Ecosyste.ms: Papers

10.3389/fonc.2020.584404

In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster
Cited by: 6
Author(s): Yuwei Zhang, Guofang Zhao, Fatma Ahmed, Tianfei Yi, Shiyun Hu, Ting Cai, Qi Liao
Software Mentions: 11
Published: about 4 years ago

10.1371/journal.pone.0223477

Extractive single document summarization using binary differential evolution: Optimization of different sentence quality measures
Cited by: 28
Author(s): Naveen Saini, Sriparna Saha, Dhiraj Chakraborty, Pushpak Bhattacharyya
Software Mentions: 6
Published: about 5 years ago

10.1016/j.gpb.2019.08.002

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information
Cited by: 56
Author(s): Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, A. Ian Smith, Tatiana T. Marquez‐Lago, Jian Li, Jiangning Song
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.60321

Graphical-model framework for automated annotation of cell identities in dense cellular images
Cited by: 18
Author(s): Shivesh Chaudhary, Sol Ah Lee, Yueyi Li, Dhaval Patel, Hang Lu
Software Mentions: 4
Published: over 3 years ago

10.1109/TPAMI.2018.2840695

DeepIGeoS: A Deep Interactive Geodesic Framework for Medical Image Segmentation
Cited by: 262
Author(s): Guotai Wang, María A. Zuluaga, Wenqi Li, Rosalind Pratt, Premal A. Patel, Michaël Aertsen, Tom Doel, Anna L. David, Jan Deprest, Sébastien Ourselin, Tom Vercauteren
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms19092483

IDP–CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields
Cited by: 18
Author(s): Yumeng Liu, Xiaolong Wang, Bin Liu
Software Mentions: 4
Published: over 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

10.1155/2020/7090918

Chinese Emergency Event Recognition Using Conv-RDBiGRU Model
Cited by: 5
Author(s): Haoran Yin, Jinxuan Cao, Luzhe Cao, Guodong Wang
Software Mentions: 4
Published: over 4 years ago

10.1186/s13321-018-0327-2

LSTMVoter: chemical named entity recognition using a conglomerate of sequence labeling tools
Cited by: 29
Author(s): Wahed Hemati, Alexander Mehler
Software Mentions: 4
Published: almost 6 years ago

10.1007/s11060-016-2363-y

Development of the SIOPE DIPG network, registry and imaging repository: a collaborative effort to optimize research into a rare and lethal disease
Cited by: 40
Author(s): Sophie E M Veldhuijzen van Zanten, Joshua Baugh, Brooklyn Chaney, Dennis de Jongh, Esther Sánchez Aliaga, Frederik Barkhof, Johan Noltes, Ruben De Wolf, Jet Van Dijk, Antonio Cannarozzo, Carin M. Damen-Korbijn, Jan A. Lieverst, Niclas Colditz, Marion Hoffmann, Monika Warmuth‐Metz, Brigitte Bison, David Jones, Dominik Sturm, Gerrit H. Gielen, Chris Jones, Esther Hulleman, Raphaël Calmon, David Castel, Pascale Varlet, G Giraud, Irene Slavc, Stefaan Van Gool, Sandra Jacobs, Filip Jadrijević-Cvrlje, David Sumerauer, Karsten Nysom, Virve Pentikäinen, Sanna-Maria Kivivuori, Pierre Leblond, Natasha Entz-Werle, André O. von Bueren, Antonis Kattamis, Darren Hargrave, Péter Hauser, Miklós Garami, Halldora K. Thorarinsdottir, Jane Pears, Lorenza Gandola, Giedrė Rutkauskienė, Geert O. Janssens, Ingrid Kristin Torsvik, Marta Perek-Polnik, Maria João Gil-da-Costa, Olga Zheludkova, Л. И. Шац, Ladislav Deak, Lidija Kitanovski, Ofelia Cruz, Andrés Morales La Madrid, Stefan Holm, Nicolas U. Gerber, Rejin Kebudi, Richard G. Grundy, Enrique López-Aguilar, Marta Zapata‐Tarrés, John Emmerik, Tim Hayden, Simon Bailey, Veronica Biassoni, Maura Massimino, Jacques Grill, W. Peter Vandertop, Gertjan J. L. Kaspers, Maryam Fouladi, Christof M. Kramm, Dannis G. van Vuurden
Software Mentions: 3
Published: almost 8 years ago

