Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: lib
https://packages.ecosyste.ms/registries/pypi.org/packages/lib
Autocode standard library Python bindings
4 versions
Latest release: almost 3 years ago
2 dependent packages
63,859 downloads last month
Papers Mentioning lib 26
10.1371/journal.pcbi.1008605
Machine learning based CRISPR gRNA design for therapeutic exon skippingCited by: 5
Author(s): Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford
Software Mentions: 8
Published: almost 4 years ago
10.1371/journal.pbio.3000241
Islands of retroelements are major components of Drosophila centromeresCited by: 117
Author(s): Ching-Ho Chang, Ankita Chavan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-ting Wu, Amanda M. Larracuente, Barbara G. Mellone
Software Mentions: 6
Published: over 5 years ago
10.1186/1751-0473-8-14
GenePattern flow cytometry suiteCited by: 16
Author(s): Josef Špidlen, Aaron Barsky, Karin Breuer, Peter A. Carr, Marc‐Danie Nazaire, Barbara Hill, Qian Yu, Ted Liefeld, Michael Reich, Jill P. Mesirov, Peter Wilkinson, Richard H. Scheuermann, Rafick‐Pierre Sékaly, Ryan R. Brinkman
Software Mentions: 5
Published: over 11 years ago
10.7717/peerj-cs.533
AndroAnalyzer: android malicious software detection based on deep learningCited by: 13
Author(s): Recep Sinan Arslan
Software Mentions: 5
Published: over 3 years ago
10.3390/s16050645
An Integrated Simulation Module for Cyber-Physical Automation SystemsCited by: 18
Author(s): Francesco Ferracuti, Alessandro Freddi, Andrea Monteriù, Mariorosario Prist
Software Mentions: 4
Published: over 8 years ago
10.1186/s13059-019-1842-9
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methodsCited by: 318
Author(s): Brian J. Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, Aviv Regev
Software Mentions: 4
Published: about 5 years ago
10.1007/s10577-019-09605-1
A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular driveCited by: 29
Author(s): Brendan M Smalec, Thomas Heider, Brianna L. Flynn, Rachel J. O’Neill
Software Mentions: 3
Published: almost 6 years ago
10.1021/acs.inorgchem.0c02971
Rationalizing the Decavanadate(V) and Oxidovanadium(IV) Binding to G-Actin and the Competition with Decaniobate(V) and ATPCited by: 26
Author(s): Giuseppe Sciortino, Manuel Aureliano, Eugenio Garribba
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13059-015-0596-2
Bridger: a new framework for de novo transcriptome assembly using RNA-seq dataCited by: 246
Author(s): Zheng Chang, Guojun Li, Juntao Liu, Yu Zhang, Cody Ashby, De Li Liu, Carole L. Cramer, Xiuzhen Huang
Software Mentions: 3
Published: almost 10 years ago
10.3390/s21186050
A Novel Automate Python Edge-to-Edge: From Automated Generation on Cloud to User Application Deployment on Edge of Deep Neural Networks for Low Power IoT Systems FPGA-Based AccelerationCited by: 1
Author(s): Tarek Belabed, Vitor Ramos Gomes da Silva, Alexandre Quenon, Carlos Valderamma, Chokri Souani
Software Mentions: 3
Published: about 3 years ago
10.1128/mBio.01950-18
Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing MachineryCited by: 8
Author(s): James T. Van Leuven, Meng Mao, Denghui Xing, Gordon M. Bennett, John P. McCutcheon
Software Mentions: 3
Published: over 5 years ago
10.1534/g3.119.400596
A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing DataCited by: 15
Author(s): Tom Hill, Robert L. Unckless
Software Mentions: 2
Published: about 5 years ago
10.1186/1471-2105-10-428
TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling dataCited by: 185
Author(s): Álvaro Cuadros-Inostroza, Camila Caldana, Henning Redestig, Miyako Kusano, Jan Lisec, Hugo Peña‐Cortés, Lothar Willmitzer, Matthew A. Hannah
Software Mentions: 2
