10.1186/s13059-016-1097-7

Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery
Cited by: 64
Author(s): Andrée Delahaye‐Duriez, Prashant K. Srivastava, Kirill Shkura, Sarah R. Langley, Liisi Laaniste, Aida Moreno‐Moral, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Elena V. Gazina, Kay Richards, Steven Petrou, Rafał M. Kamiński, Enrico Petretto, Michael R. Johnson
Software Mentions: 5
Published: over 9 years ago

10.3389/fmed.2021.674338

Role of Immune Cell-Specific Hypermethylation Signatures in Classification and Risk Stratification of Breast Cancer
Cited by: 0
Author(s): Yong Chen, Fada Xia, Bo Jiang, Wenlong Wang, Xinying Li
Software Mentions: 5
Published: almost 5 years ago

10.3389/fimmu.2021.590742

High Throughput Multi-Omics Approaches for Clinical Trial Evaluation and Drug Discovery
Cited by: 30
Author(s): Jessica Zielinski, Jason J. Luke, Silvia Guglietta, Carsten Krieg
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.505441

SCCNV: A Software Tool for Identifying Copy Number Variation From Single-Cell Whole-Genome Sequencing
Cited by: 5
Author(s): Xiao Dong, Lei Zhang, Xiaoxiao Hao, Tao Wang, Jan Vijg
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.00053-18

Balances: a New Perspective for Microbiome Analysis
Cited by: 173
Author(s): Javier Rivera Pinto, J. J. Egozcue, Vera Pawlowsky‐Glahn, Roger Paredes, Marc Noguera‐Julian, M. Luz Calle
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12874-016-0229-9

Health Equity Assessment Toolkit (HEAT): software for exploring and comparing health inequalities in countries
Cited by: 64
Author(s): Ahmad Reza Hosseinpoor, Devaki Nambiar, Anne Schlotheuber, Daniel D. Reidpath, Zev Ross
Software Mentions: 5
Published: over 9 years ago

10.1186/s12872-020-01537-7

The minimal informative monitoring interval of N-terminal pro-B-type natriuretic peptide in patients with stable heart failure
Cited by: 4
Author(s): Zhehao Dai, Taku Asano, Osamu Takahashi, Nobuyuki Komiyama, Sachiko Ohde
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2020.00505

Analysis of Circular RNA-Related Competing Endogenous RNA Identifies the Immune-Related Risk Signature for Colorectal Cancer
Cited by: 16
Author(s): Wei Song, Jun Ren, Chuntao Wang, Yuhang Ge, Tao Fu
Software Mentions: 5
Published: about 6 years ago

10.1002/cam4.2312

Characterization of transcriptome profile and clinical features of a novel immunotherapy target CD204 in diffuse glioma
Cited by: 19
Author(s): Yanggang Yuan, Qitai Zhao, Songfeng Zhao, Penghua Zhang, Haibiao Zhao, Zeyun Li, Yue Du, Xin Tian, Jingli Lü
Software Mentions: 5
Published: about 7 years ago

10.1002/brb3.1788

There is No test–retest reliability of brain activation induced by robotic passive hand movement: A functional NIRS study
Cited by: 3
Author(s): Sung-Jin Bae, Yonghee Lee, Pyung Hun Chang
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2018.02457

Bacterial Abundance and Community Composition in Pond Water From Shrimp Aquaculture Systems With Different Stocking Densities
Cited by: 61
Author(s): Yustian Rovi Alfiansah, Christiane Hassenrück, Andreas Kunzmann, Arief Taslihan, Jens Harder, Astrid Gärdes
Software Mentions: 5
Published: over 7 years ago

10.2196/24348

Monitoring Information-Seeking Patterns and Obesity Prevalence in Africa With Internet Search Data: Observational Study
Cited by: 6
Author(s): Olubusola Oladeji, Chi Zhang, Tiam Moradi, Dharmesh Tarapore, Andrew Stokes, Vukosi Marivate, Moinina David Sengeh, Elaine O. Nsoesie
Software Mentions: 5
Published: about 5 years ago

