Publications

(Jul 2022) A pulmonologist’s guide to perform and analyse cross-species single lung cell transcriptomics
Peter Pennitz, Holger Kirsten, Vincent D. Friedrich, Emanuel Wyler, Cengiz Goekeri, Benedikt Obermayer, Gitta A. Heinz, Mir-Farzin Mashreghi, Maren Büttner, Jakob Trimpert, Markus Landthaler, Norbert Suttorp, Andreas C. Hocke, Stefan Hippenstiel, Mario Tönnies, Markus Scholz, Wolfgang M. Kuebler, Martin Witzenrath, Katja Hoenzke, Geraldine Nouailles
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(Jun 2022) Single cell- and spatial ‘Omics revolutionize physiology
Thomas Conrad, Janine Altmüller
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(Mar 2022) Analysis of myocardial cellular gene expression during pressure overload reveals matrix based functional intercellular communication
M., Wang, Y., Gigina, A., Korf-Klingebiel, M., Bosnjak, B., Davenport, C.F., Wiehlmann, L., Geffers, Dobreva, G., Völkers, M., Heineke, J.
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(Mar 2022) Recent advances in T-cell receptor repertoire analysis: Bridging the gap with multimodal single-cell RNA sequencing
Sebastiaan Valkiers, Nicky de Vrij, Sofie Gielis, Sara Verbandt, Benson Ogunjimi, Kris Laukens, Pieter Meysman
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(Feb 2022) Immunotherapy of cancer in single-cell RNA sequencing era: A precision medicine perspective
Nafiseh Erfanian, Afshin Derakhshani, Saeed Nasseri, Mohammad Fereidouni, Behzad Baradaran, Neda Jalili Tabrizi, Oronzo Brunetti, Renato Bernardini, Nicola Silvestris, Hossein Safarpou
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(Jan 2022) Innate lymphoid cell characterization in the rat and their correlation to gut commensal microbes
Amanda Sudworth,Filip M. Segers,Bahtiyar Yilmaz,Naomi C. Guslund,Andrew J. Macpherson,Erik Dissen,Shuo-Wang Qiao,Marit Inngjerdingen
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(Jan 2022) Single-cell RNA-seq recognized the initiator of epithelial ovarian cancer recurrence
Tongtong Kan, Shupeng Zhang, Shengtao Zhou, Ya Zhang, Yun Zhao, Yinghua Gao, Tao Zhang, Feng Gao, Xin Wang, Linjie Zhao & Mengsu Yang
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(Oct 2021) High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy
Camelia Quek, Xinyu Bai , Georgina V. Long 1, Richard A. Scolyer , and James S. Wilmott
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(Oct 2021) Microfluidics applications for high-throughput single cell sequencing
Wen‑min Zhou, Yan‑yan Yan, Qiao‑ru Guo, Hong Ji, Hui Wang, Tian‑tian Xu, Bolat Makabel, Christian Pilarsky, Gen He, Xi‑yong Yu and Jian‑ye Zhang
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(Sep 2021) Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics
Luyao Liu, Xiaobin Dong, Yunping Tu, Guijun Miao, Zhongping Zhang, Lulu Zhang, Zewen Wei, Duli Yu & Xianbo Qiu
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(Sep 2021) PsiNorm: a scalable normalization for single-cell RNA-seq data
Matteo Borella, Graziano Martello, Davide Risso, Chiara Romualdi
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(Aug 2021) Single-cell analysis of cell fate bifurcation in the chordate Ciona
Konner M. Winkley, Wendy M. Reeves & Michael T. Veeman
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(Aug 2021) Stochastic gene expression drives mesophyll protoplast regeneration
Mengxue Xu, Qingwei DuCaihuan, TianYing Wang, and Yuling Jiao
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(Jul 2021) OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security
Yuri V. Gogolev , Sunny Ahmar , Bala Ani Akpinar, Hikmet Budak, Alexey S. Kiryushkin, Vladimir Y. Gorshkov, Goetz Hensel, Kirill N. Demchenko, Igor Kovalchuk, Freddy Mora-Poblete, Tugdem Muslu, Ivan D. Tsers, Narendra Singh Yadav and Viktor Korzun
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(Jul 2021) Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq
Martin Philpott, Jonathan Watson, Anjan Thakurta, Tom Brown Jr, Tom Brown Sr, Udo Oppermann & Adam P. Cribbs
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(May 2021) High-throughput full-length single-cell RNA-seq automation
Lira Mamanova, Zhichao Miao, Ayesha Jinat, Peter Ellis, Lesley Shirley & Sarah A. Teichmann
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(May 2021) What are the applications of single-cell RNAsequencing in cancer research: a systematic review
Lvyuan Li, Fang Xiong, Yumin Wang, Shanshan Zhang, Zhaojian Gong, Xiayu Li,Yi He, Lei Shi,Fuyan Wang, Qianjin Liao, Bo Xiang, Ming Zhou, Xiaoling Li, Yong Li, Guiyuan Li, Zhaoyang Zeng,Wei Xiongmand Can Guo
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(Apr 2021) Spinal macrophages resolve nociceptive hypersensitivity after peripheral injury
Jesse K.Niehaus, BonnieTaylor-Blake, LipinLoo, Jeremy M.Simon, Mark J.Zylka
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(Mar 2021) Neurodegeneration in human brain organoids infected with herpes simplex virus type 1
Agnieszka Rybak-Wolf, Emanuel Wyler, Ivano Legnini, Anna Loewa, Petar Glažar, Seung Joon Kim, Tancredi Massimo Pentimalli, Anna Oliveras Martinez, Benjamin Beyersdorf, Andrew Woehler, Markus Landthaler and Nikolaus Rajewsky