10.7717/peerj.3219

CRF: detection of CRISPR arrays using random forest
Cited by: 8
Author(s): Kai Wang, Chun Liang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1008895

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Cited by: 62
Author(s): Melissa J. Hubisz, Amy L. Williams, Adam Siepel
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0102366

Semi-Supervised Morphosyntactic Classification of Old Icelandic
Cited by: 2
Author(s): Kryztof Urban, Timothy R. Tangherlini, Aurelijus Vijūnas, Peter Broadwell
Software Mentions: 3
Published: over 10 years ago

10.1017/gmh.2015.21

Development of a scoring system for non-specialist ratings of clinical competence in global mental health: a qualitative process evaluation of the Enhancing Assessment of Common Therapeutic Factors (ENACT) scale
Cited by: 53
Author(s): Brandon A. Kohrt, Megan Ramaiya, Sauharda Rai, Anvita Bhardwaj, Mark J. D. Jordans
Software Mentions: 3
Published: almost 10 years ago

10.1186/2041-1480-1-3

Analysis of syntactic and semantic features for fine-grained event-spatial understanding in outbreak news reports
Cited by: 7
Author(s): Hutchatai Chanlekha, Nigel Collier
Software Mentions: 3
Published: almost 15 years ago

10.1186/1758-2946-7-S1-S3

tmChem: a high performance approach for chemical named entity recognition and normalization
Cited by: 219
Author(s): Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13063-020-04859-1

Downstream or upstream administration of P2Y12 receptor blockers in non-ST elevated acute coronary syndromes: study protocol for a randomized controlled trial
Cited by: 1
Author(s): Giuseppe Tarantini, Marco Mojoli, Ferdinando Varbella, Roberto Caporale, Stefano Rigattieri, Giuseppe Andò, Plinio Cirillo, Simona Pierini, Andrea Santarelli, Paolo Sganzerla, Nicoletta De Cesare, Ugo Limbruno, Alessandro Lupi, Roberto Ricci, Carlo Cernetti, Luca Favero, Francesco Saia, Loris Roncon, Valeria Gasparetto, Marco Ferlini, Federico Ronco, Luca Ferri, Daniela Trabattoni, Alessandra Russo, Vincenzo Guiducci, Carlo Penzo, Fabio Tarantino, Ciro Mauro, Alfredo Marchese, Battistina Castiglioni, Alessio La Manna, Matteo Martinato, Darío Gregori, Dominick J. Angiolillo, Giuseppe Musumeci
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijerph13090912

Utilizing Chinese Admission Records for MACE Prediction of Acute Coronary Syndrome
Cited by: 19
Author(s): Danqing Hu, Zhengxing Huang, Terence Chan, Wei Dong, Xudong Lü, Huilong Duan
Software Mentions: 3
Published: about 8 years ago

10.3390/ijerph17176142

Factors Influencing Walking and Exercise Adherence in Healthy Older Adults Using Monitoring and Interfacing Technology: Preliminary Evidence
Cited by: 4
Author(s): Andrea Albergoni, Florentina J. Hettinga, Wim Stut, Francesco Sartor
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms17020191

Prioritization of Susceptibility Genes for Ectopic Pregnancy by Gene Network Analysis
Cited by: 11
Author(s): Ji‐Long Liu, Miao Zhao
Software Mentions: 3
Published: almost 9 years ago

10.1155/2021/9962109

Breast Cancer Segmentation Methods: Current Status and Future Potentials
Cited by: 33
Author(s): Epimack Michael, He Ma, Hong Li, Frank Kulwa, Jing Li
Software Mentions: 2
Published: over 3 years ago

10.1155/2017/4898963

A Novel Approach towards Medical Entity Recognition in Chinese Clinical Text
Cited by: 21
Author(s): Jun Liang, Xuemei Xian, Xiaoli He, Ming Xu, Sheng Dai, Junyi Xin, Xu Jie, Jian Yu, Jianbo Lei
Software Mentions: 2
Published: almost 8 years ago

10.3762/bjnano.6.190

Framework for automatic information extraction from research papers on nanocrystal devices
Cited by: 8
Author(s): Thaer M. Dieb, Masaharu Yoshioka, Shinjiro Hara, Mary Newton
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2105-13-265

Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods
Cited by: 3
Author(s): Tudor Groza, Jane Hunter, Andreas Zankl
Software Mentions: 2
Published: about 12 years ago

