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: cran: LSC
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/LSC
Local Statistical Complexity - Automatic Pattern Discovery in
Spatio-Temporal Data
2 versions
Latest release: almost 11 years ago
0 downloads
Papers Mentioning LSC 42
10.1093/gigascience/giab003
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing dataCited by: 25
Author(s): Shanika L. Amarasinghe, Matthew E. Ritchie, Quentin Gouil
Software Mentions: 6
Published: almost 4 years ago
10.1038/srep43793
Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genomeCited by: 24
Author(s): Guogui Ning, Cheng Xu, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Software Mentions: 5
Published: over 7 years ago
10.1016/j.immuni.2017.12.010
The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized MacrophagesCited by: 153
Author(s): Zsolt Czimmerer, Bence Dániel, Attila Horváth, Dominik Rückerl, Gergely Nagy, Máté Kiss, Matthew Peloquin, Marietta Margit Budai, Ixchelt Cuaranta-Monroy, Zoltán Simándi, László Steiner, Béla Nagy, Szilárd Póliska, Csaba Bankó, Zsolt Bacsó, Ira G. Schulman, Sascha Sauer, Jean Deleuze, Judith E. Allen, Szilvia Benkő, László Nagy
Software Mentions: 5
Published: almost 7 years ago
10.1111/tpj.14179
Computational aspects underlying genome to phenome analysis in plantsCited by: 47
Author(s): Anthony Bolger, Hendrik Poorter, Kathryn Dumschott, Marie E. Bolger, Daniel Arend, Sonia Osorio, Heidrun Gundlach, Klaus Mayer, Matthias Lange, Uwe Scholz, Björn Usadel
Software Mentions: 4
Published: almost 6 years ago
10.3389/fgene.2019.00384
Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome SequencingCited by: 81
Author(s): Bo Wang, Vivek Kumar, Andrew Olson, Doreen Ware
Software Mentions: 4
Published: over 5 years ago
10.3389/fpls.2021.698602
Investigation Into Different Wood Formation Mechanisms Between Angiosperm and Gymnosperm Tree Species at the Transcriptional and Post-transcriptional LevelCited by: 2
Author(s): Hui Li, Guanghui Chen, Hongying Pang, Qiao Wang, Xinren Dai
Software Mentions: 4
Published: over 3 years ago
10.1186/s13068-018-1060-9
Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analysesCited by: 33
Author(s): Xing Qin, Xiaoyun Su, Huiying Luo, Rui Ma, Bin Yao, Fuying Ma
Software Mentions: 4
Published: over 6 years ago
10.12688/f1000research.10571.2
Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysisCited by: 332
Author(s): Jason L. Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu‐Jie Wang, David Buck, Kin Fai Au
Software Mentions: 4
Published: over 7 years ago
10.3390/genes8100257
Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinaleCited by: 18
Author(s): Li He, Shuhua Fu, Zhichao Xu, Jun Yan, Jiang Xu, Hong Zhou, Jianguo Zhou, Xinlian Chen, Ying Liu, Kin Fai Au, Hui Yao
Software Mentions: 3
Published: about 7 years ago
10.3389/fgene.2019.00253
Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA SequencingCited by: 100
Author(s): Liangzhen Zhao, Hangxiao Zhang, Markus V. Kohnen, Kasavajhala V. S. K. Prasad, Lianfeng Gu, Anireddy S. N. Reddy
Software Mentions: 3
Published: over 5 years ago
10.1186/s13059-019-1883-0
Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long readsCited by: 11
Author(s): Laura H. Tung, Mingfu Shao, Carl Kingsford
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12864-020-07124-6
Multi-tissue transcriptome analysis using hybrid-sequencing reveals potential genes and biological pathways associated with azadirachtin A biosynthesis in neem (azadirachta indica)Cited by: 9
Author(s): Huiyan Wang, Ning Wang, Yi-Xin Huo
Software Mentions: 2
Published: about 4 years ago
10.3389/fmed.2021.643175
Production of Mass-Separated Erbium-169 Towards the First Preclinical in vitro InvestigationsCited by: 9
