10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0149237

Optimizing Viral Discovery in Bats
Cited by: 35
Author(s): Caroline Young, Kevin J. Olival
Software Mentions: 9
Published: over 10 years ago

10.1038/s41598-020-76315-8

Robustly forecasting maize yields in Tanzania based on climatic predictors
Cited by: 18
Author(s): Rahel Laudien, Bernhard Schauberger, David Makowski, Christoph Gornott
Software Mentions: 9
Published: over 5 years ago

10.1016/j.celrep.2019.11.077

Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids
Cited by: 42
Author(s): Jitu W. George, Huihui Fan, Benjamin K. Johnson, Tyler J. Carpenter, Kelly K. Foy, Anindita Chatterjee, Amanda L. Patterson, Julie Koeman, Marie Adams, Zachary Madaj, David Chesla, Erica E. Marsh, Timothy J. Triche, Hui Shen, Jose Teixeira
Software Mentions: 9
Published: over 6 years ago

10.1186/s13059-015-0702-5

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Cited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: almost 11 years ago

10.1016/j.molcel.2018.11.006

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains
Cited by: 117
Author(s): Jean-Philippe Lambert, S. Picaud, Takao Fujisawa, Huayun Hou, P. Savitsky, Liis Uusküla-Reimand, Gagan D. Gupta, Hala Abdouni, Zhen‐Yuan Lin, Monika Tucholska, James D.R. Knight, Beatriz Gonzalez-Badillo, Nicole St‐Denis, Joseph A. Newman, Manuel Stucki, Laurence Pelletier, Nuno Bandeira, Michael D. Wilson, P. Filippakopoulos, Anne‐Claude Gingras
Software Mentions: 9
Published: over 7 years ago

10.1038/s41598-019-50540-2

Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands
Cited by: 23
Author(s): Franziska Wemheuer, Bernd Wemheuer, Rolf Daniel, Stefan Vidal
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.ppat.1009577

Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF
Cited by: 11
Author(s): Xiaogang Cheng, Ancy Joseph, Victor Castro, Alice Chen-Liaw, Zachary L. Skidmore, Takaharu Ueno, Jun–ichi Fujisawa, Daniel A. Rauch, Grant A. Challen, Michael P. Martinez, Patrick Green, Malachi Griffith, Jacqueline E. Payton, John Edwards, Lee Ratner
Software Mentions: 9
Published: about 5 years ago

10.1186/s40249-020-00677-4

Factors associated with mobile phone ownership and potential use for rabies vaccination campaigns in southern Malawi
Cited by: 15
Author(s): Orla Marron, Gareth J. Thomas, Jordana L. Burdon Bailey, Dagmar Mayer, Paul Orion Grossman, Frederic Lohr, Andrew D Gibson, Luke Gamble, Patrick Chikungwa, Julius L.C. Chulu, Ian Handel, Barend Mark de Clare Bronsvoort, Richard J. Mellanby, Stella Mazeri
Software Mentions: 9
Published: about 6 years ago

10.1155/2020/9762067

14-CpG-Based Signature Improves the Prognosis Prediction of Hepatocellular Carcinoma Patients
Cited by: 8
Author(s): Hongye Jiang, Gang Ning, Yensheng Wang, Weibiao Lv
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0165881

High Interannual Variability in Connectivity and Genetic Pool of a Temperate Clingfish Matches Oceanographic Transport Predictions
Cited by: 14
Author(s): Maria Klein, Sara Teixeira, Jorge Assis, Ester A. Serrão, Emanuel João Gonçalves, Rita Alexandra Borges
Software Mentions: 9
Published: over 9 years ago

10.3390/metabo10030086

Local Phenomena Shape Backyard Soil Metabolite Composition
Cited by: 9
Author(s): Tra D Nguyen, Mahbobeh Lesani, Ines Forrest, Yunpeng Lan, Danya A. Dean, Quentin M. R. Gibaut, Yanting Guo, Ekram Hossain, Marcela Olvera, Hannah Panlilio, Adwaita R. Parab, Chao‐Yi Wu, Jean A. Bernatchez, Robert H. Cichewicz, Laura-Isobel McCall
Software Mentions: 9
Published: over 6 years ago