Published: almost 15 years ago
10.1186/s12870-018-1585-x
Comparative transcriptomics identifies patterns of selection in rosesCited by: 13
Author(s): Shubin Li, Mingyu Zhong, Xue Dong, Xiaoling Jiang, Yuxing Xu, Yibo Sun, Fang Cheng, Li D, Kaixue Tang, Wang Si-qing, Silan Dai, Jin‐Yong Hu
Software Mentions: 2
Published: almost 6 years ago
10.1111/1755-0998.12297
Genome assembly and annotation of a<i>Drosophila simulans</i>strain from MadagascarCited by: 46
Author(s): Nicola Palmieri, Viola Nolte, Jun Chen, Christian Schlötterer
Software Mentions: 2
Published: over 10 years ago
10.1155/2020/4932572
Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat’s Claw) against the Main Protease 3CLpro of SARS-CoV-2 by Molecular ModelingCited by: 19
Author(s): Andrés F. Yepes-Pérez, Oscar Herrera-Calderon, José-Emilio Sánchez-Aparicio, Laura Tiessler-Sala, Jean‐Didier Maréchal, Wilson Cardona‐G
Software Mentions: 2
Published: about 4 years ago
10.3389/fgene.2021.739781
Chromosome-Scale Genome Assembly and Transcriptome Assembly of Kawakawa Euthynnus affinis; A Tuna-Like SpeciesCited by: 3
Author(s): Miloš Havelka, Eitaro Sawayama, Taiju Saito, Kazutoshi Yoshitake, Daiki Saka, Toshinao Ineno, Shuichi Asakawa, Motohiro Takagi, Ryoji Goto, Takahiro Matsubara
Software Mentions: 2
Published: about 3 years ago
10.1093/gigascience/gix108
Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumeriliCited by: 13
Author(s): Elena Sarropoulou, Arvind Sundaram, Elisavet Kaitetzidou, Georgios Kotoulas, Gregor D. Gilfillan, Nikos Papandroulakis, Constantinos C. Mylonas, Antoniοs Magoulas
Software Mentions: 2
Published: about 7 years ago
10.1038/srep34998
Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognitionCited by: 26
Author(s): S.J. Choi, Changill Ban
Software Mentions: 2
Published: about 8 years ago
10.1534/g3.120.401411
A Reference Genome from the Symbiotic Hydrozoan,<i>Hydra viridissima</i>Cited by: 12
Author(s): Mayuko Hamada, Noriyuki Satoh, Konstantin Khalturin
Software Mentions: 1
Published: about 4 years ago
10.1186/s12860-020-00294-x
Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivityCited by: 10
Author(s): Elliot D. Drew, Robert W. Janes
Software Mentions: 1
Published: over 4 years ago
10.1107/S2059798320014540
Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metalsCited by: 7
Author(s): Thorsten B. Blum, D. Housset, Max T. B. Clabbers, Eric Van Genderen, Maria Bacia‐Verloop, U. Zander, A.A. McCarthy, Guy Schoehn, Wai Li Ling, Jan Pieter Abrahams
Software Mentions: 1
Published: almost 4 years ago
10.3390/s21051915
Tactile Sensors for Parallel Grippers: Design and CharacterizationCited by: 8
Author(s): Andrea Cirillo, Marco Costanzo, Gianluca Laudante, Salvatore Pirozzi
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0153507
Modeling Dynamic Systems with Efficient Ensembles of Process-Based ModelsCited by: 21
Author(s): Nikola Simidjievski, Ljupčo Todorovski, Sašo Džeroski
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0017957
The Notch-2 Gene Is Regulated by Wnt Signaling in Cultured Colorectal Cancer CellsCited by: 56
Author(s): Jonas Ungerbäck, Nils Elander, John Grünberg, Mikael Sigvardsson, Peter Söderkvist
Software Mentions: 1
Published: over 13 years ago
10.1093/gigascience/giy097
The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)Cited by: 15
Author(s): Hansheng Zhao, Songbo Wang, Jiongliang Wang, Chunhai Chen, Shijie Hao, Lianfu Chen, Baowei Fei, Kai Han, Rongsheng Li, Chengcheng Shi, Huayu Sun, Sining Wang, Hao Xu, Kebin Yang, Xiurong Xu, Xuemeng Shan, Jingjing Shi, Aiqin Feng, Guangyi Fan, Xin Liu, Shancen Zhao, Chi Zhang, Qiang Gao, Zhimin Gao, Zehui Jiang
Software Mentions: 1
Published: over 6 years ago