10.1186/s12889-017-4590-3

Smoking-related general and cause-specific mortality in Estonia
Cited by: 15
Author(s): Gea Kõks, Krista Fischer, Sulev Kõks
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12862-018-1225-y

Certainty of paternity in two coucal species with divergent sex roles: the devil takes the hindmost
Cited by: 15
Author(s): Ignas Safari, Wolfgang Goymann
Software Mentions: 5
Published: almost 8 years ago

10.1186/1741-7007-7-70

Genetical genomic determinants of alcohol consumption in rats and humans
Cited by: 136
Author(s): Boris Tabakoff, Laura Saba, Morton P. Printz, Pam Flodman, Colin A. Hodgkinson, David Goldman, George F. Koob, H. G. Richardson, Katerina Kechris, Richard L. Bell, Norbert Hübner, Matthias Heinig, Michal Pravenec, Jonathan Mangion, Lucie Legault, M Dongier, Katherine M. Conigrave, John B. Whitfield, John B. Saunders, Bridget F. Grant, Paula L. Hoffman
Software Mentions: 5
Published: over 16 years ago

10.1016/j.ebiom.2021.103538

Airway microbial communities, smoking and asthma in a general population sample
Cited by: 21
Author(s): Elena Turek, Michael J. Cox, Michael Hunter, Jennie Hui, Phillip James, Saffron A.G. Willis‐Owen, Leah Cuthbertson, Alan James, A.W. Musk, Miriam F. Moffatt, William Cookson
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12859-021-04154-z

Tamock: simulation of habitat-specific benchmark data in metagenomics
Cited by: 0
Author(s): Samuel M. Gerner, Alexandra B. Graf, Thomas Rattei
Software Mentions: 5
Published: about 5 years ago

10.1177/0748730418813785

LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data
Cited by: 47
Author(s): Jordan M. Singer, Jacob J. Hughey
Software Mentions: 5
Published: over 7 years ago

10.1093/gigascience/giy149

PhenoMeNal: processing and analysis of metabolomics data in the cloud
Cited by: 58
Author(s): Kristian Peters, J. H. Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M. D. Ebbels, Carles Foguet, Robert C. Glen, Alejandra González-Beltrán, Ulrich L. Günther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Íbrahím Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, Pablo Moreno-Ger, Steffen Neumann, Jon Ander Novella, Claire O’Donovan, Jake T M Pearce, Alina Peluso, Marco Piras, Luca Pireddu, Michelle A.C. Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Vitaly A. Selivanov, Ola Spjuth, Daniel Schober, Etienne Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael Van Vliet, Mark R. Viant, Ralf Weber, Gianluigi Zanetti, Christoph Steinbeck
Software Mentions: 5
Published: over 7 years ago

10.3389/fpls.2018.00641

Detailed Phytochemical Analysis of High- and Low Artemisinin-Producing Chemotypes of Artemisia annua
Cited by: 22
Author(s): Tomasz Czechowski, Tony R. Larson, Theresa M. Catania, David Harvey, Cenxi Wei, Michel Essome, Geoffrey D. Brown, Ian A. Graham
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-019-6314-9

Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause
Cited by: 32
Author(s): Thomas J. Colgan, Sive Finlay, Mark J. F. Brown, James C. Carolan
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-020-03838-2

Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference
Cited by: 3
Author(s): Robert J. Moore, Michael Barnathan, Brian Fristensky, Yán Li, Greg Knowles, Paul Gardner-Stephen, Angelo Bueti, Peter Anderson, Jianguang Qin, Andrew S. Ball
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2019.01333

A Novel Prognostic Index Based on Alternative Splicing in Papillary Renal Cell Carcinoma
Cited by: 2
Author(s): Zhipeng Wu, Jinhui Liu, Rui Sun, Dongming Chen, Kai Wang, Changchun Cao, Xianlin Xu
Software Mentions: 5
Published: over 6 years ago