10.3390/microorganisms9091814

Presence of Human Pathogens of the Borrelia burgdorferi sensu lato Complex Shifts the Sequence Read Abundances of Tick Microbiomes in Two German Locations
Cited by: 7
Author(s): Angeline Hoffmann, Thomas Müller, Volker Fingerle, Matthias Noll
Software Mentions: 9
Published: almost 5 years ago

10.3389/fpls.2021.638738

Capturing and Selecting Senescence Variation in Wheat
Cited by: 11
Author(s): Elizabeth A. Chapman, Simon Orford, Jean-Luc Da Lage, Simon Griffiths
Software Mentions: 9
Published: about 5 years ago

10.3389/fbioe.2019.00257

The Construction and Analysis of ceRNA Network and Patterns of Immune Infiltration in Mesothelioma With Bone Metastasis
Cited by: 23
Author(s): Runzhi Huang, Jiawen Wu, Zixuan Zheng, Guanghua Wang, Dianwen Song, Penghui Yan, Huabin Yin, Peng Hu, Xiaolong Zhu, Haiyun Wang, Qi Lv, Tong Meng, Zongqiang Huang, Jie Zhang
Software Mentions: 9
Published: over 6 years ago

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: about 6 years ago

10.3389/fmicb.2020.575707

Evaluating the Potential Antibiotic Resistance Status in Environment Based on the Trait of Microbial Community
Cited by: 9
Author(s): Zhiguo Su, Bei Huang, Quanquan Mu, Donghui Wen
Software Mentions: 9
Published: over 5 years ago

10.1534/g3.120.401436

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat
Cited by: 18
Author(s): Sophie A Harrington, Anna E Backhaus, Ajit Singh, Keywan Hassani‐Pak, Cristóbal Uauy
Software Mentions: 9
Published: over 5 years ago

10.3389/fneur.2020.01021

Medical Informatics Platform (MIP): A Pilot Study Across Clinical Italian Cohorts
Cited by: 10
Author(s): Alberto Redolfi, Silvia De Francesco, Fulvia Palesi, Samantha Galluzzi, Cristina Muscio, Gloria Castellazzi, Pietro Tiraboschi, Giovanni Savini, Anna Nigri, Gabriella Bottini, Maria Grazia Bruzzone, Matteo Cotta Ramusino, Stefania Ferraro, C Wheeler-Kingshott, Fabrizio Tagliavini, Giovanni B. Frisoni, Philippe Ryvlin, Jean-François Demonet, Ferath Kherif, Stefano F. Cappa, Egidio D’Angelo
Software Mentions: 9
Published: almost 6 years ago

10.1016/j.mad.2021.111437

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice
Cited by: 6
Author(s): Matías Fuentealba, Daniel K. Fabian, Handan Melike Dönertaş, Janet Thornton, Linda Partridge
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0129213

Association between Influenza A Virus Infection and Pigs Subpopulations in Endemically Infected Breeding Herds
Cited by: 35
Author(s): Andrés Díaz, Andrés Pérez, Srinand Sreevatsan, Peter Davies, Marie Culhane, Montserrat Torremorell
Software Mentions: 9
Published: about 11 years ago

10.1186/s13040-021-00267-6

eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals
Cited by: 11
Author(s): Theodore G. Drivas, Anastasia Lucas, Marylyn D. Ritchie
Software Mentions: 9
Published: almost 5 years ago

10.15252/msb.20209620

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
Cited by: 166
Author(s): Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I. Jordan, Nir Yosef
Software Mentions: 9
Published: over 5 years ago

10.3389/fpls.2021.612843

Development and Validation of Methodology for Estimating Potato Canopy Structure for Field Crop Phenotyping and Improved Breeding
Cited by: 10
Author(s): Filipe Colwell, Jock Souter, Glenn Bryan, Lindsey Compton, Neil Boonham, Ankush Prashar
Software Mentions: 9
Published: over 5 years ago

10.3389/fpsyg.2018.02327

Use or Consequences: Probing the Cognitive Difference Between Two Measures of Divergent Thinking
Cited by: 44
Author(s): Richard W. Hass, Roger E. Beaty
Software Mentions: 9
Published: over 7 years ago

10.7717/peerj.9089

Resampling-based methods for biologists
Cited by: 35
Author(s): John Fieberg, Kelsey Vitense, Douglas H. Johnson
Software Mentions: 9
Published: about 6 years ago

