/baw063

PGD: a pangolin genome hub for the research community
Cited by: 4
Author(s): Tze King Tan, Ka Yun Tan, Riitta Hari, Aini Mohamed Yusoff, George T.F. Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mikhail Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O’Brien, Siew Woh Choo
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.56969

Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
Cited by: 22
Author(s): Arpan C. Ghosh, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yanhui Hu, Víctor Barrera, Shannan Ho Sui, Norbert Perrimon
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.120.401160

Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment
Cited by: 31
Author(s): Yuheng Du, Qizhao Huang, Cédric Arisdakessian, Lana X. Garmire
Software Mentions: 4
Published: over 6 years ago

10.1186/s12941-020-00408-5

Dysbiosis of urine microbiota in obstructive urinary retention patients revealed by next-generation sequencing
Cited by: 4
Author(s): Shan Jiang, Saisai Lu, Xiaomin Chen, Fengxia Li, Ce Zhu, Yuanyuan Zheng, Xiaobing Wang, Shihao Xu
Software Mentions: 4
Published: over 5 years ago

10.1186/1745-6150-3-24

In silico regulatory analysis for exploring human disease progression
Cited by: 8
Author(s): Dustin T. Holloway, Mark A. Kon, Charles DeLisi
Software Mentions: 4
Published: about 18 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.pone.0216453

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function
Cited by: 12
Author(s): Claire Duvallet, Kara Larson, Scott B. Snapper, Sonia Iosim, Ann Lee, Katherine Freer, Kara May, Eric J. Alm, Rachel Rosen
Software Mentions: 4
Published: about 7 years ago

10.1007/s00294-020-01096-6

Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality
Cited by: 11
Author(s): Anton Levitan, Andrew N. Gale, Emma Dallon, Darby W. Kozan, Kyle W. Cunningham, Roded Sharan, Judith Berman
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.01953

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe
Cited by: 106
Author(s): Leho Tedersoo, Sten Anslan, Mohammad Bahram, Rein Drenkhan, Karin Pritsch, Franz Buegger, Allar Padari, Niloufar Hagh‐Doust, Vladimir Mikryukov, Daniyal Gohar, Rasekh Amiri, Indrek Hiiesalu, Reimo Lutter, Raul Rosenvald, Elisabeth Rähn, Kalev Adamson, Tiia Drenkhan, Hardi Tullus, Katrin Jürimaa, Ivar Sibul, Eveli Otsing, Sergei Põlme, Marek Metslaid, Kaire Loit, Ahto Agan, Rasmus Puusepp, Inge Varik, Urmas Kõljalg, Kessy Abarenkov
Software Mentions: 4
Published: almost 6 years ago

10.3389/fcell.2021.711253

TLR5 Supports Development of Placental Labyrinthine Zone in Mice
Cited by: 1
Author(s): Jensen H.C. Yiu, Samson Wing Ming Cheung, Jieling Cai, Kam-Suen Chan, Jing Chen, Lai Yee Cheong, Hau-Tak Chau, Aimin Xu, Raymond Li, Connie W. Woo
Software Mentions: 4
Published: about 5 years ago

10.1186/1746-1596-8-34

CognitionMaster: an object-based image analysis framework
Cited by: 41
Author(s): Stephan Wienert, Daniel Heim, Manato Kotani, Bjoern Lindequist, Albrecht Stenzinger, Masaru Ishii, Peter Hufnagl, Michael Beil, Manfred Dietel, Carsten Denkert, Frederick Klauschen
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-017-00650-6

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration
Cited by: 34
Author(s): Deepak Kumaresan, Adam T. Cross, Benjamin Moreira‐Grez, Khalil Kariman, Paul Nevill, Jason C. Stevens, Richard J. N. Allcock, Anthony G. O'Donnell, Kingsley W. Dixon, Andrew S. Whiteley
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms19092500

Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites
Cited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: almost 8 years ago

10.1111/mec.15401

Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent
Cited by: 34
Author(s): Anna Tigano, Jocelyn P. Colella, Matthew D. MacManes
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

10.3389/fcimb.2021.663068

Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis
Cited by: 7
Author(s): Jiung Wen Chen, Jer Horng Wu, Wei Fan Chiang, Yuh Ling Chen, Wei Wu, Li-Wha Wu
Software Mentions: 4
Published: almost 5 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

10.1111/mec.15635

On the way to specificity ‐ Microbiome reflects sponge genetic cluster primarily in highly structured populations
Cited by: 17
Author(s): Cristina Díez‐Vives, Sergi Taboada, Carlos Leiva, Kathrin Busch, Ute Hentschel, Ana Riesgo
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpsyt.2020.00839