10.1093/bioinformatics/btw088

fqtools: an efficient software suite for modern FASTQ file manipulation
Cited by: 21
Author(s): Alastair Droop
Software Mentions: 5
Published: over 10 years ago

10.1186/s40168-015-0146-x

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Cited by: 91
Author(s): Yue Jiang, Xuejian Xiong, Jayne S. Danska, John Parkinson
Software Mentions: 5
Published: over 10 years ago

10.1099/mgen.0.000271

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network
Cited by: 5
Author(s): Charles H. D. Williamson, Nathan E. Stone, Amalee E. Nunnally, Heidie Hornstra, David M. Wagner, Chandler C. Roe, Adam J. Vazquez, Nivedita Nandurkar, Jacob Vinocur, Joel Terriquez, John D. Gillece, Jason Travis, Darrin Lemmer, Paul Keim, Jason W. Sahl
Software Mentions: 5
Published: about 7 years ago

10.7717/peerj.3720

Atropos: specific, sensitive, and speedy trimming of sequencing reads
Cited by: 168
Author(s): John P. Didion, Marcel Martin, Francis S. Collins
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0220436

Affect regulation training reduces symptom severity in depression – A randomized controlled trial
Cited by: 28
Author(s): Matthias Berking, Eva Eichler, Maike Luhmann, Alice Diedrich, Wolfgang Hiller, Winfried Rief
Software Mentions: 5
Published: almost 7 years ago

10.2196/15371

Transfer Learning for Risk Classification of Social Media Posts: Model Evaluation Study
Cited by: 21
Author(s): Derek Howard, Marta M. Maslej, Justin Lee, Jacob Ritchie, Geoffrey Woollard, Leon French
Software Mentions: 5
Published: about 6 years ago

10.1155/2021/6648093

Integrated Analysis to Identify a Redox-Related Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 16
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: about 5 years ago

10.1515/med-2020-0114

CCTs as new biomarkers for the prognosis of head and neck squamous cancer
Cited by: 11
Author(s): Yanbo Dong, Siyu Lu, Zhenxiao Wang, Liangfa Liu
Software Mentions: 5
Published: over 6 years ago

10.1155/2021/2042114

Identification of Prognostic Metabolism-Related Genes in Clear Cell Renal Cell Carcinoma
Cited by: 8
Author(s): Yusa Chen, Yumei Liang, Ying Chen, Shan Ouyang, Kanghan Liu, Yin Wu
Software Mentions: 5
Published: almost 5 years ago

10.3390/ijms21218016

Enhancer of Zeste Homolog 2 (EZH2) Mediates Glucolipotoxicity-Induced Apoptosis in β-Cells
Cited by: 3
Author(s): Tina Dahlby, Christian Simon, Marie Balslev Backe, Mattias Salling Dahllöf, Edward B. Holson, Bridget K. Wagner, Marianne Böni-Schnetzler, Michał Marzec, Morten Lundh, Thomas Mandrup‐Poulsen
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms21030751

Effect of Bortezomib on Global Gene Expression in PC12-Derived Nerve Cells
Cited by: 10
Author(s): Karolina Łuczkowska, Dorota Rogińska, Zofia Ulańczyk, Bogusław Machaliński
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pbio.2002940

The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity
Cited by: 46
Author(s): Rukeia El-Athman, Nikolaï Genov, J Mazùch, Kaiyang Zhang, Yong A. Yu, Luise Fuhr, Marconi Abreu, Yin Li, Thomas Wallach, Achim Kramer, Clemens A. Schmitt, Angela Relógio
Software Mentions: 5
Published: over 8 years ago