Author(s): Zeynep Talip, Francesca Borgna, Cristina Müller, J. Ulrich, Charlotte Duchemin, J.P. Ramos, T. Stora, U. Köster, Youcef Nedjadi, Vadim Gadelshin, Valentin Fedosseev, F. Juget, Claude Bailat, Adelheid Fankhauser, S. G. Wilkins, Laura Lambert, B. A. Marsh, D. V. Fedorov, E. Chevallay, P. Fernier, Roger Schibli, Nicholas P. van der Meulen
Software Mentions: 2
Published: over 3 years ago
10.3390/genes9010043
Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant TranscriptomesCited by: 54
Author(s): Dong An, Hieu X. Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Software Mentions: 2
Published: almost 7 years ago
10.1186/s13059-018-1605-z
A comparative evaluation of hybrid error correction methods for error-prone long readsCited by: 83
Author(s): Shuhua Fu, Anqi Wang, Kin Fai Au
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0046679
Improving PacBio Long Read Accuracy by Short Read AlignmentCited by: 278
Author(s): Kin Fai Au, Jason G. Underwood, Lawrence Lee, Wing Hung Wong
Software Mentions: 2
Published: about 12 years ago
10.1093/bib/bbv029
Denoising DNA deep sequencing data—high-throughput sequencing errors and their correctionCited by: 235
Author(s): David Laehnemann, Arndt Borkhardt, Alice C. McHardy
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2105-15-211
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence informationCited by: 446
Author(s): Marten Boetzer, Walter Pirovano
Software Mentions: 2
Published: over 10 years ago
10.1038/s41598-020-70565-2
Kinetic analysis of effects of temperature and time on the regulation of venom expression in Bungarus multicinctusCited by: 10
Author(s): Xiao Yin, Shuai Guo, Jihai Gao, Lu Luo, Xuejiao Liao, Mingqian Li, He Su, Zhixing Huang, Jiang Xu, Jin Pei, Shilin Chen
Software Mentions: 2
Published: about 4 years ago
10.1038/s41598-021-91873-1
Time-domain based evaluation of detection efficiency in liquid scintillation countingCited by: 2
Author(s): K. Mitev, Chavdar Dutsov, P. Cassette, Benoît Sabot
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2020.621301
The Draft Genome Sequence of a New Land-Hopper Platorchestia hallaensisCited by: 1
Author(s): Ajit Kumar Patra, Oksung Chung, Ji Yong Yoo, Sang Ho Baek, Tae Won Jung, Min-Seop Kim, Moon Geun Yoon, Yali Yang, Jeong-Hyeon Choi
Software Mentions: 2
Published: almost 4 years ago
10.3390/ijerph18063237
Life Stressors in Patients with Inflammatory Bowel Disease: Comparison with a Population-Based Healthy Control Group in the Czech RepublicCited by: 7
Author(s): Hana Bednaříková, Natália Kaščáková, Jana Fürstová, Zuzana Zelinková, Přemysl Falt, Jozef Hašto, Peter Tavel
Software Mentions: 1
Published: over 3 years ago
10.1186/s12859-016-1316-y
LSCplus: a fast solution for improving long read accuracy by short read alignmentCited by: 19
Author(s): Ruifeng Hu, Guibo Sun, Xiaobo Sun
Software Mentions: 1
Published: almost 8 years ago
10.1186/s12859-017-1610-3
HALC: High throughput algorithm for long read error correctionCited by: 51
Author(s): Ergude Bao, Lingxiao Lan
Software Mentions: 1
Published: over 7 years ago
10.1186/s12864-020-07227-0
A comprehensive evaluation of long read error correction methodsCited by: 55
Author(s): Haowen Zhang, Chirag Jain, Srinivas Aluru
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12864-019-6286-9
A hybrid and scalable error correction algorithm for indel and substitution errors of long readsCited by: 5
Author(s): Arghya Kusum Das, Sayan Goswami, Kisung Lee, Seung-Jong Park
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12870-021-03091-6
Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcriptsCited by: 1
Author(s): Hui Zhang, Jingjing Jin, Guoyun Xu, Zefeng Li, Zheyu Niu, Qingyuan Zheng, Hongkun Lv, Pingping Li, Lifeng Jin, Qiansi Chen, Peijian Cao, Huina Zhou
Software Mentions: 1
Published: over 3 years ago
10.1093/bioinformatics/btu538
LoRDEC: accurate and efficient long read error correctionCited by: 561
