cran: LSC | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giab003

long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data
Cited 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 genome
Cited 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: almost 8 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 Macrophages
Cited 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 plants
Cited 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 Sequencing
Cited 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 Level
Cited 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 analyses
Cited by: 33
Author(s): Xing Qin, Xiaoyun Su, Huiying Luo, Rui Ma, Bin Yao, Fuying Ma
Software Mentions: 4
Published: almost 7 years ago

10.12688/f1000research.10571.2

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Cited 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 officinale
Cited 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 Sequencing
Cited 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: almost 6 years ago

10.1186/s13059-019-1883-0

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads
Cited by: 11
Author(s): Laura H. Tung, Mingfu Shao, Carl Kingsford
Software Mentions: 3
Published: about 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 Investigations
Cited 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 Transcriptomes
Cited 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 reads
Cited 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 Alignment
Cited 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 correction
Cited 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 information
Cited 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 multicinctus
Cited 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: over 4 years ago

10.1038/s41598-021-91873-1

Time-domain based evaluation of detection efficiency in liquid scintillation counting
Cited 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 hallaensis
Cited 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 Republic
Cited by: 7
Author(s): Hana Bednaříková, Natália Kaščáková, Jana Fürstová, Zuzana Zelinková, Přemysl Falt, Jozef Hašto, Peter Tavel
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-016-1316-y

LSCplus: a fast solution for improving long read accuracy by short read alignment
Cited by: 19
Author(s): Ruifeng Hu, Guibo Sun, Xiaobo Sun
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-017-1610-3

HALC: High throughput algorithm for long read error correction
Cited 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 methods
Cited by: 55
Author(s): Haowen Zhang, Chirag Jain, Srinivas Aluru
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-019-6286-9

A hybrid and scalable error correction algorithm for indel and substitution errors of long reads
Cited by: 5
Author(s): Arghya Kusum Das, Sayan Goswami, Kisung Lee, Seung-Jong Park
Software Mentions: 1
Published: about 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 transcripts
Cited 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 correction
Cited by: 561
Author(s): Leena Salmela, Éric Rivals
Software Mentions: 1
Published: over 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 bracteata
Cited by: 0
Author(s): Nurohaida Ab Aziz, Salwani Shaffie, Azimah Abd Rahman, Hokchai Yam, Nazalan Najimudin, Amir Hamzah Ahmad Ghazali
Software Mentions: 1
Published: almost 4 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 Reads
Cited 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 Approaches
Cited by: 24
Author(s): Hsin-Hung Lin, Yu-Chieh Liao
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0061980

Paraquat Modulates Alternative Pre-mRNA Splicing by Modifying the Intracellular Distribution of SRPK2
Cited 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 cells
Cited 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 Maize
Cited 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 miltiorrhiza
Cited 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 Applications
Cited 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 nicotianae
Cited 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 Lipopolysaccharide
Cited 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 Learning
Cited 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 Estimates
Cited 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 reads
Cited 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

Projects: cran: LSC

Papers Mentioning LSC 42