10.1093/femsec/fiab097

Host species shape the community structure of culturable endophytes in fruits of wild berry species (<i>Vaccinium myrtillus</i> L., <i>Empetrum nigrum</i> L. and <i>Vaccinium vitis-idaea</i> L.)
Cited by: 9
Author(s): Minh-Phuong Nguyen, Kaisa Lehosmaa, Françoise Martz, Janne J. Koskimäki, Anna Maria Pirttilä, Hely Häggman
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12911-021-01459-0

Transformers-sklearn: a toolkit for medical language understanding with transformer-based models
Cited by: 14
Author(s): Feihong Yang, Xuwen Wang, Hetong Ma, Jiao Li
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12864-019-5692-3

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Cited by: 14
Author(s): Marc Lorentzen, Hugo Campbell-Sills, Tue Sparholt Jørgensen, Tue Kjærgaard Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick Lucas
Software Mentions: 9
Published: about 7 years ago

10.3390/insects12070639

Estimation of the Recent Expansion Rate of Ruspolia nitidula (Orthoptera) on a Regional and Landscape Scale
Cited by: 3
Author(s): Oto Kaláb, Petr Pyszko, Petr Kočárek
Software Mentions: 9
Published: almost 5 years ago

10.1186/s40246-019-0242-2

Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis
Cited by: 4
Author(s): Carlos Ruiz‐Arenas, Alejandro Cáceres, Vı́ctor Moreno, Juan R. González
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0018337

mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components
Cited by: 7
Author(s): Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Raimo Pohjanvirta
Software Mentions: 9
Published: almost 15 years ago

10.1016/j.csbj.2018.01.003

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Cited by: 184
Author(s): Chang Xu
Software Mentions: 9
Published: over 8 years ago

10.3389/fendo.2020.554922

Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes
Cited by: 6
Author(s): H Johansson, Jonas Nørskov Søndergaard, Carl Jorns, Claudia Kutter, Ewa Ellis
Software Mentions: 9
Published: over 5 years ago

10.1080/19490976.2021.1957408

Imbalance of the intestinal virome and altered viral-bacterial interactions caused by a conditional deletion of the vitamin D receptor
Cited by: 14
Author(s): Jilei Zhang, Yongguo Zhang, Yinglin Xia, Jun Sun
Software Mentions: 9
Published: over 5 years ago

10.1038/srep46112

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing
Cited by: 31
Author(s): José de Ribamar da Silva Nunes, Shikai Liu, Fábio Pértille, Caio Augusto Perazza, Priscilla Marqui Schmidt Villela, Vera Maria Fonseca de Almeida-Val, Alexandre Wagner Silva Hilsdorf, Zhanjiang Liu, Luiz Lehmann Coutinho
Software Mentions: 9
Published: about 9 years ago

10.3389/fcell.2021.643603

Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain
Cited by: 8
Author(s): Samuel E. Ross, Daniel Hesselson, Ozren Bogdanović
Software Mentions: 9
Published: over 5 years ago

10.1007/s13755-020-00105-9

Predicting risk of stillbirth and preterm pregnancies with machine learning
Cited by: 43
Author(s): Aki Koivu, Mikko Sairanen
Software Mentions: 9
Published: over 6 years ago

10.3390/ijms21145044

Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth
Cited by: 10
Author(s): Elena Spada, Luciano Calzari, Luigi Corsaro, Teresa Fazia, Monica Mencarelli, Anna Maria Di Blasio, Luisa Bernardinelli, G. Zangheri, Michele Vignali, Davide Gentilini
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: over 6 years ago

10.1186/1471-2105-13-136

Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: about 14 years ago

10.1128/AEM.00121-20

Assessment of Soil Features on the Growth of Environmental Nontuberculous Mycobacterial Isolates from Hawai'i
Cited by: 15
Author(s): Cody Glickman, Ravleen Virdi, Nabeeh A. Hasan, L. Elaine Epperson, Leeza Brown, Stephanie N. Dawrs, James Crooks, Edward D. Chan, Michael Strong, Stephen T. Nelson, Jennifer R. Honda
Software Mentions: 9
Published: over 5 years ago

10.1186/1471-2164-14-892

RNA-Seq optimization with eQTL gold standards
Cited by: 24
Author(s): Shannon Ellis, Saloni Gupta, Foram N. Ashar, Joel S. Bader, Andrew B. West, Dan E. Arking
Software Mentions: 9
Published: over 12 years ago