Study Protocol: The Coaching Alternative Parenting Strategies (CAPS) Study of Parent-Child Interaction Therapy in Child Welfare Families
Cited by: 5
Author(s): Akhila Nekkanti, Rose Jeffries, Carolyn M Scholtes, Lisa Shimomaeda, Kathleen A. J. DeBow, Jessica Wells, Emma R. Lyons, Ryan J. Giuliano, Felicia J. Gutierrez, Kyndl Woodlee, Beverly W. Funderburk, Elizabeth A. Skowron
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12911-019-0750-y

A visual interactive analytic tool for filtering and summarizing large health data sets coded with hierarchical terminologies (VIADS)
Cited by: 8
Author(s): Xia Jing, Matthew Emerson, David Masters, Matthew L. Brooks, Jacob Buskirk, Nasseef Abukamail, Chang Liu, James J. Cimino, Jay H. Shubrook, Sonsoles de Lacalle, Yuchun Zhou, Vimla L. Patel
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0141225

A catalogue of novel bovine long noncoding RNA across 18 tissues
Cited by: 76
Author(s): Lambros T. Koufariotis, Yi‐Ping Phoebe Chen, Amanda J. Chamberlain, Christy Vander Jagt, Ben J. Hayes
Software Mentions: 4
Published: almost 11 years ago

10.7554/eLife.19760

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation
Cited by: 551
Author(s): Max A. Horlbeck, Luke A. Gilbert, Jacqueline E. Villalta, Brittany Susan Adamson, Ryan A. Pak, Yu‐Wen Chen, Alexander P. Fields, Chong Yon Park, Jacob E. Corn, Martin Kampmann, Jonathan S. Weissman
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0232609

The two types of society: Computationally revealing recurrent social formations and their evolutionary trajectories
Cited by: 3
Author(s): Lux Miranda, Jacob Freeman
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pntd.0007919

Polymorphism analyses and protein modelling inform on functional specialization of Piwi clade genes in the arboviral vector Aedes albopictus
Cited by: 16
Author(s): Michele Marconcini, Luis Miguel Hernández, Giuseppe Iovino, Vincent Houé, Federica Valerio, Umberto Palatini, Elisa Pischedda, Jacob E. Crawford, Bradley J. White, Teresa Lin, Rebeca Carballar-Lejarazú, Lino Ometto, Federico Forneris, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0187150

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma
Cited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2105-15-76

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
Cited by: 185
Author(s): Simon Roux, Jérémy Tournayre, Antoine Mahul, Didier Debroas, François Enault
Software Mentions: 4
Published: over 12 years ago

10.1002/dta.2895

Rapid and robust on‐scene detection of cocaine in street samples using a handheld near‐infrared spectrometer and machine learning algorithms
Cited by: 30
Author(s): Ruben F. Kranenburg, Joshka Verduin, Yannick Weesepoel, Martin Alewijn, Marcel Heerschop, G. C. M. Koomen, Peter H. J. Keizers, Frank Bakker, Fionn Wallace, Annette van Esch, Annemieke Hulsbergen, Arian C. van Asten
Software Mentions: 4
Published: about 6 years ago

10.1111/pbi.12835

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels
Cited by: 27
Author(s): M. Michelle Malmberg, Luke W. Pembleton, Rebecca C. Baillie, Michelle C. Drayton, Shimna Sudheesh, Sukhjiwan Kaur, Hiroshi Shinozuka, Preeti Verma, Germán Spangenberg, Hans D. Daetwyler, John W. Forster, Noel O. I. Cogan
Software Mentions: 4
Published: almost 9 years ago

10.3389/fninf.2020.00030

Experimental Pipeline (Expipe): A Lightweight Data Management Platform to Simplify the Steps From Experiment to Data Analysis
Cited by: 5
Author(s): Mikkel Elle Lepperød, Svenn-Arne Dragly, Alessio Paolo Buccino, Milad Hobbi Mobarhan, Anders Malthe‐Sørenssen, Torkel Hafting, Marianne Fyhn
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-14-S7-S14

Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements
Cited by: 16
Author(s): Swaraj Basu, Ferenc Müller, Remo Sanges
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-019-53892-x

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
Cited by: 46
Author(s): Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele
Software Mentions: 4
Published: over 6 years ago

10.1186/s13073-021-00835-9

CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores
Cited by: 294
Author(s): Philipp Rentzsch, Max Schubach, Jay Shendure, Martin Kircher
Software Mentions: 4
Published: over 5 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

10.1128/mBio.00586-21

Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits
Cited by: 13
Author(s): Joshua M. Wang, Andrew L. Woodruff, Matthew J. Dunn, Robert J. Fillinger, Richard J. Bennett, Matthew Anderson
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-12-184

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation
Cited by: 19
Author(s): Catherine L. Anderson, Cory L. Strope, Etsuko N. Moriyama
Software Mentions: 4
Published: about 15 years ago

10.1371/journal.pone.0236540

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes
Cited by: 38
Author(s): Beverly McClenaghan, Nicole A Fahner, David Côté, Julek Chawarski, Avery McCarthy, Hoda Rajabi, Gregory A. C. Singer, Mehrdad Hajibabaei
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-021-07666-3