10.15252/embj.2019103852

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic <scp>sRNA</scp> activation in competence control
Cited by: 47
Author(s): Jens Hör, Geneviève Garriss, Silvia Di Giorgio, Lisa-Marie Hack, Jens T. Vanselow, Konrad U. Förstner, Andreas Schlösser, Birgitta Henriques‐Normark, Jörg Vogel
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.58716

Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?
Cited by: 210
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Francesca Luca, Yi Xu, Adnan Alazizi, Yaozhu Leng, Chaur Dong Hsu, Nardhy Gomez-López
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.39188

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury
Cited by: 27
Author(s): Jordan W. Squair, Seth Tigchelaar, Kyung‐Mee Moon, Jie Liu, Wolfram Tetzlaff, Brian K. Kwon, Andrei V. Krassioukov, Christopher R. West, Leonard J. Foster, Michael A. Skinnider
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-021-92610-4

Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction
Cited by: 2
Author(s): Jun-Yan Hong, T.D.C.P. Gunasekara, Cheng He, Sanzhen Liu, Jianqin Huang, Hairong Wei
Software Mentions: 5
Published: about 5 years ago

10.1093/gigascience/giaa054

Fcirc: A comprehensive pipeline for the exploration of fusion linear and circular RNAs
Cited by: 5
Author(s): Zhaoqing Cai, Hongzhang Xue, Yue Xu, Jens Köhler, Xiaoyu Cheng, Yanjun Dai, Jie Zheng, Haiyun Wang
Software Mentions: 5
Published: about 6 years ago

10.1093/jamiaopen/ooab065

P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants
Cited by: 0
Author(s): Elias DeVoe, Gavin R. Oliver, Roman M. Zenka, Patrick R. Blackburn, Margot A. Cousin, Nicole J. Boczek, Jean-Pierre A. Kocher, Raúl Urrutia, Eric W. Klee, Michael T. Zimmermann
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0157703

A Fit-Fat Index for Predicting Incident Diabetes in Apparently Healthy Men: A Prospective Cohort Study
Cited by: 23
Author(s): Robert A. Sloan, Benjamin Haaland, Susumu S. Sawada, I-Min Lee, Xuemei Sui, Duck-chul Lee, Yassine Ridouane, Falk Müller‐Riemenschneider, Steven N. Blair
Software Mentions: 5
Published: about 10 years ago

10.1186/s13059-017-1309-9

DESMAN: a new tool for de novo extraction of strains from metagenomes
Cited by: 149
Author(s): Christopher Quince, Tom O. Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E. Darling, Gavin Collins, A. Murat Eren
Software Mentions: 5
Published: almost 9 years ago

10.3390/cancers11010053

Prognostic Gene Discovery in Glioblastoma Patients using Deep Learning
Cited by: 34
Author(s): Kelvin Wong, Robert Rostomily, Stephen T.C. Wong
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0004481

Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
Cited by: 17
Author(s): Ingmar S. Middelbos, Brittany M. Vester, Lisa K. Karr-Lilienthal, Lawrence B. Schook, Kelly S. Swanson
Software Mentions: 5
Published: over 17 years ago

10.1002/ece3.2146

Quantifying the effects of drought on abrupt growth decreases of major tree species in Switzerland
Cited by: 38
Author(s): Marco Vanoni, Harald Bugmann, Magdalena Nötzli, Christof Bigler
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0178323

Effect of climate on incidence of respiratory syncytial virus infections in a refugee camp in Kenya: A non-Gaussian time-series analysis
Cited by: 11
Author(s): Raymond Nyoka, Jimmy Omony, Samuel Mwalili, Thomas Achia, Anthony Gichangi, Henry Mwambi
Software Mentions: 5
Published: about 9 years ago

10.1128/mSystems.00003-15

Open-Source Sequence Clustering Methods Improve the State Of the Art
Cited by: 139
Author(s): Evguenia Kopylova, José A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Zhou Hong, Torbjørn Rognes, J. Gregory Caporaso, Rob Knight
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0042678

