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Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

List by Alex Eve

Preprints:

Spatial transcriptomics reveals the architecture of the tumor/microenvironment interface

Miranda V. Hunter, Reuben Moncada, Joshua M. Weiss, Itai Yanai, Richard M. White

https://www.biorxiv.org/content/10.1101/2020.11.05.368753v1

CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes

Mirjana Efremova, Miquel Vento-Tormo, Sarah A. Teichmann, Roser Vento-Tormo

https://www.biorxiv.org/content/10.1101/680926v1

A spatially resolved single cell atlas of human gastrulation

Richard C.V. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas

https://www.biorxiv.org/content/10.1101/2020.07.21.213512v1

Integrated analysis of multimodal single-cell data

Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M. Mauck III, Shiwei Zheng, Andrew Butler, Maddie J. Lee, Aaron J. Wilk, Charlotte Darby, Michael Zagar, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar B. Fleming, Bertrand Yeung, Angela J. Rogers, Juliana M. McElrath, Catherine A. Blish, Raphael Gottardo, Peter Smibert, Rahul Satija

https://www.biorxiv.org/content/10.1101/2020.10.12.335331v1

Capybara: A computational tool to measure cell identity and fate transitions

Wenjun Kong, Yuheng C. Fu, Samantha A. Morris

https://www.biorxiv.org/content/10.1101/2020.02.17.947390v2

CellOracle: Dissecting cell identity via network inference and in silico gene perturbation

Kenji Kamimoto, Christy M. Hoffmann, Samantha A. Morris

https://www.biorxiv.org/content/10.1101/2020.02.17.947416v3

CellRank for directed single-cell fate mapping

Marius Lange, Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti, Heiko Lickert, Meshal Ansari, Janine Schniering, Herbert B. Schiller, Dana Pe’er, Fabian J. Theis

https://www.biorxiv.org/content/10.1101/2020.10.19.345983v1

Query to reference single-cell integration with transfer learning

Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Ziga Avsec, Alexander V. Misharin, Fabian J. Theis

https://www.biorxiv.org/content/10.1101/2020.07.16.205997v1

Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells

Adam Gayoso, Zoë Steier, Romain Lopez, Jeffrey Regier, Kristopher L Nazor, Aaron Streets, Nir Yosef

https://www.biorxiv.org/content/10.1101/2020.05.08.083337v2

AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution

Hananeh Aliee, Fabian Theis

https://www.biorxiv.org/content/10.1101/2020.02.21.940650v1

P2

Deep learning does not outperform classical machine learning for cell-type annotation

Niklas D. Köhler, Maren Büttner, Fabian J. Theis

https://www.biorxiv.org/content/10.1101/653907v1

P7

scMET: Bayesian modelling of DNA methylation heterogeneity at single-cell resolution

Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina A. Vallejos

https://www.biorxiv.org/content/10.1101/2020.07.10.196816v2

P22

Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks

Florian Klimm, Enrique M. Toledo, Thomas Monfeuga, Fang Zhang, Charlotte M. Deane, Gesine Reinert

https://www.biorxiv.org/content/10.1101/698647v2

P24

Single-cell molecular and cellular architecture of the mouse neurohypophysis

Qiyu Chen, Dena Leshkowitz, Janna Blechman, Gil Levkowitz

https://www.biorxiv.org/content/10.1101/744466v2

P29

Differences in mitochondrial activity trigger cell competition during early mouse development

Ana Lima, Gabriele Lubatti, Jörg Burgstaller, Di Hu, Alistair Green, Aida Di Gregorio, Tamzin Zawadzki, Barbara Pernaute, Elmir Mahammadov, Marian Dore, Juan Miguel Sanchez, Sarah Bowling, Margarida Sancho, Mohammad Karimi, David Carling, Nick Jones, Shankar Srinivas, Antonio Scialdone, Tristan A. Rodriguez

https://www.biorxiv.org/content/10.1101/2020.01.15.900613v1

P32

Quantitative and molecular differences distinguish adult human medullary and extramedullary haematopoietic stem and progenitor cell landscapes

