Ecosyste.ms: Papers

10.1093/bioinformatics/btab039

mlr3proba: an R package for machine learning in survival analysis
Cited by: 38
Author(s): Raphael Sonabend, Franz J. Király, Andreas Bender, Bernd Bischl, Michel Lang
Software Mentions: 18
Published: almost 4 years ago

10.7554/eLife.55913

An image-based data-driven analysis of cellular architecture in a developing tissue
Cited by: 22
Author(s): Jonas Hartmann, Mie Wong, Elisa Cristina de Proença Rodrigues Gallo, Darren Gilmour
Software Mentions: 14
Published: over 4 years ago

10.1002/cam4.4092

Gene signatures predict biochemical recurrence‐free survival in primary prostate cancer patients after radical therapy
Cited by: 6
Author(s): Qiang Su, Zhenyu Liu, Chi Chen, Han Gao, Yongbei Zhu, Liusu Wang, Meiqing Pan, Jiangang Liu, Xin Yang, Jie Tian
Software Mentions: 12
Published: over 3 years ago

10.1093/molbev/msaa128

Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
Cited by: 25
Author(s): Xavier Grau‐Bové, Sean Tomlinson, Andrias O. O’Reilly, Nicholas J. Harding, Alistair Miles, Dominic Kwiatkowski, Martin Donnelly, David Weetman
Software Mentions: 12
Published: over 4 years ago

10.3390/ani11072131

Predicting Subclinical Ketosis in Dairy Cows Using Machine Learning Techniques
Cited by: 7
Author(s): Alicja Satoła, Edyta Bauer
Software Mentions: 12
Published: over 3 years ago

10.1371/journal.pcbi.1009136

Multidimensional analysis and detection of informative features in human brain white matter
Cited by: 14
Author(s): Adam Richie-Halford, Jason D. Yeatman, Noah Simon, Ariel Rokem
Software Mentions: 12
Published: over 3 years ago

10.15252/msb.20209522

Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma
Cited by: 19
Author(s): Samantha O'Connor, Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey J. Delrow, José L. McFaline-Figueroa, Cole Trapnell, Steven M. Pollard, Anoop P. Patel, Patrick J. Paddison, Christopher Plaisier
Software Mentions: 10
Published: over 3 years ago

10.3389/fnins.2019.00494

Automated, Efficient, and Accelerated Knowledge Modeling of the Cognitive Neuroimaging Literature Using the ATHENA Toolkit
Cited by: 6
Author(s): Michael C. Riedel, Taylor Salo, Jason Hays, Matthew D. Turner, Matthew T. Sutherland, Jessica A. Turner, Angela R. Laird
Software Mentions: 10
Published: over 5 years ago

10.1002/ece3.6594

A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
Cited by: 36
Author(s): Devon O’Rourke, Nicholas A. Bokulich, Michelle A. Jusino, Matthew D. MacManes, Jeffrey T. Foster
Software Mentions: 10
Published: over 4 years ago

10.3389/fcimb.2020.00137

Microbiotyping the Sinonasal Microbiome
Cited by: 15
Author(s): Ahmed Bassiouni, S. Paramasivan, Arron Shiffer, Matthew R. Dillon, Emily K. Cope, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis, Mohammad Javed Ali, Benjamin S. Bleier, Claudio Callejas, Marjolein Cornet, Richard Douglas, Daniel Lorena Dutra, Christos Georgalas, Richard J. Harvey, Peter H. Hwang, Amber U. Luong, Rodney J. Schlosser, Pongsakorn Tantilipikorn, Marc A. Tewfik, Sarah Vreugde, Peter John Wormald, J. Gregory Caporaso, Alkis James Psaltis
Software Mentions: 9
Published: over 4 years ago

10.26508/lsa.202000757

multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
Cited by: 16
Author(s): Aditya Bhagwat, Johannes Graumann, René Wiegandt, Mette Bentsen, Jordan M. Welker, Carsten Kuenne, Jens Preussner, Thomas Braun, Mario Looso
Software Mentions: 9
Published: over 4 years ago

10.3389/fimmu.2021.592303

Machine Learning Identifies Complicated Sepsis Course and Subsequent Mortality Based on 20 Genes in Peripheral Blood Immune Cells at 24 H Post-ICU Admission
Cited by: 35
Author(s): Shayantan Banerjee, Akram Mohammed, Hector R. Wong, Nades Palaniyar, Rishikesan Kamaleswaran
Software Mentions: 9
Published: almost 4 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: over 3 years ago