The Role of Master Regulators in the Metabolic/Transcriptional Coupling in Breast Carcinomas
Cited by: 19
Author(s): Karol Baca-López, M. Mayorga, Alfredo Hidalgo-Miranda, Nora Gutiérrez-Nájera, Enrique Hernández‐Lemus
Software Mentions: 5
Published: almost 14 years ago

10.1371/journal.pmed.1002950

The association between heat exposure and hospitalization for undernutrition in Brazil during 2000−2015: A nationwide case-crossover study
Cited by: 25
Author(s): Rongbin Xu, Qi Zhao, Micheline de Sousa Zanotti Stagliorio Coélho, Paulo Hilário Nascimento Saldiva, Michael J. Abramson, Shanshan Li, Hyewon Lee
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0248650

Elucidating the immune infiltration in acne and its comparison with rosacea by integrated bioinformatics analysis
Cited by: 14
Author(s): Lu Yang, Yanhong Shou, Yue Yang, Jianhua Xu
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0111819

Expression Analysis of All Protease Genes Reveals Cathepsin K to Be Overexpressed in Glioblastoma
Cited by: 39
Author(s): Urška Verbovšek, Helena Motaln, Ana Rotter, Nadia A. Atai, Kristina Gruden, C. J. F. Van Noorden, Tamara T. Lah
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0247669

Immune gene expression networks in sepsis: A network biology approach
Cited by: 13
Author(s): Kyung Soo Kim, Dong Wook Jekarl, Jaeeun Yoo, Seungok Lee, Myungshin Kim, Yonggoo Kim
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-35276-9

The relative effects of forest amount, forest configuration, and urban matrix quality on forest breeding birds
Cited by: 24
Author(s): Alexandra V. Shoffner, Andrew Wilson, Wenwu Tang, Sara A. Gagné
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-27047-3

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy
Cited by: 17
Author(s): Nina Marchi, Philippe Mennecier, Myriam Georges, Sophie Lafosse, Tatyana Hegay, Choduraa Dorzhu, Boris Chichlo, Laure Ségurel, Évelyne Heyer
Software Mentions: 5
Published: about 8 years ago

10.1093/g3journal/jkaa055

Transcriptome analysis of <i>Caenorhabditis elegans</i> lacking heme peroxidase SKPO-1 reveals an altered response to <i>Enterococcus faecalis</i>
Cited by: 4
Author(s): Yi Liu, Daniel Martínez-Martínez, Clara L. Essmann, Melissa R. Cruz, Filipe Cabreiro, Danielle A. Garsin
Software Mentions: 5
Published: over 5 years ago

10.3390/insects12030271

Differential Gene Expression in the Heads of Behaviorally Divergent Culex pipiens Mosquitoes
Cited by: 2
Author(s): Anna Noreuil, Megan L. Fritz
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-89926-6

Smoke from regional wildfires alters lake ecology
Cited by: 13
Author(s): Facundo Scordo, Sudeep Chandra, Erin Suenaga, Suzanne J. Kelson, Joshua Culpepper, Lucia Scaff, Flavia Tromboni, Timothy J. Caldwell, Carina Seitz, Juan Esteban Fiorenza, Craig E. Williamson, Steven Sadro, Kevin C. Rose, Simon R. Poulson
Software Mentions: 5
Published: about 5 years ago

10.1534/g3.120.401452

Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
Cited by: 10
Author(s): Mariem Nsibi, Barbara Gouble, Sylvie Bureau, Timothée Flutre, Christopher Sauvage, Jean‐Marc Audergon, Jean‐Luc Regnard
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-61558-2

Innovation in wild Barbary macaques (Macaca sylvanus)
Cited by: 16
Author(s): Federica Amici, Álvaro López Caicoya, Bonaventura Majolo, Anja Widdig
Software Mentions: 5
Published: over 6 years ago