Author(s): Leena Salmela, Éric Rivals
Software Mentions: 1
Published: about 10 years ago
10.1128/MRA.01051-20
Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Burkholderia sp. Strain USMB20, Isolated from Nodules of Mucuna bracteataCited by: 0
Author(s): Nurohaida Ab Aziz, Salwani Shaffie, Azimah Abd Rahman, Hokchai Yam, Nazalan Najimudin, Amir Hamzah Ahmad Ghazali
Software Mentions: 1
Published: over 3 years ago
10.3390/molecules23061248
Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L.Cited by: 16
Author(s): Jia Ge, Lei Cai, Guoan Bi, Chen Gao, Weibang Sun
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0109999
Whole Genome Complete Resequencing of Bacillus subtilis Natto by Combining Long Reads with High-Quality Short ReadsCited by: 33
Author(s): Masao Kamada, Sumitaka Hase, Kengo Sato, Atsushi Toyoda, Asao Fujiyama, Yasubumi Sakakibara
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0144305
Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid ApproachesCited by: 24
Author(s): Hsin-Hung Lin, Yu-Chieh Liao
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pone.0061980
Paraquat Modulates Alternative Pre-mRNA Splicing by Modifying the Intracellular Distribution of SRPK2Cited by: 20
Author(s): Silvia Vivarelli, Silvia C. Lenzken, Marc-David Ruepp, Francesco Ranzini, Andrea Maffioletti, Reinaldo Alvarez, Oliver Mühlemann, Silvia M.L. Barabino
Software Mentions: 1
Published: over 11 years ago
10.3389/fgene.2014.00215
Using a medium-throughput comet assay to evaluate the global DNA methylation status of single cellsCited by: 21
Author(s): Angélique Lewies, Etresia van Dyk, Johannes F. Wentzel, P. J. Pretorius
Software Mentions: 1
Published: over 10 years ago
10.3389/fpls.2017.00694
A Comprehensive Analysis of Alternative Splicing in Paleopolyploid MaizeCited by: 53
Author(s): Wenbin Mei, Sanzhen Liu, James C. Schnable, Cheng‐Ting Yeh, Nathan M. Springer, Patrick S. Schnable, W. Brad Barbazuk
Software Mentions: 1
Published: over 7 years ago
10.3389/fpls.2016.00100
Global Identification of the Full-Length Transcripts and Alternative Splicing Related to Phenolic Acid Biosynthetic Genes in Salvia miltiorrhizaCited by: 42
Author(s): Zhichao Xu, Hongmei Luo, Aijia Ji, Xin Zhang, Jingyuan Song, Shilin Chen
Software Mentions: 1
Published: almost 9 years ago
10.1016/j.gpb.2015.08.002
PacBio Sequencing and Its ApplicationsCited by: 1,445
Author(s): Anthony Rhoads, Kin Fai Au
Software Mentions: 1
Published: about 9 years ago
10.1186/s13742-016-0108-7
Genomes and virulence difference between two physiological races of Phytophthora nicotianaeCited by: 36
Author(s): Hui Liu, Xiao Ma, Haiqin Yu, Dunhuang Fang, Yongping Li, Xiao Wang, Wenwen Wang, Yang Dong, Bingguang Xiao
Software Mentions: 1
Published: almost 9 years ago
10.1186/1465-9921-6-116
Respiratory epithelial cells require Toll-like receptor 4 for induction of Human β-defensin 2 by LipopolysaccharideCited by: 96
Author(s): Ruth MacRedmond, Catherine M. Greene, Clifford C. Taggart, Noel G. McElvaney, Shane O’Neill
Software Mentions: 1
Published: about 19 years ago
10.1038/s41598-018-28364-3
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative LearningCited by: 6
Author(s): Olivia Choudhury, Ankush Chakrabarty, Scott J. Emrich
Software Mentions: 1
Published: over 6 years ago
10.3390/s16081168
Computing the Deflection of the Vertical for Improving Aerial Surveys: A Comparison between EGM2008 and ITALGEO05 EstimatesCited by: 17
Author(s): Riccardo Barzaghi, Daniela Carrión, Massimiliano Pepe, G. Prezioso
Software Mentions: 1
Published: over 8 years ago
10.1186/s13015-016-0075-7
Jabba: hybrid error correction for long sequencing readsCited by: 61
Author(s): Giles Miclotte, Mahdi Heydari, Piet Demeester, Stéphane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
Software Mentions: 1
Published: over 8 years ago