Skip to main content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Volume 6(1);  2021

Innovations

Fluorescent-dependent comparative Ct method for qPCR gene expression analysis in IVF clinical pre-implantation embryonic testing
Arnav Lal, William E Roudebush, Monica Mainigi, Renee J Chosed
Biol Methods Protoc. 2021; 6(1): bpab001. Published online 2021 Jan 18. doi: 10.1093/biomethods/bpab001
PMCID:
PMC7998709
Abstract Article PDF–550K
Single well, single-common primer pair, dual probe, duplex qPCR assay for the quantification of mRNA splicing variants
Janice Wang, Winifred P Wong, Emma O Link, Shantel Olivares, Cade T Adelman, Anne S Henkel, Malek El Muayed
Biol Methods Protoc. 2021; 6(1): bpab002. Published online 2021 Feb 9. doi: 10.1093/biomethods/bpab002
PMCID:
PMC7903517
Abstract Article PDF–468K
Sequence-specific inhibition of reverse transcription by recombinant CRISPR/dCas13a ribonucleoprotein complexes in vitro
Toshitsugu Fujita, Shoko Nagata, Miyuki Yuno, Hodaka Fujii
Biol Methods Protoc. 2021; 6(1): bpab009. Published online 2021 Apr 19. doi: 10.1093/biomethods/bpab009
PMCID:
PMC8106441
Abstract Article PDF–427K
OptM: estimating the optimal number of migration edges on population trees using Treemix
Robert R Fitak
Biol Methods Protoc. 2021; 6(1): bpab017. Published online 2021 Sep 16. doi: 10.1093/biomethods/bpab017
PMCID:
PMC8476930
Abstract Article PDF–306K

Methods Article

Heterozygous KCNH2 variant phenotyping using Flp-In HEK293 and high-throughput automated patch clamp electrophysiology
Chai-Ann Ng, Jessica Farr, Paul Young, Monique J Windley, Matthew D Perry, Adam P Hill, Jamie I Vandenberg
Biol Methods Protoc. 2021; 6(1): bpab003. Published online 2021 Mar 19. doi: 10.1093/biomethods/bpab003
PMCID:
PMC8046900
Abstract Article PDF–2.2M
Optimization and biological validation of an in vitro assay using the transfected Dm28c/pLacZ Trypanosoma cruzi strain
Julián Ernesto Nicolás Gulin, Daniela Marisa Rocco, Victoria Alonso, Pamela Cribb, Jaime Altcheh, Facundo García-Bournissen
Biol Methods Protoc. 2021; 6(1): bpab004. Published online 2021 Jul 13. doi: 10.1093/biomethods/bpab004
PMCID:
PMC8355463
Abstract Article PDF–408K
Circular DNA enrichment sequencing reveals the viral/satellites genetic diversity associated with the third epidemic of cotton leaf curl disease
Nasim Ahmed, Imran Amin, Syed Shan-e-Ali Zaidi, Saleem Ur Rahman, Muhammad Farooq, Claude Maurice Fauquet, Shahid Mansoor
Biol Methods Protoc. 2021; 6(1): bpab005. Published online 2021 Mar 25. doi: 10.1093/biomethods/bpab005
PMCID:
PMC8046901
Abstract Article PDF–1.0M
Novel metric for hyperbolic phylogenetic tree embeddings
Hirotaka Matsumoto, Takahiro Mimori, Tsukasa Fukunaga
Biol Methods Protoc. 2021; 6(1): bpab006. Published online 2021 Mar 27. doi: 10.1093/biomethods/bpab006
PMCID:
PMC8058397
Abstract Article PDF–501K
A two-step PCR assembly for construction of gene variants across large mutational distances
Shreya Routh, Anamika Acharyya, Riddhiman Dhar
Biol Methods Protoc. 2021; 6(1): bpab007. Published online 2021 Apr 2. doi: 10.1093/biomethods/bpab007
PMCID:
PMC8062255
Abstract Article PDF–545K
MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads
Malte B Hallgren, Søren Overballe-Petersen, Ole Lund, Henrik Hasman, Philip T L C Clausen
Biol Methods Protoc. 2021; 6(1): bpab008. Published online 2021 Apr 21. doi: 10.1093/biomethods/bpab008
PMCID:
PMC8106442
Abstract Article PDF–256K
Development of a LAMP assay using a portable device for the real-time detection of cotton leaf curl disease in field conditions
Amna Rafiq, Waqas Rafique Ali, Muhammad Asif, Nasim Ahmed, Waheed S Khan, Shahid Mansoor, Sadia Zafar Bajwa, Imran Amin
Biol Methods Protoc. 2021; 6(1): bpab010. Published online 2021 May 6. doi: 10.1093/biomethods/bpab010
PMCID:
PMC8164779
Abstract Article PDF–597K
Cryopreservation of clonal and polyclonal populations of Chlamydomonas reinhardtii
Jacob Boswell, Charles Ross Lindsey, Emily Cook, Frank Rosenzweig, Matthew Herron
Biol Methods Protoc. 2021; 6(1): bpab011. Published online 2021 Jun 21. doi: 10.1093/biomethods/bpab011
PMCID:
PMC8263314
Abstract Article PDF–454K
A comparison of the efficiency of RNA extraction from extracellular vesicles using the Qiagen RNeasy MinElute versus Enzymax LLC RNA Tini Spin columns and qPCR of miRNA
Rachael Anne Dunlop, Sandra Anne Banack, Paul Alan Cox
Biol Methods Protoc. 2021; 6(1): bpab015. Published online 2021 Jul 21. doi: 10.1093/biomethods/bpab015
PMCID:
PMC8344526
Abstract Article PDF–471K
A genome-wide circular RNA transcriptome in rat
Disha Sharma, Paras Sehgal, Sridhar Sivasubbu, Vinod Scaria
Biol Methods Protoc. 2021; 6(1): bpab016. Published online 2021 Sep 7. doi: 10.1093/biomethods/bpab016
PMCID:
PMC8435660
Abstract Article PDF–741K
Wildlife pathogen detection: evaluation of alternative DNA extraction protocols
Vasiliki Mantzana-Oikonomaki, Martine Maan, Joana Sabino-Pinto
Biol Methods Protoc. 2021; 6(1): bpab018. Published online 2021 Sep 17. doi: 10.1093/biomethods/bpab018
PMCID:
PMC8529346
Abstract Article PDF–290K
Bright fluorescent nucleic acid detection with CRISPR-Cas12a and poly(thymine) templated copper nanoparticles
Janna F M Bogers, Nicole F Berghuis, Ruud W Busker, Angelo van Booma, Armand Paauw, Hans C van Leeuwen
Biol Methods Protoc. 2021; 6(1): bpaa020. Published online 2020 Oct 8. doi: 10.1093/biomethods/bpaa020
Correction in:
Biol Methods Protoc. 2022; 7(1): bpac016.
PMCID:
PMC7891128
Abstract Article PDF–465K
MultiPep: a hierarchical deep learning approach for multi-label classification of peptide bioactivities
Alexander G B Grønning, Tim Kacprowski, Camilla Schéele
Biol Methods Protoc. 2021; 6(1): bpab021. Published online 2021 Nov 23. doi: 10.1093/biomethods/bpab021
PMCID:
PMC8665375
Abstract Article PDF–431K
Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples
Sara D’Andreano, Anna Cuscó, Olga Francino
Biol Methods Protoc. 2021; 6(1): bpaa026. Published online 2020 Dec 23. doi: 10.1093/biomethods/bpaa026
PMCID:
PMC7820110
Abstract Article PDF–279K
Intestinal crypt-derived enteroid coculture in presence of peristaltic longitudinal muscle myenteric plexus
Daniel E Levin, Arabinda Mandal, Mark A Fleming, Katherine H Bae, Brielle Gerry, Sean R Moore
Biol Methods Protoc. 2021; 6(1): bpaa027. Published online 2020 Dec 23. doi: 10.1093/biomethods/bpaa027
PMCID:
PMC7891127
Abstract Article PDF–766K

