bioconductor: ADAM | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-82043-4

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Cited by: 10
Author(s): Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Software Mentions: 11
Published: almost 4 years ago

10.3389/fmolb.2019.00025

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Cited by: 22
Author(s): Dalibor Trapl, Izabela Horvacanin, Václav Mareška, Furkan Özçelik, Gözde Ünal, Vojtěch Spiwok
Software Mentions: 11
Published: over 5 years ago

10.3389/fncom.2021.674028

Accurate Prediction of Children's ADHD Severity Using Family Burden Information: A Neural Lasso Approach
Cited by: 1
Author(s): Juan C. Laria, David Delgado-Gómez, Inmaculada Peñuelas-Calvo, Enrique Baca‐García, Rosa E. Lillo
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.47994

DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning
Cited by: 304
Author(s): Jacob M. Graving, Daniel H. Chae, Hemal Naik, Liang Li, Benjamin Koger, Blair R. Costelloe, Iain D. Couzin
Software Mentions: 7
Published: about 5 years ago

10.1186/s12864-020-07013-y

Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework
Cited by: 3
Author(s): Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars, H. Peter Hofstee
Software Mentions: 6
Published: about 4 years ago

10.1186/s13321-021-00536-w

Learning protein-ligand binding affinity with atomic environment vectors
Cited by: 21
Author(s): Rocco Meli, Andrew Anighoro, Michael J. Bodkin, Garrett M. Morris, Philip C. Biggin
Software Mentions: 6
Published: over 3 years ago

10.3389/fnins.2018.00368

From ERPs to MVPA Using the Amsterdam Decoding and Modeling Toolbox (ADAM)
Cited by: 94
Author(s): Johannes J. Fahrenfort, Joram van Driel, Simon van Gaal, Christian N. L. Olivers
Software Mentions: 6
Published: over 6 years ago

10.1186/s13326-019-0212-6

Exploring semantic deep learning for building reliable and reusable one health knowledge from PubMed systematic reviews and veterinary clinical notes
Cited by: 6
Author(s): Mercedes Arguello-Casteleiro, Robert Stevens, Julio Des-Diz, Chris Wroe, M.J. Fernandez-Prieto, Nava Maroto, Diego Maseda-Fernandez, George Demetriou, Simon Peters, P. J. W. Noble, Phil Jones, Joanna Dukes‐McEwan, Alan Radford, John Keane, Goran Nenadić
Software Mentions: 6
Published: about 5 years ago

10.3389/fncom.2019.00046

A Closed-Loop Toolchain for Neural Network Simulations of Learning Autonomous Agents
Cited by: 5
Author(s): Jakob Jordan, Philipp Weidel, Abigail Morrison
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1009021

MiMeNet: Exploring microbiome-metabolome relationships using neural networks
Cited by: 33
Author(s): Derek Reiman, Brian T. Layden, Yang Dai
Software Mentions: 5
Published: over 3 years ago

10.1128/mSphere.01263-20

Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale
Cited by: 17
Author(s): Abraham G Moller, Kyle Winston, Sang Yong Ji, Junting Wang, Michelle N. Hargita Davis, Claudia Solís-Lemus, Timothy D. Read
Software Mentions: 5
Published: over 3 years ago

10.1093/bioinformatics/btx727

Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks
Cited by: 31
Author(s): Žiga Avsec, Mohammadamin Barekatain, Jianghua Cheng
Software Mentions: 5
Published: about 7 years ago

10.3390/s20164575

Comparative Analysis on Machine Learning and Deep Learning to Predict Post-Induction Hypotension
Cited by: 17
Author(s): Ji‐Hyun Lee, Jiyoung Woo, Ah Reum Kang, Young-Seob Jeong, Woohyun Jung, Misoon Lee, Sang Hyun Kim
Software Mentions: 5
Published: over 4 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: over 6 years ago