10.3389/fcell.2021.648806

Construction of a Prognostic Immune-Related LncRNA Risk Model for Lung Adenocarcinoma
Cited by: 16
Author(s): Yue Li, Ruoyi Shen, Anqi Wang, Jian Zhao, Jieqi Zhou, Weijie Zhang, Ruochen Zhang, Jianjie Zhu, Zeyi Liu, Jian-An Huang
Software Mentions: 5
Published: over 5 years ago

10.1016/j.bbapap.2013.02.032

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
Cited by: 67
Author(s): Yasset Perez‐Riverol, Rui Wang, Henning Hermjakob, Markus Müller, Vladimir Vesada, Juan Antonio Vizcaíno
Software Mentions: 5
Published: over 12 years ago

10.1186/1471-2105-14-263

Ontology based molecular signatures for immune cell types via gene expression analysis
Cited by: 12
Author(s): Terrence F. Meehan, Nicole Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl
Software Mentions: 5
Published: almost 13 years ago

10.1186/1471-2105-6-98

ProGenExpress: Visualization of quantitative data on prokaryotic genomes
Cited by: 6
Author(s): Michael Watson
Software Mentions: 5
Published: about 21 years ago

10.3389/fcell.2021.641960

Immune-Related Long Non-coding RNA Signature and Clinical Nomogram to Evaluate Survival of Patients Suffering Esophageal Squamous Cell Carcinoma
Cited by: 14
Author(s): Tong Zhu, Zhifeng Ma, Haiyong Wang, Desheng Wei, Bin Wang, Chu Zhang, Linhai Fu, Zhupeng Li, Guangmao Yu
Software Mentions: 5
Published: over 5 years ago

10.1098/rspb.2021.0454

Long-term exposure to artificial light at night in the wild decreases survival and growth of a coral reef fish
Cited by: 13
Author(s): Jules Schligler, Daphne Cortese, Ricardo Beldade, Stephen E. Swearer, Suzanne C. Mills
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2021.648331

Fibrillarin-GFP Facilitates the Identification of Meiotic Competent Oocytes
Cited by: 6
Author(s): Ting Wang, Jie Na
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2021.736540

Characterization of Molecular Heterogeneity Associated With Tumor Microenvironment in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy
Cited by: 9
Author(s): Weimin Zhong, Yinan Li, Yazhou Yuan, Hongbin Zhong, Chaoqun Huang, Jiwei Huang, Yao Lin, Jian Huang
Software Mentions: 5
Published: almost 5 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

10.1371/journal.pone.0197386

A bioavailable strontium isoscape for Western Europe: A machine learning approach
Cited by: 105
Author(s): Clément P. Bataille, Isabella C.C. von Holstein, Jason E. Laffoon, Malte Willmes, Xiao Ming Liu, Gareth R. Davies
Software Mentions: 5
Published: about 8 years ago

10.1111/1365-2656.12055

Male reproductive strategy explains spatiotemporal segregation in brown bears
Cited by: 110
Author(s): Sam M. J. G. Steyaert, Jonas Kindberg, Jon E. Swenson, Andreas Zedrosser
Software Mentions: 5
Published: over 13 years ago

10.3389/fcvm.2021.631650

Integrated DNA Methylation and Gene Expression Analysis Identified S100A8 and S100A9 in the Pathogenesis of Obesity
Cited by: 7
Author(s): Ningyuan Chen, Miao Liu, Wei Lin, Donghua Zou, Ling Huang, Jian Huang, Wei Shi, Li-Lin Li, Yu-Xing Luo, Hao Liang, Shang‐Ling Pan, Junhua Peng
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0244363

Backbone: An R package for extracting the backbone of bipartite projections
Cited by: 20
Author(s): Rachel Domagalski, Zachary P. Neal, Bruce E. Sagan
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0188512

Wrapped: An R package for circular data
Cited by: 8
Author(s): Saralees Nadarajah, Yuanyuan Zhang
Software Mentions: 5
Published: over 8 years ago