10.15252/msb.20209667

Using single‐plant‐omics in the field to link maize genes to functions and phenotypes
Cited by: 17
Author(s): Daniel Felipe Cruz, Sam Meyer, Joke Ampe, Heike Sprenger, Dorota Herman, Tom Van Hautegem, Jolien De Block, Dirk Inzé, Hilde Nelissen, Steven Maere
Software Mentions: 8
Published: about 4 years ago

10.3389/fgene.2021.651812

MRPC: An R Package for Inference of Causal Graphs
Cited by: 2
Author(s): Md. Bahadur Badsha, Evan A Martin, Audrey Qiuyan Fu
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-021-04126-3

Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources
Cited by: 6
Author(s): Neel Patel, William S. Bush
Software Mentions: 7
Published: over 3 years ago

10.3390/nu11123045

Nutrient Estimation from 24-Hour Food Recalls Using Machine Learning and Database Mapping: A Case Study with Lactose
Cited by: 20
Author(s): Elizabeth Chin, Gabriel Simmons, Yasmine Bouzid, Annie Kan, D. D. Burnett, Ilias Tagkopoulos, Danielle G. Lemay
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pcbi.1007553

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes
Cited by: 18
Author(s): David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2021.665849

Decisive Effects of Life Stage on the Gut Microbiota Discrepancy Between Two Wild Populations of Hibernating Asiatic Toads (Bufo gargarizans)
Cited by: 3
Author(s): Xuehang Song, Jingwei Zhang, Jinghan Song, Yuanyuan Zhai
Software Mentions: 6
Published: over 3 years ago

10.3390/brainsci10110851

Functional and Structural Connectome Features for Machine Learning Chemo-Brain Prediction in Women Treated for Breast Cancer with Chemotherapy
Cited by: 4
Author(s): Vincent Chin‐Hung Chen, Tung-Yeh Lin, Dah-Cherng Yeh, Jyh‐Wen Chai, Jun‐Cheng Weng
Software Mentions: 6
Published: about 4 years ago

10.1016/j.cell.2016.09.027

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells
Cited by: 620
Author(s): Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Saltó, Amit Zeisel, Lars E. Borm, Simon Stott, Enrique M. Toledo, J. Carlos Villaescusa, Peter Lönnerberg, Jesper Ryge, Roger A. Barker, Ernest Arenas, Sten Linnarsson
Software Mentions: 6
Published: about 8 years ago

10.15252/emmm.202013257

Urinary proteome profiling for stratifying patients with familial Parkinson’s disease
Cited by: 66
Author(s): Sebastian Virreira Winter, Özge Karayel, Mike Strauss, Shalini Padmanabhan, Matthew Surface, Kalpana Merchant, Matthias Mann
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12933-019-0879-0

Machine-learning to stratify diabetic patients using novel cardiac biomarkers and integrative genomics
Cited by: 45
Author(s): Quincy A. Hathaway, Skyler M. Roth, Mark V. Pinti, Daniel C. Sprando, Amina Kunovac, Andrya J. Durr, Chris C. Cook, Garrett K. Fink, Tristen B. Cheuvront, Jasmine H. Grossman, Ghadah A. Aljahli, Andrew Taylor, Andrew Giromini, Jessica L. Allen, John M. Hollander
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-90335-y

Whole brain functional recordings at cellular resolution in zebrafish larvae with 3D scanning multiphoton microscopy
Cited by: 15
Author(s): Matteo Bruzzone, Enrico Chiarello, Marco Albanesi, Maria Elena Miletto Petrazzini, Aram Megighian, Claudia Lodovichi, Marco Dal Maschio
Software Mentions: 6
Published: over 3 years ago

10.15252/msb.20198871

Paralog dependency indirectly affects the robustness of human cells
Cited by: 40
Author(s): Rohan Dandage, Christian R. Landry
Software Mentions: 6
Published: over 5 years ago

10.1186/s12911-017-0518-1

Word2Vec inversion and traditional text classifiers for phenotyping lupus
Cited by: 49
Author(s): Clayton A. Turner, Alexander Jacobs, Cassios K. Marques, Jim C. Oates, Diane L. Kamen, Paul E. Anderson, Jihad S. Obeid
Software Mentions: 6
Published: over 7 years ago

10.1002/minf.202000005

Using Machine Learning Methods and Structural Alerts for Prediction of Mitochondrial Toxicity
Cited by: 30
Author(s): Jennifer Hemmerich, Florentina Troger, Barbara Füzi, Gerhard Ecker
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2020.596589