10.1038/s41598-020-60932-4

An empirical comparison of neural networks and machine learning algorithms for EEG gait decoding
Cited by: 44
Author(s): Sho Nakagome, Trieu Phat Luu, Yongtian He, Akshay Sujatha Ravindran, José L. Contreras-Vidal
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-019-6323-8

Bias in estimates of variance components in populations undergoing genomic selection: a simulation study
Cited by: 9
Author(s): Hongding Gao, Per Madsen, G.P. Aamand, Jørn Rind Thomasen, Anders Christian Sørensen, Just Jensen
Software Mentions: 5
Published: almost 5 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 4 years ago

10.1371/journal.pone.0201483

HSRA: Hadoop-based spliced read aligner for RNA sequencing data
Cited by: 11
Author(s): Roberto R. Expósito, Jorge González-Domínguez, Juan Touriño
Software Mentions: 5
Published: over 6 years ago

10.1038/s41597-019-0103-9

Multitask learning and benchmarking with clinical time series data
Cited by: 414
Author(s): Hrayr Harutyunyan, Hrant Khachatrian, David C. Kale, Greg Ver Steeg, Aram Galstyan
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giy052

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files
Cited by: 3
Author(s): Xiaobo Sun, Jingjing Gao, Peng Jin, Celeste Eng, Esteban G. Burchard, Terri H. Beaty, Ingo Ruczinski, Rasika A. Mathias, Kathleen C. Barnes, Fusheng Wang, Zhaohui S. Qin
Software Mentions: 5
Published: over 6 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: about 3 years ago

10.3389/fonc.2020.00272

Inferring Personalized and Race-Specific Causal Effects of Genomic Aberrations on Gleason Scores: A Deep Latent Variable Model
Cited by: 2
Author(s): Zhong Chen, Andrea Edwards, Chindo Hicks, Kun Zhang
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.5551

BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments
Cited by: 11
Author(s): Maria Luiza Mondelli, Thiago Tavares Magalhães, Guilherme Loss, Michael Wilde, Ian Foster, Marta Mattoso, Daniel S. Katz, Hélio J. C. Barbosa, Ana Tereza Ribeiro de Vasconcelos, Kary Ocaña, Luiz M. R. Gadelha
Software Mentions: 4
Published: about 6 years ago

10.1186/s13326-015-0026-0

Ambiguity and variability of database and software names in bioinformatics
Cited by: 8
Author(s): Geraint Duck, Aleksandar Kovačević, David L. Robertson, Robert Stevens, Goran Nenadić
Software Mentions: 4
Published: over 9 years ago

10.1186/1752-0509-7-135

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Cited by: 134
Author(s): Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolás Rodríguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalvès, Julien Dorier, Michel Le Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xénarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Sáez-Rodríguez, Tomáš Helikar
Software Mentions: 4
Published: almost 12 years ago

10.3389/fphar.2021.708050

A Comparison of Nine Machine Learning Mutagenicity Models and Their Application for Predicting Pyrrolizidine Alkaloids
Cited by: 5
Author(s): Christoph Helma, Verena Schöning, Jürgen Drewe, Philipp Boss
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers13030577

Optimizing the Procedure to Manufacture Clinical-Grade NK Cells for Adoptive Immunotherapy
Cited by: 16
Author(s): Adrián Fernández, Alfonso Navarro-Zapata, Adela Escudero, Nerea Matamala, Beatriz Ruz-Caracuel, Isabel Mirones, Alicia Pernas, Marta Cobo, Gema Casado, Diego Lanzarot, Carlos Rodríguez-Antolín, María Vela, Cristina Ferreras, Carmen Mestre, Aurora Viejo, Alejandra Leivas, Javier Martı́nez, Lucía Fernández, Antonio Pérez‐Martínez
Software Mentions: 4
Published: almost 4 years ago