10.3389/fnbeh.2019.00036

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain
Cited by: 13
Author(s): Scott D Cinel, Steven J. Taylor
Software Mentions: 9
Published: over 7 years ago

10.12688/f1000research.27062.2

SAPHIR: a Shiny application to analyze tissue section images
Cited by: 0
Author(s): Elodie Germani, Hugues Lelouard, Mathieu Fallet
Software Mentions: 9
Published: about 5 years ago

10.18632/aging.103508

Radiomics-based prediction of survival in patients with head and neck squamous cell carcinoma based on pre- and post-treatment 18F-PET/CT
Cited by: 26
Author(s): Zheran Liu, Yuan Cao, Wei Diao, Yue Cheng, Zhiyun Jia, Xingchen Peng
Software Mentions: 9
Published: almost 6 years ago

10.3389/fmicb.2020.01398

Microbiome Shifts Associated With the Introduction of Wild Atlantic Horseshoe Crabs (Limulus polyphemus) Into a Touch-Tank Exhibit
Cited by: 9
Author(s): Ariel D. Friel, Sean A. Neiswenter, Cale O. Seymour, Lauren Rose Bali, Ginger McNamara, Fabian Leija, Jack Jewell, Brian P. Hedlund
Software Mentions: 9
Published: almost 6 years ago

10.7717/peerj.2562

Beech cupules as keystone structures for soil fauna
Cited by: 7
Author(s): Nereida Melguizo‐Ruiz, Gerardo Jiménez‐Navarro, Jordi Moya‐Laraño
Software Mentions: 9
Published: over 9 years ago

10.1186/gb-2014-15-3-r47

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines
Cited by: 571
Author(s): Paul Geeleher, Nancy J. Cox, R. Stephanie Huang
Software Mentions: 9
Published: over 12 years ago

10.1371/journal.pone.0193164

Mosquito pornoscopy: Observation and interruption of Aedes aegypti copulation to determine female polyandric event and mixed progeny
Cited by: 10
Author(s): Danilo O. Carvalho, Samira Chuffi, Rafaella Sayuri Ioshino, I. C. S. Marques, Regina Fini, Maria Karina Costa, Helena Rocha Corrêa de Araújo, André Luis Costa-da-Silva, Bianca Burini Kojin, Margareth Lara Capurro
Software Mentions: 9
Published: over 8 years ago

10.18632/aging.203455

Construction of an immune-related lncRNA signature as a novel prognosis biomarker for LUAD
Cited by: 9
Author(s): Hang Chen, Wei Shen, Saiqi Ni, Menglu Sang, Shibo Wu, Yinyu Mu, Kaitai Liu, Ni Li, Linwen Zhu, Guodong Xu
Software Mentions: 9
Published: almost 5 years ago

10.3389/fimmu.2021.709173

The Role of Hemoglobin Subunit Delta in the Immunopathy of Multiple Sclerosis: Mitochondria Matters
Cited by: 6
Author(s): Afshin Derakhshani, Hossein Safarpour, Behzad Baradaran, Nima Hemmat, Patrizia Leone, Zahra Asadzadeh, Mehrdad Pashazadeh, Behzad Baradaran, Vito Racanelli
Software Mentions: 9
Published: almost 5 years ago

10.1186/1752-0509-7-125

sybil – Efficient constraint-based modelling in R
Cited by: 105
Author(s): Gabriel Gelius-Dietrich, Abdelmoneim Amer Desouki, Claus Jonathan Fritzemeier, Martin J. Lercher
Software Mentions: 9
Published: over 12 years ago

10.3390/insects12070646

Are There Personality Differences between Rural vs. Urban-Living Individuals of a Specialist Ground Beetle, Carabus convexus?
Cited by: 10
Author(s): Tibor Magura, Szabolcs Mizser, Roland Horváth, D Nagy, Mária Tóth, Réka Csicsek, Gábor L. Löveï
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-021-88943-9

Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages
Cited by: 17
Author(s): Ankit T. Hinsu, Nilam J. Tulsani, Ketankumar Panchal, Ramesh Pandit, Basanti Jyotsana, Nishant A. Dafale, N. B. Patil, Hemant J. Purohit, Chaitanya Joshi, Subhash J. Jakhesara
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-018-30701-5