The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession
Cited by: 24
Author(s): Stacey J. Doherty, Robyn A. Barbato, A. Stuart Grandy, W. Kelley Thomas, Sylvain Monteux, Ellen Dorrepaal, Margareta Johansson, Jessica G. Ernakovich
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0144820

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data
Cited by: 2
Author(s): Ryan Bressler, Richard Kreisberg, Brady Bernard, John E. Niederhuber, Joseph G. Vockley, Ilya Shmulevich, Theo Knijnenburg
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0204920

Predicting acute kidney injury at hospital re-entry using high-dimensional electronic health record data
Cited by: 8
Author(s): Samuel J. Weisenthal, Caroline M. Quill, Samir A. Farooq, Henry Kautz, Martin S. Zand
Software Mentions: 5
Published: about 6 years ago

10.1039/d0sc04263c

One class classification as a practical approach for accelerating π–π co-crystal discovery
Cited by: 12
Author(s): Aikaterini Vriza, Angelos B. Canaj, Rebecca Vismara, Laurence J. Kershaw Cook, Troy D. Manning, Michael W. Gaultois, Peter A. Wood, Vitaliy Kurlin, Neil G. Berry, Matthew S. Dyer, Matthew J. Rosseinsky
Software Mentions: 5
Published: almost 4 years ago

10.1128/mSystems.00093-19

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry
Cited by: 14
Author(s): Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon, Willem Waegeman, Vincent J. Denef
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-88939-5

GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds
Cited by: 6
Author(s): Marawan Ahmed, Horia Jalily Hasani, Subha Kalyaanamoorthy, Khaled Barakat
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms21197281

SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features
Cited by: 10
Author(s): António Preto, Irina S. Moreira
Software Mentions: 5
Published: about 4 years ago

10.3390/microorganisms8010134

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota
Cited by: 34
Author(s): Rodrigo García-López, Fernanda Cornejo‐Granados, Alonso A. López-Zavala, Filiberto Sánchez-López, Andrés Cota-Huízar, Rogerio R. Sotelo‐Mundo, Abraham Guerrero, Alfredo Mendoza-Vargas, Bruno Gómez‐Gil, Adrián Ochoa-Leyva
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13321-017-0232-0

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set
Cited by: 207
Author(s): Eelke B. Lenselink, Niels ten Dijke, Brandon J. Bongers, George Papadatos, Herman van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, Gerard J. P. van Westen
Software Mentions: 5
Published: over 7 years ago

10.15252/msb.202010138

Natural variants suppress mutations in hundreds of essential genes
Cited by: 10
Author(s): Leopold Parts, Amandine Batté, Maykel Lopes, Michael Wai-Keong Yuen, Meredith Laver, Bryan-Joseph San Luis, Jia-Xing Yue, Carles Pons, Elise Eray, Patrick Aloy, Gianni Liti, Jolanda van Leeuwen
Software Mentions: 5
Published: over 3 years ago

10.15252/msb.20167490

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
Cited by: 163
Author(s): Kevin Drew, Chanjae Lee, Ryan L. Huizar, Fan Tu, Blake Borgeson, Claire D. McWhite, Yun Ma, John B. Wallingford, Edward M. Marcotte
Software Mentions: 5
Published: over 7 years ago

10.15252/msb.20199270

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance
Cited by: 22
Author(s): Stephan Kamrad, Jan Großbach, María Rodríguez-López, Michael Mülleder, StJohn Townsend, Valentina Cappelletti, Gorjan Stojanovski, Clara Correia‐Melo, Paola Picotti, Andreas Beyer, Markus Ralser, Jürg Bähler
Software Mentions: 5
Published: over 4 years ago

10.1002/hbm.25368

Brain age prediction: A comparison between machine learning models using region‐ and voxel‐based morphometric data
Cited by: 52
Author(s): Lea Baecker, Jessica Dafflon, Pedro F. da Costa, Rafael Garcia‐Dias, Sandra Vieira, Cristina Scarpazza, Vince D. Calhoun, João Ricardo Sato, Andrea Mechelli, Walter Hugo Lopez Pinaya
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-021-02294-2

seqQscorer: automated quality control of next-generation sequencing data using machine learning
Cited by: 9
Author(s): Steffen Albrecht, Maximilian Sprang, Miguel A. Andrade‐Navarro, Jean-Fred Fontaine
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0234908