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(Mar 2021) Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids
Thomas M. Rawlings, Komal Makwana, Deborah M. Taylor, Matteo A. Molè, Katherine J. Fishwick, Maria Tryfonos, Joshua Odendaal, Amelia Hawkes, Magdalena Zernicka-Goetz, Geraldine M. Hartshorne,Jan J. Brosens, Emma S. Lucas
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(Mar 2021) Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells
Costanza Borrelli, Tomas Valenta, Kristina Handler, Karelia Vélez, Alessandra Gurtner,Giulia Moro, Atefeh Lafzi, Laura de Vargas Roditi, George Hausmann, Isabelle C. Arnold ,Andreas E. Moor & Konrad Basler
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(Feb 2021) Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer
Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D,Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S,Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M,Cremaschi P, Claessens F, Visakorpi T, Tammela TLJ, Murtola T, Granberg KJ, LambAD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A
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(Feb 2021) Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function
Adam P. Cribbs, Panagis Filippakopoulos, Martin Philpott, Graham Wells, Henry Penn, Henrik Oerum, Viia Valge-Archer, Marc Feldmann and Udo Oppermann
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(Feb 2021) Single nucleus transcriptomics data integration recapitulates the major cell types in human liver
Klev Diamanti , Juan Salvador Inda Díaz , Amanda Raine , Gang Pan , Claes Wadelius , Marco Cavalli
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(Jan 2021) Highly accurate barcode and UMI error correction using dual nucleotide dimer blocks allows direct single-cell nanopore transcriptome sequencing
Martin Philpott, Jonathan Watson, Anjan Thakurta, Tom Brown Jr, Tom Brown Sr, Udo Oppermann, Adam P Cribbs
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(Jan 2021) UniverSC: a flexible cross-platform single-cell data processing pipeline
S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
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(Dec 2020) Characterization of iCell cardiomyocytes using single-cell RNA-sequencing methods
Christina Schmid, Christian T.Wohnhaas,Tobias Hildebrandt, Patrick Baum, Georg Rasta
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(Sep 2020) Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
Tracy M. Yamawaki, Daniel R. Lu, Daniel C. Ellwanger, Dev Bhatt, Paolo Manzanillo, Hong Zhou, Oh Kyu Yoon, Oliver Homann, Songli Wang, Chi-Ming Li
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(May 2020) Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention
Wyler Emanuel, Mösbauer Kirstin, Franke Vedran, Diag Asija, Gottula Lina Theresa, Arsie Roberto, Klironomos Filippos, Koppstein David, Ayoub Salah, Buccitelli Christopher, Richter Anja, Legnini Ivano, Ivanov Andranik, Mari Tommaso, Del Giudice Simone, Papies Jan Patrick, Müller Marcel Alexander, Niemeyer Daniela, Selbach Matthias, Akalin Altuna, Rajewsky Nikolaus, Drosten Christian, Landthaler Markus
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(May 2020) Single-Cell RNA Sequencing and Its Combination with Protein and DNA Analyses
Jane Ru Choi , Kar Wey Yong , Jean Yu Choi and Alistair C. Cowie
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(Apr 2020) Cell Atlas technologies and insights into tissue architecture
Anna Wilbrey-Clark ; Kenny Roberts ; Sarah A. Teichmann
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(Mar 2020) Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism
Adam P. Cribbs https://orcid.org/0000-0001-5288-3077 adam.cribbs@imm.ox.ac.uk, Stefan Terlecki-Zaniewicz, Martin Philpott, +13 , Jeroen Baardman, David Ahern, Morten Lindow, Susanna Obad, Henrik Oerum, Brante Sampey, Palwinder K. Mander, Henry Penn, Paul Wordsworth, Paul Bowness, Menno de Winther, Rab K. Prinjha , Marc Feldmann , and Udo Oppermann
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(Feb 2020) Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics
CharlotteRich-Griffin, Annika Stechemesser, Jessica Finch, Emma Lucas, Sascha Ott, Patrick Schäfer
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(Jan 2020) Recurrent pregnancy loss is associated with a pro-senescent decidual response during the peri-implantation window
Emma S. Lucas, Pavle Vrljicak, Joanne Muter, Maria M. Diniz-da-Costa, Paul J. Brighton, Chow-Seng Kong, Julia Lipecki, Katherine J. Fishwick, Joshua Odendaal, Lauren J. Ewington, Siobhan Quenby, Sascha Ott & Jan J. Brosens
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(Jan 2020) Single cell and genetic analyses reveal conserved populations and signaling mechanisms of gastrointestinal stromal niches
Ji-Eun Kim, Lijiang Fei, Wen-Chi Yin, Sabrina Coquenlorge, Abilasha Rao-Bhatia, Xiaoyun Zhang, Sammy Shun Wai Shi, Ju Hee Lee, Noah A. Hahn, Wasi Rizvi, Kyoung-Han Kim, Hoon-Ki Sung, Chi-chung Hui, Guoji Guo & Tae-Hee Kim
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(Jan 2020) A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