10.3389/fnins.2019.01321

Analyzing Neuroimaging Data Through Recurrent Deep Learning Models
Cited by: 63
Author(s): Armin W. Thomas, Hauke R. Heekeren, Klaus Robert Müller, Wojciech Samek
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-019-3220-8

Modeling aspects of the language of life through transfer-learning protein sequences
Cited by: 292
Author(s): Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes, Burkhard Rost
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0133660

GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems
Cited by: 6
Author(s): Sherif H. Elmeligy Abdelhamid, Chris J. Kuhlman, Madhav V. Marathe, Henning S. Mortveit, S. S. Ravi
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.63377

DeepEthogram, a machine learning pipeline for supervised behavior classification from raw pixels
Cited by: 61
Author(s): James P Bohnslav, Nivanthika K Wimalasena, Kelsey J Clausing, Yu Dai, David A. Yarmolinsky, Tomás Cruz, Adam D Kashlan, M. Eugenia Chiappe, Lauren L. Orefice, Clifford J. Woolf, Christopher D. Harvey
Software Mentions: 4
Published: about 3 years ago

10.3390/ijms21124310

Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram
Cited by: 46
Author(s): Michał Burdukiewicz, Katarzyna Sidorczuk, Dominik Rafacz, Filip Pietluch, Jarosław Chilimoniuk, Stefan Rödiger, Przemysław Gagat
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms21165847

Deep Learning Modeling of Androgen Receptor Responses to Prostate Cancer Therapies
Cited by: 11
Author(s): Oliver Snow, Nada Lallous, Martin Ester, Artem Cherkasov
Software Mentions: 4
Published: over 4 years ago

10.1186/s12870-018-1611-z

Phytohormone treatment induces generation of cryptic peptides with antimicrobial activity in the Moss Physcomitrella patens
Cited by: 25
Author(s): Igor Fesenko, Regina Azarkina, Ilya Kirov, Andrei Kniazev, Anna Filippova, Ekaterina N. Grafskaia, В. Н. Лазарев, Victor G. Zgoda, Ivan Butenko, Olga Bukato, Irina Lyapina, Dmitry Nazarenko, S. N. Elansky, Anna Mamaeva, В. Т. Иванов, Vadim M. Govorun
Software Mentions: 4
Published: almost 6 years ago

10.3390/s21072430

Time Series Forecasting of Univariate Agrometeorological Data: A Comparative Performance Evaluation via One-Step and Multi-Step Ahead Forecasting Strategies
Cited by: 17
Author(s): Saurabh Suradhaniwar, Soumyashree Kar, Surya S. Durbha, J. Adinarayana
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms21239070

A Computational Framework Based on Ensemble Deep Neural Networks for Essential Genes Identification
Cited by: 45
Author(s): Nguyen Quoc Khanh Le, Duyen Thi, Truong Nguyen Khanh Hung, Luu Ho Thanh Lam, Chih-Min Lin, Ngan Thi Kim Nguyen
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13601-018-0204-0

5th Pediatric Allergy and Asthma Meeting (PAAM)
Cited by: 8
Author(s):
Software Mentions: 4
Published: over 6 years ago

10.3390/s20092594

Recognition of Patient Groups with Sleep Related Disorders using Bio-signal Processing and Deep Learning
Cited by: 21
Author(s): Delaram Jarchi, Javier Andreu-Pérez, Mehrin Kiani, Oldřich Vyšata, Jiří Kuchyňka, Aleš Procházka, Saeid Sanei
Software Mentions: 4
Published: over 4 years ago

10.1186/s13321-021-00535-x

Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier
Cited by: 8
Author(s): Jennifer Handsel, Brian Matthews, Nicola Knight, Simon J. Coles
Software Mentions: 4
Published: about 3 years ago

10.3390/s16050645

An Integrated Simulation Module for Cyber-Physical Automation Systems
Cited by: 18
Author(s): Francesco Ferracuti, Alessandro Freddi, Andrea Monteriù, Mariorosario Prist
Software Mentions: 4
Published: over 8 years ago