Machine learning and natural language processing methods to identify ischemic stroke, acuity and location from radiology reports
Cited by: 59
Author(s): Charlene Ong, Agni Orfanoudaki, Rebecca Zhang, Francois Pierre M. Caprasse, Meghan R. Hutch, Liang Ma, Darian Fard, Oluwafemi Balogun, Matthew Miller, Margaret A. Minnig, Hanife Saglam, Brenton Prescott, David M. Greer, Stelios M. Smirnakis, Dimitris Bertsimas
Software Mentions: 5
Published: over 4 years ago

10.3390/s21082728

Virtual Sensing and Sensors Selection for Efficient Temperature Monitoring in Indoor Environments
Cited by: 13
Author(s): Andrea Brunello, Andrea Urgolo, Federico Pittino, András Montvay, Angelo Montanari
Software Mentions: 4
Published: over 3 years ago

10.1002/aps3.1238

Phenotypic variation of cassava root traits and their responses to drought
Cited by: 27
Author(s): Jitrana Kengkanna, Phissinee Jakaew, Suwaluk Amawan, Natalie Busener, Alexander Bucksch, Patompong Saengwilai
Software Mentions: 4
Published: over 5 years ago

10.1101/2021.03.17.435863

Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies
Cited by: 31
Author(s): Allison J Greaney, Tyler N Starr, Christopher O. Barnes, Yiska Weisblum, Fabian Schmidt, Marina Caskey, Christian Gaebler, Alice Cho, Marianna Agudelo, Shlomo Finkin, Zijun Wang, Daniel Poston, Frauke Muecksch, Théodora Hatziioannou, Paul D. Bieniasz, Davide F. Robbiani, Michel C. Nussenzweig, Pamela J. Björkman, Jesse D. Bloom
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-39142-0

Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning
Cited by: 30
Author(s): Aidan O’Brien, Laurence O.W. Wilson, Gaétan Burgio, Denis C. Bauer
Software Mentions: 4
Published: almost 6 years ago

10.1002/advs.201902862

Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression
Cited by: 75
Author(s): Peng Zheng, Jian Yang, Yifan Li, Jing Wu, Weiwei Liang, Bangmin Yin, Xunmin Tan, Yu Huang, Tingjia Chai, Hanping Zhang, Jiajia Duan, Jingjing Zhou, Zuoli Sun, Chen Xu, Subhi Marwari, Jianbo Lai, Tingting Huang, Yanli Du, Peifen Zhang, Seth W. Perry, Ma‐Li Wong, Júlio Licinio, Shaohua Hu, Peng Xie, Gang Wang
Software Mentions: 4
Published: almost 5 years ago

10.3389/fncom.2020.580632

DNNBrain: A Unifying Toolbox for Mapping Deep Neural Networks and Brains
Cited by: 11
Author(s): Xiayu Chen, Ming Zhou, Zhengxin Gong, Wei Xu, Xingyu Liu, Taicheng Huang, Zonglei Zhen, Jia Liu
Software Mentions: 4
Published: about 4 years ago

10.15252/msb.20199356

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease
Cited by: 129
Author(s): Jakob Bader, Philipp E. Geyer, Johannes B. Müller-Reif, Maximilian T. Strauss, Manja Koch, Frank Leypoldt, Pèter Köertvelyessy, Daniel Bittner, Carola G. Schipke, Enise I. Incesoy, Oliver Peters, Nikolaus Deigendesch, Mikael Simons, Majken K. Jensen, Henrik Zetterberg, Matthias Mann
Software Mentions: 4
Published: over 4 years ago

10.1111/tpj.14312

μ<scp>CT</scp> trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives
Cited by: 19
Author(s): Nathan Hughes, Hugo R. Oliveira, Nick Fradgley, Fiona Corke, James Cockram, John H. Doonan, Cândida Nibau
Software Mentions: 4
Published: over 5 years ago

10.1002/hbm.25144

High‐density intracranial recordings reveal a distinct site in anterior dorsal precentral cortex that tracks perceived speech
Cited by: 10
Author(s): Julia Berezutskaya, Clarissa Baratin, Zachary V. Freudenburg, N.F. Ramsey
Software Mentions: 4
Published: over 4 years ago

10.1111/jcmm.15441

Molecular classification and immunologic characteristics of immunoreactive high‐grade serous ovarian cancer
Cited by: 1
Author(s): Zheran Liu, Huimeng Wu, Jiachen Deng, Haoqing Wang, Zixuan Wang, An‐Gang Yang, Bowen Liang, Ji Luo, Jianyong Li, Ye Xu, Xiaoli Tang, Fang Fu, Libin Deng
Software Mentions: 4
Published: over 4 years ago