Karen Davey, Daniel Wong, Filip Konopacki, Eugene Kwa, Heike Fiegler, View ORCID ProfileChristopher R. Sibley
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(Jan 2020) A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs
E Alessio, RS Bonadio, L Buson, F Chemello
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(Dec 2019) Single-cell sequencing and its applications in head and neck cancer
Zongtai Qiae,Thomas Barrettae, Anuraag S.Parikh, Itay Tiroshd, Sidharth V.Puram
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(Dec 2019) Dissecting the human immune system with single cell RNA sequencing technology
Gang Xu, Yang Liu, Hanjie Li, Lei Liu, Shuye Zhang, Zheng Zhang
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(Nov 2019) Single-Cell Analysis Using Droplet Microfluidics
Kinga Matuła, Francesca Rivello, Wilhelm T. S. Huck
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(Aug 2019) Single-Cell Genomics
Carmela Paolillo, Eric Londin, Paolo Fortina
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(Jul 2019) Micro-fluidics in Disease Diagnosis: Past, Present, and Future-An Overview
Madhav Gajananrao Raje, Manasi Raje
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(Jul 2019) DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Christian T. Wohnhaas, Germán G. Leparc, Francesc Fernandez-Albert, David Kind, Florian Gantner, Coralie Viollet, Tobias Hildebrandt & Patrick Baum
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(Jul 2019) Inside out: optimization of lipid nanoparticle formulations for exterior complexation and in vivo delivery of saRNA
Anna K. Blakney, Paul F. McKay, Bárbara Ibarzo Yus, Yoann Aldon & Robin J. Shattock
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(Jul 2019) Single-Cell Genomics: Technology and Applications
RamanPreet Kaur, Abhilash Ludhiadch, Anjana Munshi
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(May 2019) Droplet-based single cell RNAseq tools: a practical guide
Robert Salomon, Dominik Kaczorowski, Fatima Valdes-Mora, Robert E Nordon, Adrian Neild, Nona Farbehi, Nenad Bartonicek, David Gallego-Ortega
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(May 2019) The Skin You Are In: Design-of-Experiments Optimization of Lipid Nanoparticle Self-Amplifying RNA Formulations in Human Skin Explants
Anna K. Blakney, Paul F. McKay, Bárbara Ibarzo Yus, Judith E. Hunter, Elizabeth A. Dex, and Robin J. Shattock
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(Apr 2019) Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics
Vincent Croset, Christoph D Treiber , Scott Waddell
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(Feb 2019) Revolutionizing immunology with single-cell RNA sequencing
Haide Chen, Fang Ye & Guoji Guo
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(Dec 2018) Recent advances in microfluidic technology for manipulation and analysis of biological cells
MK Alam, E Koomson, H Zou, C Yi, CW Li, T Xu, Mengsu Yang
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(Noc 2018) Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
Atefeh Lafzi, Catia Moutinho, Simone Picelli & Holger Heyn
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(Nov 2018) Single-Cell Transcriptomics in Cancer Immunobiology: The Future of Precision Oncology
Fatima Valdes-Mora, Kristina Handler, Andrew M. K. Law, Robert Salomon, Samantha R. Oakes, Christopher, J. Ormandy and David Gallego-Ortega
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(Jul 2018) Reconstruction of the Decidual Pathways in Human Endometrial Cells Using Single-Cell RNA-Seq
Emma S Lucas, Pavle Vrljicak, Maria M Diniz-da-Costa, Paul J Brighton, Chow S Kong, Julia Lipecki, Katherine Fishwick, Joanne Muter, Sascha Ott, Jan J Brosens
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(Jun 2018) Immunoglobulin gene analysis as a tool for investigating human immune responses
Deborah Dunn-Walters, Catherine Townsend, Emma Sinclair, Alex Stewart
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(May 2018) Preparing scRNA-seq for the Clinic & the Field
Camille Mojica Rey
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(May 2018) Single-cell sequencing leads a new era of profiling transcriptomic landscape
Huidan Zhang, Naiwen Cui, Yamei Cai, Fengyang Lei, Fengyang, David A Weitz
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(Mar 2018) Platforms for single-cell collection and analysis
Lukas Valihrach, Peter Androvic and Mikael Kubista
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(Jan 2018) How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives
Alessandra Dal Molin, Barbara Di Camillo
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(Oct 2017) How low can you go? Pushing the limits of low-input ChIP-seq
JA Dahl, GD Gilfillan
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(Aug 2017) Microfluidics as a strategic player to decipher single-cell omics?
O Caen, H Lu, P Nizard, V Taly
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(Jan 2017) A review on macroscale and microscale cell lysis methods
M Shehadul Islam, A Aryasomayajula…
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