Nicole Mende, Hugo P Bastos, Antonella Santoro, Kendig Sham, Krishnaa T. Mahbubani, Abbie Curd, Hitoshi Takizawa, Nicola K Wilson, Bertie Göttgens, Kourosh Saeb-Parsy, Elisa Laurenti

https://www.biorxiv.org/content/10.1101/2020.01.26.919753v2

P38

Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors

Marieke Lavaert, Kai Ling Liang, Niels Vandamme, Jong-Eun Park, Juliette Roels, Monica S. Kowalczyk, Bo Li, Orr Ashenberg, Marcin Tabaka, Danielle Dionne, Timothy L. Tickle, Michal Slyper, Orit Rozenblatt-Rosen, Bart Vandekerckhove, Georges Leclercq, Aviv Regev, Pieter Van Vlierberghe, Martin Guilliams, Sarah A. Teichmann, Yvan Saeys, Tom Taghon

https://www.biorxiv.org/content/10.1101/2020.04.07.007237v1

P28

Molecular and cellular pathology of monogenic Alzheimer’s disease at single cell resolution

Federica Marinaro, Moritz Haneklaus, Zhechun Zhang, Alessio Strano, Lewis Evans, Louis-François Handfield, Natalie S. Ryan, Nick C. Fox, Martin Hemberg, Sharad Ramanathan, Frederick J. Livesey

https://www.biorxiv.org/content/10.1101/2020.07.14.202317v1

P15

Primed smooth muscle cells acting as first responder cells in disease

Matt D Worssam, Jordi Lambert, Sebnem Oc, Annabel L Taylor, Lina Dobnikar, Joel Chappell, Jennifer L Harman, Nichola L Figg, Alison Finigan, Kirsty Foote, Anna K Uryga, Martin R Bennett, Mikhail Spivakov, Helle F Jørgensen

https://www.biorxiv.org/content/10.1101/2020.10.19.345769v1

P71

Spatial mapping of cell types by integration of transcriptomics data

Alma Andersson, Joseph Bergenstråhle, Michaela Asp, Ludvig Bergenstråhle, Aleksandra Jurek, José Fernández Navarro, Joakim Lundeberg

https://www.biorxiv.org/content/10.1101/2019.12.13.874495v1

Genome-wide Spatial Expression Profiling in FFPE Tissues

Eva Gracia Villacampa, Ludvig Larsson, Linda Kvastad, Alma Andersson, Joseph Carlson, Joakim Lundeberg

https://www.biorxiv.org/content/10.1101/2020.07.24.219758v1

The spatial landscape of gene expression isoforms in tissue sections

Kevin Lebrigand, Joseph Bergenstråhle, Kim Thrane, Annelie Mollbrink, Pascal Barbry, Rainer Waldmann, Joakim Lundeberg

https://www.biorxiv.org/content/10.1101/2020.08.24.252296v1

Spage2vec: Unsupervised detection of spatial gene expression constellations

Gabriele Partel, Carolina Wählby

https://www.biorxiv.org/content/10.1101/2020.02.12.945345v1

Molecular architecture of the developing mouse brain

Gioele La Manno, Kimberly Siletti, Alessandro Furlan, Daniel Gyllborg, Elin Vinsland, Christoffer Mattsson Langseth, Irina Khven, Anna Johnsson, Mats Nilsson, Peter Lönnerberg, Sten Linnarsson

https://www.biorxiv.org/content/10.1101/2020.07.02.184051v1

Hybridization-based In Situ Sequencing (HybISS): spatial transcriptomic detection in human and mouse brain tissue

Daniel Gyllborg, Christoffer Mattsson Langseth, Xiaoyan Qian, Sergio Marco Salas, Markus M. Hilscher, Ed S. Lein, Mats Nilsson

https://www.biorxiv.org/content/10.1101/2020.02.03.931618v1

Human brain organoids reveal accelerated development of cortical neuron classes as a shared feature of autism risk genes

Bruna Paulsen, Silvia Velasco, Amanda J Kedaigle, Martina Pigoni, Giorgia Quadrato, Anthony Deo, Xian Adiconis, Ana Uzquiano, Kwanho Kim, Sean K Simmons, Kalliopi Tsafou, Alex Albanese, Rafaela Sartore, Catherine Abbate, Ashley Tucewicz, Samantha Smith, Kwanghun Chung, Kaspar Lage, Aviv Regev, Joshua Z Levin, Paola Arlotta

https://www.biorxiv.org/content/10.1101/2020.11.10.376509v1

Categories: bioinformatics , cancer biology , developmental biology , immunology , systems biology

Tags: single cell

Posted on: 11th November 2020 , updated on: 12th November 2020

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