10.3390/s17010066

A Comparison Study of Classifier Algorithms for Cross-Person Physical Activity Recognition
Cited by: 29
Author(s): Yago Sáez, Alejandro Baldominos, Pedro Isasi
Software Mentions: 4
Published: almost 8 years ago

10.3390/s20174940

Application of Convolutional Neural Network-Based Feature Extraction and Data Fusion for Geographical Origin Identification of Radix Astragali by Visible/Short-Wave Near-Infrared and Near Infrared Hyperspectral Imaging
Cited by: 19
Author(s): Qinlin Xiao, Xiulin Bai, Pan Gao, Yong He
Software Mentions: 4
Published: over 4 years ago

10.3390/s21175896

Enhanced Changeover Detection in Industry 4.0 Environments with Machine Learning
Cited by: 4
Author(s): Eddi Miller, Vladyslav Borysenko, Moritz Heusinger, Niklas Niedner, Bastian Engelmann, Jan Schmitt
Software Mentions: 3
Published: over 3 years ago

10.1002/aps3.11380

Digitally deconstructing leaves in 3D using X‐ray microcomputed tomography and machine learning
Cited by: 20
Author(s): Guillaume Théroux‐Rancourt, Matthew R. Jenkins, Craig R. Brodersen, Andrew J. McElrone, Elisabeth J. Forrestel, J. Mason Earles
Software Mentions: 3
Published: over 4 years ago

10.1186/s13062-019-0257-6

Diverse approaches to predicting drug-induced liver injury using gene-expression profiles
Cited by: 18
Author(s): G Rex Sumsion, Michael S. Bradshaw, Jeremy Beales, Emi Ford, Griffin R. G. Caryotakis, Daniel J. Garrett, Emily D. LeBaron, Ifeanyichukwu O. Nwosu, Stephen R. Piccolo
Software Mentions: 3
Published: almost 5 years ago

10.3390/bios9010029

Differentiation of Patients with Balance Insufficiency (Vestibular Hypofunction) versus Normal Subjects Using a Low-Cost Small Wireless Wearable Gait Sensor
Cited by: 9
Author(s): Tam Nguyên, Jonathan H. Young, Amanda Rodriguez, Steven Zupancic, Donald Y. C. Lie
Software Mentions: 3
Published: almost 6 years ago

10.1002/cam4.2233

Toward automatic prediction of <i>EGFR</i> mutation status in pulmonary adenocarcinoma with 3D deep learning
Cited by: 72
Author(s): Wei Zhao, Jiancheng Yang, Bingbing Ni, Dexi Bi, Yingli Sun, Min Xu, Xiaoxia Zhu, Cheng Li, Liang Jin, Pan Gao, Peijun Wang, Yanqing Hua, Ming Li
Software Mentions: 3
Published: over 5 years ago

10.1186/s40168-020-00900-2

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2
Cited by: 115
Author(s): Jennifer Lu, Steven L. Salzberg
Software Mentions: 3
Published: over 4 years ago

10.1111/mpp.12877

Show me your secret(ed) weapons: a multifaceted approach reveals a wide arsenal of type III‐secreted effectors in the cucurbit pathogenic bacterium <i>Acidovorax citrulli</i> and novel effectors in the <i>Acidovorax</i> genus
Cited by: 26
Author(s): Irene Jiménez‐Guerrero, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Naama Wagner, Dafna Shkedy, Mei Zhao, Lorena Pizarro, Maya Bar, R. R. Walcott, Guido Sessa, Tal Pupko, Saul Burdman
Software Mentions: 3
Published: about 5 years ago

10.15252/msb.202110243

Tensor‐structured decomposition improves systems serology analysis
Cited by: 9
Author(s): Zhixin Cyrillus Tan, Madeleine C Murphy, Hakan S Alpay, Scott D Taylor, Aaron S. Meyer
Software Mentions: 3
Published: over 3 years ago

10.15252/msb.20188557

<i>De novo</i> gene signature identification from single‐cell <scp>RNA</scp> ‐seq with hierarchical Poisson factorization
Cited by: 75
Author(s): Hanna Mendes Levitin, Jinzhou Yuan, Yim Ling Cheng, Francisco J. R. Ruiz, Erin C. Bush, Jeffrey N. Bruce, Peter Canoll, Antonio Iavarone, Anna Lasorella, David M. Blei, Peter A. Sims
Software Mentions: 3
Published: almost 6 years ago