10.1016/j.molmet.2019.12.006

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures
Cited by: 91
Author(s): Vivek Rai, Daniel Quang, Michael R. Erdos, Darren A. Cusanovich, Riza M. Daza, Narisu Narisu, Luli S. Zou, John P. Didion, Yuanfang Guan, Jay Shendure, Stephen C. J. Parker, Francis S. Collins
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.56261

Training deep neural density estimators to identify mechanistic models of neural dynamics
Cited by: 99
Author(s): Pedro J. Gonçalves, Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, William F Podlaski, Sara A. Haddad, Tim P. Vogels, David S. Greenberg, Jakob H. Macke
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-019-2952-9

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data
Cited by: 19
Author(s): Savvas Kinalis, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger
Software Mentions: 4
Published: over 5 years ago

10.3390/s21061945

A Straightforward and Efficient Instance-Aware Curved Text Detector
Cited by: 2
Author(s): Fan Zhao, Sidi Shao, Lin Zhang, Zhiquan Wen
Software Mentions: 4
Published: over 3 years ago

10.1016/j.media.2020.101871

Accurate brain age prediction with lightweight deep neural networks
Cited by: 199
Author(s): Peng Han, Weikang Gong, Christian F. Beckmann, Andrea Vedaldi, Stephen M. Smith
Software Mentions: 4
Published: almost 4 years ago

10.1007/s10858-019-00265-1

Using Deep Neural Networks to Reconstruct Non-uniformly Sampled NMR Spectra
Cited by: 58
Author(s): D. Flemming Hansen
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-14-361

Detection of attractors of large Boolean networks via exhaustive enumeration of appropriate subspaces of the state space
Cited by: 31
Author(s): Nikolaos Berntenis, Martin Ebeling
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13742-015-0058-5

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
Cited by: 15
Author(s): Alexey Siretskiy, T. Sundqvist, Mikhail Voznesenskiy, Ola Spjuth
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj-cs.371

Multi skin lesions classification using fine-tuning and data-augmentation applying NASNet
Cited by: 11
Author(s): Elia Cano, José Mendoza-Avilés, Mariana Areiza, Noemi Guerra, José Longino Mendoza-Valdés, Carlos Rovetto
Software Mentions: 3
Published: over 3 years ago

10.3390/genes11121475

MirLocPredictor: A ConvNet-Based Multi-Label MicroRNA Subcellular Localization Predictor by Incorporating k-Mer Positional Information
Cited by: 13
Author(s): Muhammad Nabeel Asim, Muhammad Imran Malik, Christoph Zehe, Johan Trygg, Andreas Dengel, Sheraz Ahmed
Software Mentions: 3
Published: almost 4 years ago

10.3389/fonc.2020.598721

Deep CNN Model Using CT Radiomics Feature Mapping Recognizes EGFR Gene Mutation Status of Lung Adenocarcinoma
Cited by: 24
Author(s): Baihua Zhang, Shouliang Qi, Pan Xu, Chen Li, Yu-Dong Yao, Wei Qian, Yubao Guan
Software Mentions: 3
Published: almost 4 years ago

10.3390/e21121222

Deep Learning and Artificial Intelligence for the Determination of the Cervical Vertebra Maturation Degree from Lateral Radiography
Cited by: 35
Author(s): Masrour Makaremi, Camille Lacaule, Ali Mohammad-Djafari
Software Mentions: 3
Published: almost 5 years ago

10.3389/frai.2020.534696

Deep Learning for Understanding Satellite Imagery: An Experimental Survey
Cited by: 34
Author(s): Sharada P. Mohanty, Jakub Czakon, Kamil Kaczmarek, A. Pyskir, Piotr Tarasiewicz, Saket Kunwar, Janick Rohrbach, Dave Luo, Manjunath Prasad, Sascha Fleer, Jan Philip Göpfert, Akshat Tandon, Guillaume Mollard, Nikhil Rayaprolu, Marcel Salathé, Malte Schilling
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2019.00978

Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data
Cited by: 24
Author(s): Carlos Torroja, Fátima Sánchez‐Cabo
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0232683

Physics-informed neural networks for solving nonlinear diffusivity and Biot’s equations
Cited by: 67
Author(s): Teeratorn Kadeethum, Thomas Martini Jørgensen, Hamidreza M. Nick
Software Mentions: 3
Published: over 4 years ago

10.1016/j.spasta.2018.02.002

Spatial mapping with Gaussian processes and nonstationary Fourier features
Cited by: 39
Author(s): Jean-François Ton, Seth Flaxman, Dino Sejdinović, Samir Bhatt
Software Mentions: 3
Published: almost 6 years ago

10.3233/SHTI190211

Recurrent Deep Network Models for Clinical NLP Tasks: Use Case with Sentence Boundary Disambiguation.
Cited by: 1
Author(s): Benjamin C. Knoll, Elizabeth Lindemann, Arian L. Albert, Genevieve B. Melton, Serguei Pakhomov
Software Mentions: 3
Published: over 5 years ago

10.1186/s13742-016-0132-7

Recommendations on e-infrastructures for next-generation sequencing
Cited by: 18
Author(s): Ola Spjuth, Erik Bongcam‐Rudloff, Johan Dahlberg, Martin Dahlö, Aleksi Kallio, Luca Pireddu, Francesco Vezzi, Eija Korpelainen
Software Mentions: 3
Published: over 8 years ago

10.1093/database/bax049

Benchmarking distributed data warehouse solutions for storing genomic variant information
Cited by: 9
Author(s): Marek Wiewiórka, Dawid P Wysakowicz, Michał Okoniewski, Tomasz Gambin
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2021.636743

DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data
Cited by: 21
Author(s): Floyd Maseda, Zixuan Cang, Qing Nie
Software Mentions: 3
Published: over 3 years ago

10.3390/s21165319

DoA Estimation for FMCW Radar by 3D-CNN
Cited by: 5
Author(s): Tzu-Hsien Sang, Feng-Tso Chien, Chia Chih Chang, Kuan Yu Tseng, Bo Sheng Wang, Jiun-In Guo
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0213270

Comparison of infinitesimal and finite locus models for long-term breeding simulations with direct and maternal effects at the example of honeybees
Cited by: 10
Author(s): Manuel Plate, Richard Bernstein, Andreas Hoppe, Kaspar Bienefeld
Software Mentions: 3
Published: over 5 years ago

10.1186/s12911-021-01608-5

Modeling and prediction of pressure injury in hospitalized patients using artificial intelligence
Cited by: 13
Author(s): Charles M. Anderson, Zerihun Bekele, Yongkai Joshua Qiu, Dana Tschannen, Ivo D. Dinov
Software Mentions: 3
Published: about 3 years ago

10.1186/s12911-021-01553-3

Medical recommender systems based on continuous-valued logic and multi-criteria decision operators, using interpretable neural networks
Cited by: 18
Author(s): Juan G. Díaz Ochoa, Orsolya Csiszár, Thomas Schimper
Software Mentions: 3
Published: over 3 years ago

10.1080/14686996.2017.1401424

ChemTS: an efficient python library for <i>de novo</i> molecular generation
Cited by: 170
Author(s): Xiufeng Yang, Jinzhe Zhang, Kazuki Yoshizoe, Kei Terayama, Koji Tsuda
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-65369-3

Measuring Cancer Hallmark Mediation of the TET1 Glioma Survival Effect with Linked Neural-Network Based Mediation Experiments
Cited by: 2
Author(s): Thomas Luechtefeld, Nole Lin, Channing J. Paller, Katherine J. Kuhns, John Laterra, Joseph Bressler
Software Mentions: 3
Published: over 4 years ago