10.3389/fgene.2014.00362

Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae
Cited by: 31
Author(s): Kate Armstrong, Graham N. Stone, James A. Nicholls, Eugenio Valderrama, Arne A. Anderberg, Jenny E. E. Smedmark, Laurent Gautier, Yamama Naciri, Richard I. Milne, James E. Richardson
Software Mentions: 5
Published: over 11 years ago

10.1534/g3.119.400560

Genome Size Evolution Differs Between<i>Drosophila</i>Subgenera with Striking Differences in Male and Female Genome Size in<i>Sophophora</i>
Cited by: 6
Author(s): Carl E. Hjelmen, Heath Blackmon, Valerie Renee Holmes, Crystal Burrus, J. Spencer Johnston
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0213820

Impacts of climate change on high priority fruit fly species in Australia
Cited by: 20
Author(s): Sabira Sultana, John B. Baumgartner, Bernard C. Dominiak, Jane E Royer, Linda J. Beaumont
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-020-01977-6

Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome
Cited by: 67
Author(s): Jacob Schreiber, Timothy Durham, Jeffrey A. Bilmes, William Stafford Noble
Software Mentions: 5
Published: over 6 years ago

10.18632/aging.203121

Identification of microenvironment related potential biomarkers of biochemical recurrence at 3 years after prostatectomy in prostate adenocarcinoma
Cited by: 9
Author(s): Xiaoru Sun, Lu Wang, Hongkai Li, Chuandi Jin, Yuanyuan Yu, Lei Hou, Xinhui Liu, Yifan Yu, Ran Yan, Fuzhong Xue
Software Mentions: 5
Published: about 5 years ago

10.1093/gigascience/giab057

VC@Scale: Scalable and high-performance variant calling on cluster environments
Cited by: 3
Author(s): Tanveer Ahmad, Zaid Al-Ars, Peter Hofstee
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0199999

Detecting cerebrovascular changes in the brain caused by hypertension in atrial fibrillation group using acoustocerebrography
Cited by: 1
Author(s): Wioletta Dobkowska-Chudoń, Mirosław Wrobel, P. Karłowicz, A Dąbrowski, Andrzej Krupienicz, Tomasz Targowski, Andrzej Nowicki, Robert Olszewski
Software Mentions: 5
Published: about 8 years ago

10.1098/rsos.202093

Habitat filtering differentially modulates phylogenetic and functional diversity relationships between predatory arthropods
Cited by: 4
Author(s): Aurélien Ridel, Denis Lafage, Pierre Devogel, Thomas Lacoue-Labarthe, Julien Pétillon
Software Mentions: 5
Published: about 5 years ago

10.7150/jca.49409

Identification of marker genes and cell subtypes in castration-resistant prostate cancer cells
Cited by: 6
Author(s): Xiaodan Lin, Nanping Lin, Tingting Lin, Yupeng Wu, Peng Huang, Zhi‐Bin Ke, Yunzhi Lin, Shao‐Hao Chen, Qing‐Shui Zheng, Yong Wei, Xue-Yi Xue, Rongjin Lin, Ning Xu
Software Mentions: 5
Published: over 5 years ago

10.2196/15918

Enabling Agile Clinical and Translational Data Warehousing: Platform Development and Evaluation
Cited by: 5
Author(s): Helmut Spengler, C. Lang, Tanmaya Mahapatra, Ingrid Gatz, Klaus A. Kuhn, Fabian Praßer
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2020.00101

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa
Cited by: 26
Author(s): Elle M. Barnes, Erin L. Carter, James D. Lewis
Software Mentions: 5
Published: over 6 years ago

10.1093/bioinformatics/btz284

clustermq enables efficient parallelization of genomic analyses
Cited by: 5
Author(s): Michaël Schubert
Software Mentions: 5
Published: about 7 years ago

10.3325/cmj.2020.61.564

Bayesian meta-analysis now – let's do it
Cited by: 9
Author(s): Branimir K. Hackenberger
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02302-5