10.3390/plants9020174

Using Rapid Chlorophyll Fluorescence Transients to Classify Vitis Genotypes
Cited by: 8
Author(s): Jorge Marques da Silva, Andreia Figueiredo, Jorge Cunha, José Eduardo Eiras-Dias, Sara Silva, Leonardo Vanneschi, Pedro Mariano
Software Mentions: 3
Published: almost 5 years ago

10.1002/ece3.7929

Assessing age, breeding stage, and mating activity as drivers of variation in the reproductive microbiome of female tree swallows
Cited by: 6
Author(s): Jessica Hernandez, Catherine Hucul, Emily Reasor, Taryn J Smith, Joel W. McGlothlin, David C. Haak, Lisa K. Belden, Ignacio T. Moore
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.5963

Gut microbiota in reintroduction of giant panda
Cited by: 16
Author(s): Jingsi Tang, Chengdong Wang, Hemin Zhang, Jiangchao Zhao, Wei Guo, Saurabh Mishra, Fanli Kong, Bo Zeng, Ruihong Ning, Desheng Li, Jiandong Yang, Mingyao Yang, Mingwang Zhang, Qingyong Ni, Yan Li, Ying Liu
Software Mentions: 3
Published: almost 5 years ago

10.3390/e22111274

Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets
Cited by: 3
Author(s): Alexander Chervov, Jonathan Bac, Andreï Zinovyev
Software Mentions: 3
Published: about 4 years ago

10.1002/fsn3.1484

Rapid identification of chrysanthemum teas by computer vision and deep learning
Cited by: 16
Author(s): Chunlin Li, Weiying Lu, Boyan Gao, Hanae Kimura, Yanfang Li, Jing Wang
Software Mentions: 3
Published: almost 5 years ago

10.3389/fncir.2020.00042

Automated Curation of CNMF-E-Extracted ROI Spatial Footprints and Calcium Traces Using Open-Source AutoML Tools
Cited by: 9
Author(s): Lina M. Tran, Andrew J. Mocle, Adam I. Ramsaran, Alexander D. Jacob, Paul W. Frankland, Sheena A. Josselyn
Software Mentions: 3
Published: over 4 years ago

10.1007/s11357-020-00297-8

Plasma dilution improves cognition and attenuates neuroinflammation in old mice
Cited by: 33
Author(s): Melod Mehdipour, Taha Mehdipour, Colin M. Skinner, Nathan Wong, Chao Liu, Chia Chien Chen, Ok Hee Jeon, Yi Zuo, Michael J. Conboy, Irina M. Conboy
Software Mentions: 3
Published: about 4 years ago

10.1002/hbm.25152

The maternal brain: Region‐specific patterns of brain aging are traceable decades after childbirth
Cited by: 42
Author(s): Ann-Marie G. de Lange, Cláudia Barth, Tobias Kaufmann, Melis Anatürk, Sana Suri, Klaus P. Ebmeier, Lars T. Westlye
Software Mentions: 3
Published: over 4 years ago

10.1002/hbm.25589

Dyconnmap: Dynamic connectome mapping—A neuroimaging python module
Cited by: 6
Author(s): Avraam D. Marimpis, Stavros I. Dimitriadis, Rainer Goebel
Software Mentions: 3
Published: over 3 years ago

10.1186/s42238-020-00028-y

Relationship among subjective responses, flavor, and chemical composition across more than 800 commercial cannabis varieties
Cited by: 12
Author(s): Alethia de la Fuente, Federico Zamberlán, Andrés Sánchez Ferrán, Facundo Carrillo, Enzo Tagliazucchi, Carla Pallavicini
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-48872-0

Multi-study reanalysis of 2,213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures
Cited by: 12
Author(s): Raeuf Roushangar, George I. Mias
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-87876-7

Quantitative imaging of membrane contact sites for sterol transfer between endo-lysosomes and mitochondria in living cells
Cited by: 12
Author(s): Alice Dupont Juhl, Christian W. Heegaard, Stephan Werner, Gerd Schneider, Kathiresan Krishnan, Douglas F. Covey, Daniel Wüstner
Software Mentions: 3
Published: over 3 years ago

10.12688/f1000research.8001.1

Chromas from chromatin: sonification of the epigenome
Cited by: 2
Author(s): Davide Cittaro, Dejan Lazarevic, Paolo Provero
Software Mentions: 2
Published: almost 9 years ago