10.1177/2472555218820805

Evaluation of Machine Learning Classifiers to Predict Compound Mechanism of Action When Transferred across Distinct Cell Lines
Cited by: 12
Author(s): Scott J. Warchal, John C. Dawson, Neil O. Carragher
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0246096

Machine learning for buildings’ characterization and power-law recovery of urban metrics
Cited by: 5
Author(s): Alaa Krayem, Aram Yeretzian, Ghaleb Faour, Sara Najem
Software Mentions: 3
Published: almost 4 years ago

10.1089/cmb.2019.0337

Semisupervised Generative Autoencoder for Single-Cell Data
Cited by: 12
Author(s): Trung Ngô Trọng, Juha Mehtonen, Gerardo González, Roger Kramer, Ville Hautamäki, Merja Heinäniemi
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-30619-y

Hybrid optical-electronic convolutional neural networks with optimized diffractive optics for image classification
Cited by: 266
Author(s): Julie Chang, Vincent Sitzmann, Deping Xiong, Wolfgang Heidrich, Gordon Wetzstein
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0221606

Predicting 30-day hospital readmissions using artificial neural networks with medical code embedding
Cited by: 24
Author(s): Wenshuo Liu, Cooper Stansbury, Karandeep Singh, Andrew M. Ryan, Devraj Sukul, Elham Mahmoudi, Akbar K. Waljee, Ji Zhu, Brahmajee K. Nallamothu
Software Mentions: 3
Published: over 4 years ago

10.1002/hbm.25286

Comparing machine and deep <scp>learning‐based</scp> algorithms for prediction of clinical improvement in psychosis with functional magnetic resonance imaging
Cited by: 19
Author(s): Jason Smucny, Ian Davidson, Cameron S. Carter
Software Mentions: 2
Published: about 4 years ago

10.26508/lsa.201900512

ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user’s research
Cited by: 25
Author(s): Francisco Ramos‐Martín, Thibault Annaval, Sébastien Buchoux, Catherine Sarazin, Nicola D’Amelio
Software Mentions: 2
Published: about 5 years ago

10.1093/gigascience/giz044

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Cited by: 22
Author(s): Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
Software Mentions: 2
Published: over 5 years ago

10.3390/insects12050466

Utilizing Red Spotted Apollo Butterfly Transcriptome to Identify Antimicrobial Peptide Candidates against Porphyromonas gingivalis
Cited by: 2
Author(s): Kang-Woon Lee, Jaegoo Kim, Karpagam Veerappan, Hak-Jae Chung, Sathishkumar Natarajan, Ki‐Young Kim, Jun Hyung Park
Software Mentions: 2
Published: over 3 years ago

10.1186/gb-2008-9-s2-s8

Linking genes to literature: text mining, information extraction, and retrieval applications for biology
Cited by: 198
Author(s): Martin Krallinger, Alfonso Valencia, Lynette Hirschman
Software Mentions: 2
Published: about 16 years ago

10.1093/gigascience/giy098

Bioinformatics applications on Apache Spark
Cited by: 49
Author(s): Runxin Guo, Yi Zhao, Quan Zou, Xiaodong Fang, Shaoliang Peng
Software Mentions: 2
Published: over 6 years ago

10.3389/frobt.2018.00110

Stage-Wise Learning of Reaching Using Little Prior Knowledge
Cited by: 4
Author(s): François de La Bourdonnaye, Céline Teulière, Jochen Triesch, Thierry Chateau
Software Mentions: 2
Published: about 6 years ago

10.3389/fphys.2021.667828

Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations
Cited by: 1
Author(s): J. Quetzalcóatl Toledo-Marín, Geoffrey Fox, James P. Sluka, James A. Glazier
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-12-295

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
Cited by: 47
Author(s): Franziska Hinkelmann, Madison Brandon, Bonny Guang, Rustin McNeill, Grigoriy Blekherman, Alan Veliz-Cuba, Reinhard Laubenbacher
Software Mentions: 2
Published: over 13 years ago