Electrophysiological correlates of the interplay between low-level visual features and emotional content during word reading
Cited by: 22
Author(s): Sebastian Schindler, Antonio Schettino, Gilles Pourtois
Software Mentions: 9
Published: almost 8 years ago

10.1186/s13059-018-1596-9

Comparison of computational methods for the identification of topologically associating domains
Cited by: 155
Author(s): Marie Zufferey, Daniele Tavernari, Elisa Oricchio, Giovanni Ciriello
Software Mentions: 9
Published: over 7 years ago

10.1371/journal.pcbi.1009064

coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data
Cited by: 7
Author(s): Pengcheng Zeng, Zhixiang Lin
Software Mentions: 9
Published: about 5 years ago

10.1186/s13071-016-1916-4

Circulation of Dirofilaria repens and Dirofilaria immitis in Moldova
Cited by: 25
Author(s): Tatiana Șuleșco, Heidrun von Thien, Lidia Toderaș, Ion Toderaş, Renke Lühken, Egbert Tannich
Software Mentions: 9
Published: over 9 years ago

10.1098/rsos.160815

Concurrence in the ability for lipid synthesis between life stages in insects
Cited by: 20
Author(s): Bertanne Visser, Denis S. Willett, Jeffrey A. Harvey, Hans T. Alborn
Software Mentions: 9
Published: over 9 years ago

10.3390/ijerph17197127

Relationship between Quality of Life and the Complexity of Default Mode Network in Resting State Functional Magnetic Resonance Image in Down Syndrome
Cited by: 6
Author(s): María Carbó‐Carreté, Cristina Cañete‐Massé, María Dolores Figueroa-Jiménez, Maribel Peró‐Cebollero, Joan Guàrdia‐Olmos
Software Mentions: 9
Published: over 5 years ago

10.1002/1878-0261.12595

Aberrant expression of RSK1 characterizes high‐grade gliomas with immune infiltration
Cited by: 14
Author(s): Glaucia Noeli Maroso Hajj, Fernanda F. da Silva, Bárbara de Bellis, Fernanda C. S. Lupinacci, Hermano Martins Bellato, Juvanier R. Cruz, Claudionor Nogueira Costa Segundo, Igor Vilela Faquini, Leuridan Cavalcante Torres, Paulo Sanematsu, María Dirlei Begnami, Vilma R. Martins, Martín Roffé
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0222547

Endothelial dysfunction and low-grade inflammation in the transition to renal replacement therapy
Cited by: 13
Author(s): April C.E. van Gennip, Natascha J. H. Broers, Karlien J. ter Meulen, Bernard Canaud, Maarten H. L. Christiaans, T. Cornelis, M. Gelens, Marc Hermans, Constantijn Konings, Jeroen B. van der Net, Frank M. van der Sande, Casper G. Schalkwijk, Frank Stifft, Joris J. J. M. Wirtz, Jeroen P. Kooman, Remy J H Martens
Software Mentions: 9
Published: almost 7 years ago

10.1186/s12864-021-07995-3

Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris)
Cited by: 4
Author(s): Oscar E. Ospina, Alan R. Lemmon, Mysia Dye, Christopher Zdyrski, Sean Holland, Daniel Stribling, Michelle L Kortyna, Emily Moriarty Lemmon
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.ppat.1009459

Specialized 16SrX phytoplasmas induce diverse morphological and physiological changes in their respective fruit crops
Cited by: 9
Author(s): Jannicke Gallinger, Kerstin Zikeli, Matthias R. Zimmermann, Louisa Görg, Axel Mithöfer, Michael Reichelt, E. Seemüller, Jürgen Gross, Alexandra C. U. Furch
Software Mentions: 9
Published: over 5 years ago

10.18632/aging.103204

Comparison of prognostic prediction models for rectal gastrointestinal stromal tumor
Cited by: 2
Author(s): Jiaxin Liu, Pei‐Yun Zhou, Zheng Tang, Wei Yuan, Shen Shanshan, Ren Lang, Xing Zhengwen, Yong Fang, Xiaodong Gao, Anwei Xue, Kuntang Shen, Yayi Hou
Software Mentions: 9
Published: about 6 years ago

10.3389/fmicb.2018.02571

PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method
Cited by: 97
Author(s): Yi Xiong, Qiankun Wang, Junchen Yang, Xiaolei Zhu, Dong‐Qing Wei
Software Mentions: 9
Published: over 7 years ago