10.1002/cyto.a.23794

Label‐Free Identification of White Blood Cells Using Machine Learning
Cited by: 62
Author(s): Mariam Nassar, Minh Doan, Andrew Filby, Olaf Wolkenhauer, Darin K. Fogg, Justyna Piasecka, Catherine A. Thornton, Anne E. Carpenter, Huw D. Summers, Paul Rees, Holger Hennig
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0234904

Development and validation of a robotic multifactorial fall-risk predictive model: A one-year prospective study in community-dwelling older adults
Cited by: 20
Author(s): Alberto Cella, Alice De Luca, Valentina Squeri, Sara Parodi, Francesco Vallone, Angela Giorgeschi, Barbara Senesi, Ekaterini Zigoura, Katerin Leslie Quispe Guerrero, Giacomo Siri, Lorenzo De Michieli, Jody A. Saglia, Carlo Sanfilippo, Alberto Pilotto
Software Mentions: 2
Published: over 4 years ago

10.3389/fnhum.2019.00457

Revealing Relationships Among Cognitive Functions Using Functional Connectivity and a Large-Scale Meta-Analysis Database
Cited by: 5
Author(s): Hiroki Kurashige, Jun Kaneko, Yuichi Yamashita, Rieko Osu, Yohei Otaka, Takashi Hanakawa, Manabu Honda, Hideaki Kawabata
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pmed.1003416

Predicting suicide attempt or suicide death following a visit to psychiatric specialty care: A machine learning study using Swedish national registry data
Cited by: 35
Author(s): Qi Chen, Yanli Zhang-James, Eric J. Barnett, Paul Lichtenstein, Jussi Jokinen, Brian M. D’Onofrio, Stephen V. Faraone, Henrik Larsson, Seena Fazel
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1005641

Classification and analysis of a large collection of in vivo bioassay descriptions
Cited by: 13
Author(s): Magdalena Zwierzyna, John P. Overington
Software Mentions: 2
Published: over 7 years ago

10.12688/wellcomeopenres.16718.1

An automated approach to identify scientific publications reporting pharmacokinetic parameters
Cited by: 6
Author(s): Ferran Gonzalez Hernandez, Simon J. Carter, Juha Iso-Sipilä, Paul C. Goldsmith, Ahmed Almousa, Silke Gastine, Watjana Lilaonitkul, Frank Kloprogge, Joseph F. Standing
Software Mentions: 2
Published: over 3 years ago

10.15252/msb.20199405

Drug mechanism‐of‐action discovery through the integration of pharmacological and <scp>CRISPR</scp> screens
Cited by: 55
Author(s): Emanuel Gonçalvès, Aldo Segura‐Cabrera, Clare Pacini, Gabriele Picco, Fiona M. Behan, Patricia Jaaks, Elizabeth A. Coker, Dieudonne van der Meer, Andrew Barthorpe, Howard Lightfoot, Tatiana Mironenko, Alexandra Beck, Laura L. Richardson, Wanjuan Yang, Ermira Lleshi, James A. Hall, Charlotte Tolley, Caitlin Hall, Iman Mali, Frances Thomas, James A. Morris, Andrew R. Leach, James T. Lynch, Ben Sidders, Claire Crafter, Francesco Iorio, Stephen E. Fawell, Mathew J. Garnett
Software Mentions: 2
Published: over 4 years ago

10.3389/fonc.2021.644994

Preoperative Assessment for Event-Free Survival With Hepatoblastoma in Pediatric Patients by Developing a CT-Based Radiomics Model
Cited by: 5
Author(s): Yi Jiang, Jingjing Sun, Yuwei Xia, Yan Cheng, Linjun Xie, Xia Guo, Yingkun Guo
Software Mentions: 2
Published: over 3 years ago

10.3389/fphar.2019.01675

Applying Machine Learning to Ultrafast Shape Recognition in Ligand-Based Virtual Screening
Cited by: 14
Author(s): Etienne Bonanno, Jean-Paul Ebejer
Software Mentions: 2
Published: almost 5 years ago

10.15252/msb.20199243

Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability
Cited by: 32
Author(s): Mojca Mattiazzi Ušaj, Nil Sahin, Helena Friesen, Carles Pons, Matej Ušaj, Myra Paz David Masinas, Ermira Shuteriqi, Aleksei Shkurin, Patrick Aloy, Quaid Morris, Charles Boone, Brenda Andrews
Software Mentions: 2
Published: almost 5 years ago

10.1029/2019GL085870

Probing Slow Earthquakes With Deep Learning
Cited by: 32
Author(s): Bertrand Rouet‐Leduc, Claudia Hulbert, Ian W. McBrearty, P. A. Johnson
Software Mentions: 2
Published: almost 5 years ago