10.3390/genes12020319

Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks
Cited by: 3
Author(s): Ionut Sebastian Mihai, Debojyoti Das, Gabija Maršalkaite, Johan Henriksson
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-018-2507-5

Deep clustering of protein folding simulations
Cited by: 64
Author(s): Debsindhu Bhowmik, Shang Gao, M. Todd Young, Arvind Ramanathan
Software Mentions: 2
Published: almost 6 years ago

10.3389/fnins.2020.590164

A New Spiking Convolutional Recurrent Neural Network (SCRNN) With Applications to Event-Based Hand Gesture Recognition
Cited by: 36
Author(s): Yannan Xing, Gaetano Di Caterina, John J. Soraghan
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-019-3327-y

Antimicrobial peptide identification using multi-scale convolutional network
Cited by: 40
Author(s): Xin Su, Jing Xu, Yanbin Yin, Xiongwen Quan, Han Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-14-194

bioNerDS: exploring bioinformatics’ database and software use through literature mining
Cited by: 26
Author(s): Geraint Duck, Goran Nenadić, Andy Brass, David L. Robertson, Robert Stevens
Software Mentions: 2
Published: over 11 years ago

10.3389/fninf.2019.00034

Deep Learning Deformation Initialization for Rapid Groupwise Registration of Inhomogeneous Image Populations
Cited by: 6
Author(s): Sahar Ahmad, Jingfan Fan, Pei Dong, Xiaohuan Cao, Pew Thian Yap, Dinggang Shen
Software Mentions: 2
Published: over 5 years ago

10.3389/fneur.2021.720650

Automated Movement Assessment in Stroke Rehabilitation
Cited by: 3
Author(s): Tamim Ahmed, Kowshik Thopalli, Thanassis Rikakis, Pavan Turaga, Aisling Kelliher, Jia-Bin Huang, Steven L. Wolf
Software Mentions: 2
Published: over 3 years ago

10.1186/s12711-018-0439-1

Approximate Bayesian neural networks in genomic prediction
Cited by: 36
Author(s): Patrik Waldmann
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1008565

Online analysis of microendoscopic 1-photon calcium imaging data streams
Cited by: 22
Author(s): Johannes Friedrich, Andrea Giovannucci, Eftychios A. Pnevmatikakis
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1009246

Adaptation supports short-term memory in a visual change detection task
Cited by: 9
Author(s): Brian Hu, Marina Garrett, Peter A. Groblewski, Douglas R. Ollerenshaw, Jiaqi Shang, Kate Roll, Sahar Manavi, Christof Koch, Shawn R. Olsen, Ştefan Mihalaş
Software Mentions: 2
Published: about 3 years ago

10.1186/s12859-019-3159-9

PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets
Cited by: 15
Author(s): Luca Nanni, Pietro Pinoli, Arif Canakoglu, Stefano Ceri
Software Mentions: 2
Published: about 5 years ago

10.3389/fncel.2021.621252

OptiFlex: Multi-Frame Animal Pose Estimation Combining Deep Learning With Optical Flow
Cited by: 15
Author(s): Xiaole Liu, Siyang Yu, Nico A. Flierman, Sebastián Loyola, Maarten Kamermans, Tycho M. Hoogland, Chris I. De Zeeuw
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00025

Sparse Convolutional Neural Networks for Genome-Wide Prediction
Cited by: 19
Author(s): Patrik Waldmann, Christina Pfeiffer, Gábor Mészáros
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1007918

Classifying sex and strain from mouse ultrasonic vocalizations using deep learning
Cited by: 32
Author(s): Aleksandr Ivanenko, Paul V. Watkins, Marcel A. J. van Gerven, Kurt Hammerschmidt, Bernhard Englitz
Software Mentions: 2
Published: over 4 years ago

Projects: bioconductor: ADAM

Papers Mentioning ADAM 482