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Cited by: 31
Author(s): Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez‐Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, A. Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-021-04095-7

Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression
Cited by: 5
Author(s): Qinghong Dai, Tao Liu, Yongchao Gao, Honghao Zhou, Xiong Li, Wei Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-020-02247-1

Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences
Cited by: 22
Author(s): Caroline Jane Ross, Aviv Rom, Amit Spinrad, Dikla Gelbard-Solodkin, Neta Degani, Igor Ulitsky
Software Mentions: 5
Published: over 5 years ago

10.1107/S2059798318007726

Electron diffraction data processing with <i>DIALS</i>
Cited by: 96
Author(s): Max T. B. Clabbers, Tim Gruene, James M. Parkhurst, Jan Pieter Abrahams, David Waterman
Software Mentions: 5
Published: about 8 years ago

10.3390/bs11060087

From Fear to Hopelessness: The Buffering Effect of Patient-Centered Communication in a Sample of Oncological Patients during COVID-19
Cited by: 27
Author(s): Alessandro Rossi, Maria Marconi, Federica Taccini, Claudio Verusio, Stefania Mannarini
Software Mentions: 5
Published: about 5 years ago

10.1107/S1399004714017039

New methods for indexing multi-lattice diffraction data
Cited by: 53
Author(s): Richard J. Gildea, David Waterman, James M. Parkhurst, Danny Axford, Geoff Sutton, David I. Stuart, Nicholas K. Sauter, Gwyndaf Evans, Graeme Winter
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12864-016-2745-8

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
Cited by: 17
Author(s): Yongxian Yuan, Huaiqian Xu, Rufina Leung
Software Mentions: 5
Published: about 10 years ago

10.1111/1755-0998.12465

Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes
Cited by: 24
Author(s): Nina F. Ockendon, Lauren A. O’Connell, Stephen J. Bush, Jimena Monzón‐Sandoval, Holly Barnes, Tamás Székely, Hans A. Hofmann, Steve Dorus, Araxi O. Urrutia
Software Mentions: 5
Published: over 10 years ago

10.3390/e22090965

Consistent Estimation of Generalized Linear Models with High Dimensional Predictors via Stepwise Regression
Cited by: 4
Author(s): Alex Pijyan, Qi Zheng, Hyokyoung Grace Hong, Yang Li
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-021-93845-x

Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
Cited by: 12
Author(s): Priyanka Banerjee, Premanand Balraj, Nilesh Sudhakar Ambhore, S.A. Wicher, Rodney D. Britt, Christina M. Pabelick, Y. S. Prakash, Venkatachalem Sathish
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpsyg.2020.00308

A Comparison of IRT Observed Score Kernel Equating and Several Equating Methods
Cited by: 5
Author(s): Shaojie Wang, Minqiang Zhang, Sen You
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2018.00785

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies
Cited by: 44
Author(s): Robin R. Shields-Cutler, Gabe A. Al-Ghalith, Moran Yassour, Dan Knights
Software Mentions: 5
Published: about 8 years ago

10.3389/fimmu.2021.614246

Reduced Placental Transfer of Antibodies Against a Wide Range of Microbial and Vaccine Antigens in HIV-Infected Women in Mozambique
Cited by: 10
Author(s): Selena Alonso, Marta Vidal, Gemma Ruiz‐Olalla, Raquel González, Maria Nélia Manaca, Chenjerai Jairoce, Miquel Vázquez-Santiago, Reyes Balcells, Anifa Valá, Maria Rosario, Pau Cisteró, Laura Fuente-Soro, Marta Cova, Evelina Angov, Arsénio Nhacolo, Esperança Sevene, John J. Aponte, Eusébio Macete, Ruth Aguilar, Alfredo Mayor, Clara Menéndez, Carlota Dobaño, Gemma Moncunill
Software Mentions: 5
Published: over 5 years ago