10.3389/fdata.2020.00015

Improving Diagnosis of Depression With XGBOOST Machine Learning Model and a Large Biomarkers Dutch Dataset (n = 11,081)
Cited by: 42
Author(s): Amita Sharma, W. Verbeke
Software Mentions: 9
Published: about 6 years ago

10.1371/journal.pone.0190195

Additional statistical and graphical methods for analyzing site formation processes using artifact orientations
Cited by: 39
Author(s): Shannon P. McPherron
Software Mentions: 9
Published: over 8 years ago

10.1038/s41598-017-13506-w

Associations of interactions between NLRP3 SNPs and HLA mismatch with acute and extensive chronic graft-versus-host diseases
Cited by: 15
Author(s): Hidekazu Takahashi, Naoko Okayama, Natsu Yamaguchi, Yuta Miyahara, Yasuo Morishima, Yutaka Suehiro, Takahiro Yamasaki, Koji Tamada, Satoshi Takahashi, Arinobu Tojo, Shigetaka Asano, Tsuyoshi Tanabe
Software Mentions: 9
Published: over 8 years ago

10.1155/2021/9911184

Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis
Cited by: 7
Author(s): Fei Sun, Jian Zhou, Peiyu Pu, Chen Qiu, Jia rui Cao, Hao Peng
Software Mentions: 9
Published: about 5 years ago

10.1186/s40168-021-01089-8

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
Cited by: 28
Author(s): Alexander S. F. Berry, Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, Kevin T. O’Brien, Ying Chen, Samuel Murray, Lydia A. Ramharack, Robert N. Baldassano, Thomas D. Parsons, Daniel P. Beiting
Software Mentions: 9
Published: almost 5 years ago

10.3389/fgene.2014.00324

Statistical methods for detecting differentially methylated loci and regions
Cited by: 90
Author(s): Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Małgorzata Nowicka, Lukas M. Weber, Xiaobei Zhou
Software Mentions: 9
Published: almost 12 years ago

10.1093/jamiaopen/ooy059

ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data
Cited by: 12
Author(s): Benjamin S. Glicksberg, Boris Oskotsky, Nicholas Giangreco, Phyllis Thangaraj, Vivek Rudrapatna, Debajyoti Datta, Remi Frazier, Nelson Lee, Rick Larsen, Nicholas P. Tatonetti, Atul J. Butte
Software Mentions: 9
Published: over 7 years ago

10.1038/s41598-018-24454-4

The unique functioning of a pre-Columbian Amazonian floodplain fishery
Cited by: 29
Author(s): Rumsaïs Blatrix, Bruno Roux, Philippe Béarez, Gabriela Prestes-Carneiro, Marcelo Amaya, José Luis Aramayo, Leonor Rodrigues, Umberto Lombardo, José Iriarte, Jonas Gregório de Souza, Mark Robinson, Cyril Bernard, Marc Pouilly, Mélisse Durécu, Carl F. Huchzermeyer, Mashuta Kalebe, Alex Ovando, Doyle McKey
Software Mentions: 9
Published: about 8 years ago

10.1371/journal.pone.0071476

Sleepless in Town – Drivers of the Temporal Shift in Dawn Song in Urban European Blackbirds
Cited by: 90
Author(s): Anja Nordt, Reinhard Klenke
Software Mentions: 9
Published: almost 13 years ago

10.1038/s41598-021-85639-y

African soil properties and nutrients mapped at 30 m spatial resolution using two-scale ensemble machine learning
Cited by: 79
Author(s): Tomislav Hengl, Matthew A. E. Miller, Josip Križan, Keith D. Shepherd, Andrew Sila, Milan Kilibarda, Ognjen Antonijević, Luka Glušica, A. Dobermann, Stephan M. Haefele, Steve P. McGrath, Gifty E. Acquah, Jamie Collinson, Leandro Parente, Mohammadreza Sheykhmousa, Kazuki Saito, Jean‐Martial Johnson, Jordan Chamberlin, Francis B. T. Silatsa, Martin Yemefack, John Wendt, R.A. MacMillan, Ichsani Wheeler, Jonathan H. Crouch
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2021.623424