Re-examination of two diatom reference genomes using long-read sequencing
Cited by: 19
Author(s): Gina V. Filloramo, Bruce A. Curtis, Emma Blanche, John M. Archibald
Software Mentions: 4
Published: about 5 years ago

10.1038/s42003-018-0159-7

2D association and integrative omics analysis in rice provides systems biology view in trait analysis
Cited by: 3
Author(s): Wenchao Zhang, Xinbin Dai, Shizhong Xu, Patrick Xuechun Zhao
Software Mentions: 4
Published: almost 8 years ago

10.1111/acel.13443

The antagonistic pleiotropy of insulin‐like growth factor 1
Cited by: 22
Author(s): William B. Zhang, Kenny Ye, Nir Barzilai, Sofiya Milman
Software Mentions: 4
Published: about 5 years ago

10.1002/2211-5463.12484

Induction of <i>ubiquitin C</i> (<i><scp>UBC</scp></i>) gene transcription is mediated by <scp>HSF</scp>1: role of proteotoxic and oxidative stress
Cited by: 22
Author(s): Marzia Bianchi, Rita Crinelli, Vanessa Arbore, Mauro Magnani
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-020-73060-w

Automatic classification of healthy and disease conditions from images or digital standard 12-lead electrocardiograms
Cited by: 18
Author(s): Вадим Глинер, Noam Keidar, В. В. Макаров, Arutyun Avetisyan, Assaf Schuster, Yael Yaniv
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41597-021-00905-y

A resource to explore the discovery of rare diseases and their causative genes
Cited by: 5
Author(s): Friederike Ehrhart, Egon Willighagen, Martina Kutmon, Max van Hoften, Leopold Curfs, Chris T. Evelo
Software Mentions: 4
Published: over 5 years ago

10.1093/database/baab013

MENSAdb: a thorough structural analysis of membrane protein dimers
Cited by: 1
Author(s): Pedro Matos-Filipe, António Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.22039

Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq
Cited by: 48
Author(s): Pingzhu Zhou, Fei Gu, Lina Zhang, Brynn N. Akerberg, Qing Ma, Kai Li, Aibin He, Zhiqiang Lin, Sean Stevens, Bin Zhou, William T. Pu
Software Mentions: 4
Published: over 9 years ago

10.1093/gigascience/giab042

Mantis: flexible and consensus-driven genome annotation
Cited by: 19
Author(s): Pedro Queirós, Francesco Delogu, Oskar Hickl, Patrick May, Paul Wilmes
Software Mentions: 4
Published: about 5 years ago

10.1186/s12983-017-0208-y

Evidence for a postreproductive phase in female false killer whales Pseudorca crassidens
Cited by: 22
Author(s): Theoni Photopoulou, Ines Maria Ferreira, Peter B. Best, Toshio Kasuya, Helene Marsh
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.62456

Salivary and plasmatic oxytocin are not reliable trait markers of the physiology of the oxytocin system in humans
Cited by: 38
Author(s): Daniel Martins, Anthony S. Gabay, Mitul A. Mehta, Yannis Paloyelis
Software Mentions: 4
Published: over 5 years ago

10.1186/s12889-021-11790-w

Electronic data collection, management and analysis tools used for outbreak response in low- and middle-income countries: a systematic review and stakeholder survey
Cited by: 4
Author(s): Patrick Keating, Jillian Murray, Karl Schenkel, Laura Merson, Anna C. Seale
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-017-1663-3

“gnparser”: a powerful parser for scientific names based on Parsing Expression Grammar
Cited by: 10
Author(s): Dmitry Mozzherin, Alexander A. Myltsev, David J. Patterson
Software Mentions: 4
Published: about 9 years ago

10.1186/s12874-020-01046-3

Don’t dismiss logistic regression: the case for sensible extraction of interactions in the era of machine learning
Cited by: 33
Author(s): Joshua Levy, A. James O’Malley
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0080371

Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus
Cited by: 33
Author(s): C. Leyrat, Max Renner, K. Harlos, Jonathan M. Grimes
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0177459

Singularity: Scientific containers for mobility of compute
Cited by: 895
Author(s): Gregory M. Kurtzer, Vanessa Sochat, Michael Bauer
Software Mentions: 4
Published: about 9 years ago

10.1186/s13007-020-00612-6

High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography
Cited by: 63
Author(s): Shota Teramoto, Satoko Takayasu, Yuka Kitomi, Yumiko Arai‐Sanoh, Takanari Tanabata, Yusaku Uga
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.01022

Phytopathogenic Rhodococcus Have Diverse Plasmids With Few Conserved Virulence Functions
Cited by: 14
Author(s): Elizabeth A. Savory, Alexandra J. Weisberg, Danielle M. Stevens, Allison Creason, Skylar L Fuller, Emma M Pearce, Jeff H. Chang
Software Mentions: 4
Published: about 6 years ago