10.1049/htl2.12006

Prediction of hematocrit through imbalanced dataset of blood spectra
Cited by: 3
Author(s): Cristoforo Decaro, G.B. Montanari, M. Bianconi, Gaetano Bellanca
Software Mentions: 2
Published: over 3 years ago

10.1002/aps3.11377

Species complex delimitations in the genus <i>Hedychium</i> : A machine learning approach for cluster discovery
Cited by: 8
Author(s): Preeti Saryan, Shubham Gupta, Vinita Gowda
Software Mentions: 2
Published: over 4 years ago

10.15252/msb.202110267

Behavioral fingerprints predict insecticide and anthelmintic mode of action
Cited by: 16
Author(s): Adam McDermott-Rouse, Eleni Minga, Ida Barlow, Luigi Feriani, Philippa H. Harlow, Anthony J. Flemming, André E. X. Brown
Software Mentions: 2
Published: over 3 years ago

10.2196/15547

Applying Machine Learning to Daily-Life Data From the TrackYourTinnitus Mobile Health Crowdsensing Platform to Predict the Mobile Operating System Used With High Accuracy: Longitudinal Observational Study
Cited by: 11
Author(s): Rüdiger Pryss, Winfried Schlee, Burkhard Hoppenstedt, Manfred Reichert, Myra Spiliopoulou, Berthold Langguth, Marius Breitmayer, Thomas Probst
Software Mentions: 2
Published: over 4 years ago

10.15252/msb.20188290

Unraveling the hidden universe of small proteins in bacterial genomes
Cited by: 87
Author(s): Samuel Miravet-Verde, Tony Ferrar, Guadalupe Espadas-García, Rocco Mazzolini, Anas Gharrab, Eduard Sabidò, Luís Serrano, María Lluch‐Senar
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-08366-3

Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins
Cited by: 35
Author(s): Daniele Raimondi, Gabriele Orlando, Rita Pancsa, Taushif Khan, Wim Vranken
Software Mentions: 2
Published: over 7 years ago

10.1111/1751-7915.12380

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities
Cited by: 19
Author(s): Kate O’Brien, Michael S. Chimenti, Morgan B. Farnell, Tom Tabler, Thomas B. Bair, Joey Lynn Bray, Matthew W. Nonnenmann
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-021-83247-4

Conservation machine learning: a case study of random forests
Cited by: 11
Author(s): Moshe Sipper, Jason H. Moore
Software Mentions: 2
Published: almost 4 years ago

10.1002/ajmg.b.32705

Predictive modeling of schizophrenia from genomic data: Comparison of polygenic risk score with kernel support vector machines approach
Cited by: 24
Author(s): Timothy Vivian-Griffiths, Emily Baker, Karl Michael Schmidt, Matthew Bracher-Smith, James Walters, Andreas Artemiou, Peter Holmans, Michael O’Donovan, Michael John Owen, Andrew Pocklington, Valentina Escott‐Price
Software Mentions: 2
Published: about 6 years ago

10.1002/mrm.26318

Multiclass imbalance learning: Improving classification of pediatric brain tumors from magnetic resonance spectroscopy
Cited by: 28
Author(s): Niloufar Zarinabad, Martin Wilson, Sharon A. Gill, Karen Manias, Nigel P. Davies, Andrew C. Peet
Software Mentions: 2
Published: over 8 years ago

10.3390/biom10030454

Machine Learning to Identify Flexibility Signatures of Class A GPCR Inhibition
Cited by: 17
Author(s): Joseph Bemister-Buffington, A. Wolf, Sebastian Raschka, Leslie A. Kuhn
Software Mentions: 2
Published: almost 5 years ago

10.1002/advs.202100104

A Noninvasive Multianalytical Approach for Lung Cancer Diagnosis of Patients with Pulmonary Nodules
Cited by: 7
Author(s): Quan‐Xing Liu, Dong Zhou, Tiancheng Han, Lü Xiao, Bing Han, Man-Yuan Li, Guixue Yang, Qingyuan Li, Zhihua Pei, Yuanyuan Hong, Yaxi Zhang, Weizhi Chen, Hong Zheng, Ji He, Ji‐Gang Dai
Software Mentions: 2
Published: over 3 years ago

10.3390/s21186270

Automated Calibration of RSS Fingerprinting Based Systems Using a Mobile Robot and Machine Learning
Cited by: 7
Author(s): Marcin Kołakowski
Software Mentions: 2
Published: over 3 years ago