Correlations Between Tumor Mutation Burden and Immunocyte Infiltration and Their Prognostic Value in Colon Cancer
Cited by: 17
Author(s): Zhangjian Zhou, Xin Xie, Xuan Wang, Xin Zhang, Wenxin Li, Tuanhe Sun, Yifan Cai, Jianhua Wu, Chengxue Dang, Hao Zhang
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2020.578895

Radiomics Feature Activation Maps as a New Tool for Signature Interpretability
Cited by: 17
Author(s): Diem Vuong, Stephanie Tanadini‐Lang, Ze Wu, Robert J. Marks, Jan Unkelbach, Sven Hillinger, Eric Innocents Eboulet, Sandra Thierstein, Solange Peters, Miklos Pless, Matthias Gückenberger, Marta Bogowicz
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2021.610291

RNA-Binding Proteins Play an Important Role in the Prognosis of Patients With Testicular Germ Cell Tumor
Cited by: 7
Author(s): Liangyu Yao, Rong Cong, Chengjian Ji, Xiang Zhou, Jiaochen Luan, Xuhui Meng, Ninghong Song
Software Mentions: 9
Published: over 5 years ago

10.1186/s13073-020-00731-8

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Cited by: 28
Author(s): Anna Reustle, Moreno Di Marco, Carolin Meyerhoff, Annika Nelde, Juliane S. Walz, Stefan Winter, Siahei Kandabarau, Florian Büttner, Mathias Haag, Linus Backert, Daniel J. Kowalewski, Steffen Rausch, Jörg Hennenlotter, Viktoria Stühler, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Hans‐Georg Rammensee, Jens Bedke, Stefan Stevanović, Matthias Schwab, Elke Schaeffeler
Software Mentions: 9
Published: about 6 years ago

10.1371/journal.pbio.3001365

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Cited by: 34
Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Software Mentions: 9
Published: almost 5 years ago

10.1172/jci.insight.140443

Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung
Cited by: 6
Author(s): Maria Llamazares Prada, Elisa Espinet, Vedrana Mijošek, Uwe Schwartz, Pavlo Lutsik, Raluca Tamas, Mandy Richter, Annika Behrendt, Stephanie Pohl, Naja P. Benz, Thomas Muley, Arne Warth, Claus Peter Heusel, Hauke Winter, Jonathan Landry, Felix J.F. Herth, Tinne Mertens, Harry Karmouty‐Quintana, Ina Koch, Vladimı́r Beneš, Jan O. Korbel, Sebastian M. Waszak, Andreas Trumpp, David Wyatt, Heiko Stahl, Christoph Plass, Renata Z. Jurkowska
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-019-2799-0

FastqPuri: high-performance preprocessing of RNA-seq data
Cited by: 22
Author(s): Paula Pérez-Rubio, Claudio Lottaz, Julia C. Engelmann
Software Mentions: 9
Published: about 7 years ago

10.1038/s41598-017-15525-z

Single-cell Co-expression Subnetwork Analysis
Cited by: 20
Author(s): Thomas E. Bartlett, Sören Müller, Aaron A. Diaz
Software Mentions: 9
Published: over 8 years ago

10.1208/s12249-020-01660-w

Data-Driven Modeling of the Bicalutamide Dissolution from Powder Systems
Cited by: 9
Author(s): Aleksander Mendyk, Adam Pacławski, Joanna Szafraniec-Szczęsny, Agata Antosik, Witold Jamróz, Marian Paluch, Renata Jachowicz
Software Mentions: 9
Published: about 6 years ago

10.1038/s41422-021-00562-1

Distinct immune signatures discriminate between asymptomatic and presymptomatic SARS-CoV-2pos subjects
Cited by: 8
Author(s): Shanhe Yu, Caixia Di, Shijun Chen, Mingquan Guo, Jiayang Yan, Zhaoqin Zhu, Li Liu, Rilu Feng, Yinyin Xie, Ruihong Zhang, Juan Chen, Mengxi Wang, Dong Wei, Hai Fang, Tong Yin, Jinyan Huang, Sai‐Juan Chen, Hongzhou Lu, Jiang Zhu, Jieming Qu
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-021-95185-2

The food patterns of a multicenter cohort of Brazilian nulliparous pregnant women
Cited by: 3
Author(s): Maria J Miele, Renato Teixeira Souza, Iracema de Mattos Paranhos Calderon, Francisco Edson de Lucena Feitosa, Débora Farias Batista Leite, Edilberto A. Rocha Filho, Janete Vettorazzi, Jussara Mayrink, Karayna Gil Fernandes, Matias C. Vieira, Rodolfo C. Pacagnella, José Guilherme Cecatti
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13059-020-02083-3

DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning
Cited by: 23
Author(s): Yong He, Hao Yuan, Changbao Wu, Zhi Xie
Software Mentions: 9
Published: almost 6 years ago

10.15252/msb.20199389

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Cited by: 63
Author(s): Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, T. P. Speed, David M. Lin, Pengyi Yang, Jean Yee Hwa Yang
Software Mentions: 9
Published: about 6 years ago

10.3390/ijerph18010318

Mapping the Scientific Landscape of Diabetes Research in Malaysia (2000–2018): A Systematic Scientometrics Study
Cited by: 5
Author(s): Kurubaran Ganasegeran, Chee Peng Hor, Mohd Fadzly Amar Jamil, Purnima Devi Suppiah, Juliana Mohd Noor, Norshahida Abdul Hamid, Deik Roy Chuan, Mohd Rizal Abdul Manaf, Alan Swee Hock Ch’ng, Irene Looi
Software Mentions: 9
Published: over 5 years ago

10.1264/jsme2.ME18109

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields
Cited by: 33
Author(s): Turgut Yiğit Akyol, Rieko Niwa, Hideki Hirakawa, Hayato Maruyama, Takumi Sato, Takae Suzuki, Ayako Fukunaga, Takashi Sato, Shigenobu Yoshida, Keitaro Tawaraya, Masanori Saitô, Tatsuhiro Ezawa, Shusei Sato
Software Mentions: 9
Published: over 7 years ago

10.1093/jamia/ocab068

Stroke risk prediction using machine learning: a prospective cohort study of 0.5 million Chinese adults
Cited by: 26
Author(s): Matthew Chun, Robert Clarke, Benjamin J. Cairns, David A. Clifton, Derrick Bennett, Yiping Chen, Yu Guo, Pei Pei, Jun Lv, Canqing Yu, Ling Yang, Liming Li, Zhengming Chen, Tingting Zhu
Software Mentions: 9
Published: about 5 years ago

10.1038/s42003-018-0199-z

Improved reference genome for the domestic horse increases assembly contiguity and composition
Cited by: 137
Author(s): Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris Vermeesch, Brendan O’Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E. McCue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Edward Green, Donald C. Miller, Douglas F. Antczak, James N. MacLeod
Software Mentions: 9
Published: over 7 years ago

10.1186/s12859-015-0537-9

A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates
Cited by: 6
Author(s): Maud Tournoud, Audrey Larue, Marie-Angélique Cazalis, Fabienne Venet, Alexandre Pachot, Guillaume Monneret, Alain Lepape, Jean‐Baptiste Veyrieras
Software Mentions: 9
Published: about 11 years ago

10.1371/journal.pcbi.1009029

G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Cited by: 7
Author(s): Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang
Software Mentions: 9
Published: about 5 years ago

10.3389/fgene.2019.00880

LINC00460 Hypomethylation Promotes Metastasis in Colorectal Carcinoma
Cited by: 15
Author(s): Hui Zhang, Ya Lu, Jianzhong Wu, Jifeng Feng
Software Mentions: 9
Published: over 6 years ago

10.3390/ijms22042214

How Are the Flower Structure and Nectar Composition of the Generalistic Orchid Neottia ovata Adapted to a Wide Range of Pollinators?
Cited by: 8
Author(s): Emilia Brzosko, Andrzej Bajguz, Magdalena Chmur, Justyna Burzyńska, Edyta Jermakowicz, Paweł Mirski, Piotr Zieliński
Software Mentions: 9
Published: over 5 years ago

10.1186/s12864-016-2886-9

OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis
Cited by: 32
Author(s): Alfredo Rago, Donald G. Gilbert, Jeong Hyeon Choi, Timothy B. Sackton, Xiaozhu Wang, Yogeshwar D. Kelkar, John H. Werren, John K. Colbourne
Software Mentions: 9
Published: almost 10 years ago

10.1186/s13059-020-02165-2

iMOKA: k-mer based software to analyze large collections of sequencing data
Cited by: 6
Author(s): Claudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron, William Ritchie
Software Mentions: 9
Published: over 5 years ago