List of Publications

Find Samplix' scientific papers and posters.

Scientific Papers

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2024

Pushing the limits of single molecule transcript sequencing to uncover the largest disease-associated transcript isoforms in the humanneural retinal 

Merel Stemerdink, Tabea Riepe, Nick Zomer, et al.

DOI: 10.1101/2024.09.10.612265.  This article is a preprint and has not been certified by peer review. 

 

High-throughput G protein-coupled receptor-based autocrine screening for secondary metabolite production in yeast.

Saleski, T. E.Peng, H.Lengger, B.Wang, J.Jensen, M. K., & Jensen, E. D. (2024).

Biotechnology and Bioengineering114. DOI: 10.1002/bit.28797

 

Taf1 knockout is lethal in embryonic male mice and heterozygous females show weight and movement disorders 

Elisa M. CrombieAndrea J. KoreckiKaren Cleverleyet al.

Dis Model Mech (2024), dmm.050741. DOI: 10.1242/dmm.050741

 

Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA.

Dippenaar, A., Ismail, N., Heupink, T.H. et al.

Sci Rep 14, 9931 (2024). DOI: 10.1038/s41598-024-60545-1

 

Analyzing functional heterogeneity of effector cells for enhanced adoptive cell therapy applications

Anne-Christine Kiel RasmussenThomas Morgan HulenDavid Leander Petersenet al.

This article is a preprint and has not been certified by peer review 

 

T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix Xdrop® enrichment technology

Zarka, K. A., Jagd, L. M. & Douches, D. S.

Front Plant Sci 15, (2024); DOI: 10.3389/fpls.2024.1330429

 

2023

Long-read whole genome analysis of human single cells

Hård, J., Mold, J.E., Eisfeldt, J. et al.

Nat Commun 14, 5164 (2023). DOI: 10.1038/s41467-023-40898-3

 

cis-regulatory point mutation at a R2R3-Myb transcription factor contributes to speciation by reinforcement in Phlox drummondii

Austin G. GarnerAndrew CameronAndrea E. BerardiRobin Hopkins

 

A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors.

Tomaž Š, Petek M, Lukan T, Pogačar K, Stare K, Teixeira Prates E, Jacobson DA, Zrimec J, Bajc G, Butala M, Pompe Novak M, Dudley Q, Patron N, Taler-Verčič A, Usenik A, Turk D, Prat S, Coll A, Gruden K.

Plant Physiol. 2023 Mar 17;191(3):1934-1952. DOI: 10.1093/plphys/kiac579

 

Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation for X-linked genes

Giovenino, C., Trajkova, S., Pavinato, L. et al. 

Eur J Hum Genet (2023). DOI: 10.21203/rs.3.rs-2179710/v1 

 

2022

CRISPR-Powered Microfluidics in Diagnostics: A Review of Main Applications

Azimzadeh, Mostafa, Marziyeh Mousazadeh, Atieh Jahangiri-Manesh, Pouria Khashayar, and Patricia Khashayar.

Chemosensors. 2022; 10(1):3. DOI: 10.3390/chemosensors10010003

 

Unraveling Structural Rearrangements of the CFH Gene Cluster in Atypical Hemolytic Uremic Syndrome Patients Using Molecular Combing and Long-Fragment Targeted Sequencing.

Tschernoster N, Erger F, Walsh PR, McNicholas B, Fistrek M, Habbig S, Schumacher AL, Folz-Donahue K, Kukat C, Toliat MR, Becker C, Thiele H, Kavanagh D, Nürnberg P, Beck BB, Altmüller J. 

J Mol Diagn. 2022 Jun;24(6):619-631. DOI: 10.1016/j.jmoldx.2022.02.006

 

Population-wide gene disruption in the murine lung epithelium via AAV-mediated delivery of CRISPR-Cas9 components

Honglin ChenSteffen DurinckHetal Patelet al.

Mol. Ther. Methods Clin. Dev. (2022). DOI10.1016/j.omtm.2022.10.016.

 

Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells

Keyi GengLara G MerinoLinda WedemannAniek MartensMałgorzata SobotaYerma P SanchezJonas Nørskov SøndergaardRobert J WhiteClaudia Kutter

Genome Res. 2022. 32(10): 1876–1891; DOI10.1101/gr.276901.122

 

2021

Characterization of FMR1 repeat expansion and intragenic variants by indirect sequence capture

Valentina Grosso, Luca Marcolungo, Simone Maestri, et al.