Pre-Registered Study Protocols

Effect of nutritional education intervention to reduce anaemia during pregnancy in Dodoma City, Tanzania: protocol for a cluster randomized controlled trial
Mariam J Munyogwa, Nyasiro S Gibore, Agatha F Ngowi, Ipyana H Mwampagatwa
Biol Methods Protoc. 2021; 6(1): bpab012. Published online 2021 Jun 8. doi: 10.1093/biomethods/bpab012
PMCID:
PMC8242494
Abstract Article PDF–734K

New Materials

MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis
Miyuki Yuno, Shoko Nagata, Toshitsugu Fujita, Hodaka Fujii
Biol Methods Protoc. 2021; 6(1): bpab013. Published online 2021 Jul 9. doi: 10.1093/biomethods/bpab013
PMCID:
PMC8365529
Abstract Article PDF–272K
pSIR-bsr, a self-inactivating retrovirus vector expressing the blasticidin S-resistance gene
Hodaka Fujii
Biol Methods Protoc. 2021; 6(1): bpab022. Published online 2021 Dec 6. doi: 10.1093/biomethods/bpab022
PMCID:
PMC8678448
Abstract Article PDF–255K

Protocols

Quantifying the invasion and migration ability of cancer cells with a 3D Matrigel drop invasion assay
Merve Aslan, En-Chi Hsu, Shiqin Liu, Tanya Stoyanova
Biol Methods Protoc. 2021; 6(1): bpab014. Published online 2021 Jul 21. doi: 10.1093/biomethods/bpab014
PMCID:
PMC8346651
Abstract Article PDF–853K

Pre-registered Study Protocols

Effect of community-based lifestyle education intervention to reduce cardiovascular diseases risk factors among vulnerable population in Dodoma city, Tanzania: a cluster randomized controlled trial study protocol
Nyasiro S Gibore, Mariam J Munyogwa, Secilia K Ng’weshemi, Ainory P Gesase
Biol Methods Protoc. 2021; 6(1): bpab019. Published online 2021 Oct 7. doi: 10.1093/biomethods/bpab019
PMCID:
PMC8545611
Abstract Article PDF–305K
Articles from Biology Methods & Protocols are provided here courtesy of Oxford University Press
-