10.1186/s12884-017-1244-5

Assessment of DHA on reducing early preterm birth: the ADORE randomized controlled trial protocol
Cited by: 27
Author(s): Susan E. Carlson, Byron Gajewski, Christina J. Valentine, Lynette K. Rogers, Carl P. Weiner, Emily DeFranco, Catalin S. Buhimschi
Software Mentions: 2
Published: almost 8 years ago

10.1186/1758-2946-7-S1-S11

A CRF-based system for recognizing chemical entity mentions (CEMs) in biomedical literature
Cited by: 12
Author(s): Shuo Xu, Xueli An, Liehuang Zhu, Yunliang Zhang, Haodong Zhang
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-12-69

A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment
Cited by: 15
Author(s): Yufan Guo, Anna-Leena Korhonen, Maria Liakata, Ilona Silins, Johan Högberg, Ulla Stenius
Software Mentions: 2
Published: over 13 years ago

10.1186/s12883-016-0548-9

COPPADIS-2015 (COhort of Patients with PArkinson’s DIsease in Spain, 2015), a global –clinical evaluations, serum biomarkers, genetic studies and neuroimaging– prospective, multicenter, non-interventional, long-term study on Parkinson’s disease progression
Cited by: 57
Author(s): Diego Santos‐García, Pablo Mir, Esther Cubo, Lydia Vela, M.C. Rodríguez-Oroz, Marı́a José Martı́, José Matías Arbelo, Jon Infante, Jaime Kulisevsky, Pablo Martínez‐Martín
Software Mentions: 2
Published: over 8 years ago

10.1186/1465-9921-13-54

Step-down from high dose fixed combination therapy in asthma patients: a randomized controlled trial
Cited by: 26
Author(s): Alberto Papi, Gabriele Nicolini, Nunzio Crimi, Leonardo M. Fabbri, Dario Olivieri, Andrea Rossi, Pierluigi Paggiaro
Software Mentions: 2
Published: almost 13 years ago

10.3390/s20247283

MMW Radar-Based Technologies in Autonomous Driving: A Review
Cited by: 52
Author(s): Taohua Zhou, Mengmeng Yang, Kun Jiang, H. T. Wong, Diange Yang
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0060559

DomHR: Accurately Identifying Domain Boundaries in Proteins Using a Hinge Region Strategy
Cited by: 9
Author(s): Xiaoyan Zhang, Long-jian Lu, Qi Song, Qianqian Yang, Dapeng Li, Jiangming Sun, Tong-hua Li, Cong Peng
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0055656

Mining Skeletal Phenotype Descriptions from Scientific Literature
Cited by: 12
Author(s): Tudor Groza, Jane Hunter, Andreas Zankl
Software Mentions: 2
Published: almost 12 years ago

10.1186/1472-6947-12-36

Recognition of medication information from discharge summaries using ensembles of classifiers
Cited by: 36
Author(s): Son Doan, Nigel Collier, Hua Xu, Pham Hoang Duy, Từ Minh Phương
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1007641

Detecting archaic introgression using an unadmixed outgroup
Cited by: 72
Author(s): Laurits Skov, Ruoyun Hui, Vladimir Shchur, Asger Hobolth, Aylwyn Scally, Mikkel Heide Schierup, Richard Durbin
Software Mentions: 2
Published: about 6 years ago

10.1093/database/baw135

NERChem: adapting NERBio to chemical patents via full-token features and named entity feature with chemical sub-class composition
Cited by: 4
Author(s): Richard Tzong-Han Tsai, Yu Cheng Hsiao, Po Ting Lai
Software Mentions: 2
Published: almost 9 years ago

10.1093/database/baz084

The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track
Cited by: 15
Author(s): Sumit Madan, Justyna Szostak, Ravikumar Komandur Elayavilli, Richard Tzong Han Tsai, Mehdi Ali, Longhua Qian, Majid Rastegar-Mojarad, Julia Hoeng, Juliane Fluck
Software Mentions: 2
Published: almost 6 years ago

10.1093/database/baw049

Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning
Cited by: 25
Author(s): Yaoyun Zhang, Jun Xu, Hui Chen, Jingqi Wang, Yonghui Wu, Manu Prakasam, Hua Xu
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.3788

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes
Cited by: 40
Author(s): Abraham G Moller, Chun Liang
Software Mentions: 2
Published: about 7 years ago