Front. Genet. 2021. 12: 743230; DOIi: 10.3389/fgene.2021.743230

 

Generation and analysis of innovative genomically humanized knockin SOD1, TARDBP (TDP-43), and FUS mouse models

Anny Devoy, Georgia Price, Francesca De Giorgio, Rosie Bunton-Stasyshyn, David Thompson, Samanta Gasco, et al.

iScience. 2021. 24(12): 103463; DOI: 10.1016/j.isci.2021.103463

 

CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells

Keyi Geng, Lara Garcia Merino, Linda Wedemann, Aniek Martens, Malgorzata Sobota, Jonas Norskov Sondergaard, Robert J. White, Claudia Kutter

bioRxiv 2021.07.01.450727; DOI: 10.1101/2021.07.01.450727

 

Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24

Xiongwen Cao, Alexandra Khitun, Yang Luo, Zhenkun Na, Thitima Phoodokmai, Khomkrit Sappakhaw, Elizabeth Olatunji, Chayasith Uttamapinant, Sarah A. Slavoff. 

Nat Commun 12, 508, 2021. DOI: 10.1038/s41467-020-20841-6

 

Verification of CRISPR editing and finding transgenic inserts by Xdrop Indirect sequence capture followed by short- and long- read sequencing

Blondal Thorarinn, Gamba Cristina, Jagd Lea Møller, Su Ling, Demirov Dimiter, Guo Shuang, Camille M. Johnston, Eva M. Riising, Wu Xiaolin, Marie J. Mikkelsen, Szabova Ludmila, Mouritzen Peter

Methods. 2021 Jul;191:68-77. DOI: 10.1016/j.ymeth.2021.02.003.

 

 2020

Reconstruction of the birth of a male sex chromosome present in Atlantic herring

Rafati N, Chen J, Herpin A, Pettersson ME, Han F, Feng C, Wallerman O, Rubin CJ, Péron S, Cocco A, Larsson M, Trötschel C, Poetsch A, Korsching K, Bönigk W, Körschen HG, Berg F, Folkvord A, Kaupp UB, Schartl M, Andersson L.

Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24359-24368. DOI: 10.1073/pnas.2009925117

 

Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting

Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ.

Hum Mutat. 2020 Sep;41(9):1671-1679. DOI: 10.1002/humu.24063.

2020 

Corrigendum to "Generation of a set of isogenic, gene-edited iPSC lines homozygous for all main APOE variants and an APOE knock-out line" [Stem Cell Res. 34/1873-5061 (2019) 101349-55]

Schmid B, Prehn KR, Nimsanor N, Garcia BIA, Poulsen U, Jørring I, Rasmussen MA, Clausen C, Mau-Holzmann UA, Ramakrishna S, Muddashetty R, Steeg R, Bruce K, Mackintosh P, Ebneth A, Holst B, Cabrera-Socorro A.

Stem Cell Res. 2020 Sep 21;48:102005. doi: 10.1016/j.scr.2020.102005. Epub ahead of print. Erratum for: Stem Cell Res. 2019 Jan;34:101349. PMID: 32971461.

Posters

Poster identifying and isolating single immune cells based on their function

Identifying and isolating single immune cells based on their function using an Xdrop workflow

Poster Supporting engineered cell therapy

Supporting engineered cell therapy: targeted and accurate assessments of gene editing outcomes with Xdrop

Poster Unbiased amplification

Unbiased Amplification of single molecules enables even coverage of chromosomal DNA

Poster Microfluidics based

Microfluidics based, long fragment, targeted enrichment with Xdrop

Discover other applications

Screening box square

Screening

Transform discovery workflows. Effortlessly encapsulate single-cell libraries, enhancing the speed of your screening campaigns.


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Cell line development

Elevate cell line development workflow. Encapsulate and screen single mammalian cells for enhanced antibody production.


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Immunotherapy

Explore immune cell function in single-cell format assays, including cytokine, granzyme B, and cell killing assays.


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Genomics

Discover the Xdrop workflow, for CRISPR editing, CAR cassette insertion site validation, and more.