Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation by Kevin Baßler, Wataru Fujii, Theodore S. Kapellos, Erika Dudkin, Nico Reusch, Ari Horne, Benedikt Reiz, Malte D. Luecken, Collins Osei-Sarpong, Stefanie Warnat-Herresthal, Lorenzo Bonaguro, Lorenzo Bonaguro, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Allon Wagner, Allon Wagner, Patrick Günther, Carmen Pizarro, Tina Schreiber, Rainer Knoll, Rainer Knoll, Rainer Knoll, Lisa Holsten, Charlotte Kröger, Charlotte Kröger, Elena De Domenico, Elena De Domenico, Matthias Becker, Matthias Becker, Kristian Händler, Kristian Händler, Christian T. Wohnhaas, Florian Baumgartner, Meike Köhler, Heidi Theis, Heidi Theis, Michael Kraut, Michael Kraut, Marc H. Wadsworth, Marc H. Wadsworth, Travis K. Hughes, Humberto J. Ferreira, Emily Hinkley, Emily Hinkley, Ines H. Kaltheuner, Matthias Geyer, Christoph Thiele, Alex K. Shalek, Alex K. Shalek, Andreas Feißt, Daniel Thomas, Henning Dickten, Marc Beyer, Marc Beyer, Marc Beyer, Patrick Baum, Nir Yosef, Nir Yosef, Nir Yosef, Nir Yosef, Anna C. Aschenbrenner, Anna C. Aschenbrenner, Anna C. Aschenbrenner, Thomas Ulas, Thomas Ulas, Thomas Ulas, Jan Hasenauer, Jan Hasenauer, Fabian J. Theis, Fabian J. Theis, Dirk Skowasch, Joachim L. Schultze, Joachim L. Schultze, Joachim L. Schultze

Get full text

Human Monocyte Subsets and Phenotypes in Major Chronic Inflammatory Diseases by Theodore S. Kapellos, Lorenzo Bonaguro, Ioanna Gemünd, Nico Reusch, Adem Saglam, Emily R. Hinkley, Joachim L. Schultze, Joachim L. Schultze

Get full text

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation by Hisham Mohammed, Irene Hernando-Herraez, Aurora Savino, Antonio Scialdone, Iain Macaulay, Carla Mulas, Tamir Chandra, Thierry Voet, Wendy Dean, Jennifer Nichols, John C. Marioni, Wolf Reik

Get full text

hCoCena: A toolbox for network-based co-expression analysis and horizontal integration of transcriptomic datasets by Lisa Holsten, Kilian Dahm, Marie Oestreich, Matthias Becker, Thomas Ulas

Get full text

Profiling Host Respiratory Responses to SARS-CoV-2 Infection by Miao, Vincent N.

“…Single-cell genomics have revolutionized the granularity with which we can dissect cellular phenotypes in both health and disease. …”
Get full text
Get full text

Comprehensive comparative genomics reveals over 50 phyla of free-living and pathogenic bacteria are associated with diverse members of the amoebozoa by Yonas I. Tekle, Janae M. Lyttle, Maya G. Blasingame, Fang Wang

“…We used culture independent whole culture and single cell genomics/transcriptomics to investigate the association of bacteria with diverse amoebozoans. …”
Get full text

Identification of region-specific astrocyte subtypes at single cell resolution by Mykhailo Y. Batiuk, Araks Martirosyan, Jérôme Wahis, Filip de Vin, Catherine Marneffe, Carola Kusserow, Jordan Koeppen, João Filipe Viana, João Filipe Oliveira, Thierry Voet, Chris P. Ponting, T. Grant Belgard, Matthew G. Holt

Get full text

Single-cell analysis and spatial resolution of the gut microbiome by Bhoomi Madhu, Brittany M. Miller, Maayan Levy

“…Single cell genomics is a very powerful and rapidly growing field, primarily used to identify the genetic composition of microbes. …”
Get full text

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients by Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna D. Gemünd, Nikoletta Rovina, Shobhit Agrawal, Kilian Dahm, Martina van Uelft, Anna Drews, Lena Lenkeit, Niklas Bruse, Jelle Gerretsen, Jannik Gierlich, Matthias Becker, Kristian Händler, Michael Kraut, Heidi Theis, Simachew Mengiste, Elena De Domenico, Jonas Schulte-Schrepping, Lea Seep, Jan Raabe, Christoph Hoffmeister, Michael ToVinh, Verena Keitel, Gereon Rieke, Valentina Talevi, Dirk Skowasch, N. Ahmad Aziz, Peter Pickkers, Frank L. van de Veerdonk, Mihai G. Netea, Joachim L. Schultze, Matthijs Kox, Monique M. B. Breteler, Jacob Nattermann, Antonia Koutsoukou, Evangelos J. Giamarellos-Bourboulis, Thomas Ulas, German COVID-19 Omics Initiative (DeCOI)

Get full text

One bacterial cell, one complete genome. by Tanja Woyke, Damon Tighe, Konstantinos Mavromatis, Alicia Clum, Alex Copeland, Wendy Schackwitz, Alla Lapidus, Dongying Wu, John P McCutcheon, Bradon R McDonald, Nancy A Moran, James Bristow, Jan-Fang Cheng

“…No single cell genome has to our knowledge been closed and finished to date. …”
Get full text

A Population of Radio-Resistant Macrophages in the Deep Myenteric Plexus Contributes to Postoperative Ileus Via Toll-Like Receptor 3 Signaling by Jana Enderes, Shilpashree Mallesh, Reiner Schneider, Kristof J. Hupa, Mariola Lysson, Bianca Schneiker, Kristian Händler, Balthasar Schlotmann, Patrick Günther, Patrick Günther, Joachim L. Schultze, Joachim L. Schultze, Joachim L. Schultze, Jörg C. Kalff, Sven Wehner

Get full text

Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics by Stefanie Warnat-Herresthal, Konstantinos Perrakis, Bernd Taschler, Matthias Becker, Kevin Baßler, Marc Beyer, Patrick Günther, Jonas Schulte-Schrepping, Lea Seep, Kathrin Klee, Thomas Ulas, Torsten Haferlach, Sach Mukherjee, Joachim L. Schultze

Get full text

Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates by Niels JM Verstegen, Sabrina Pollastro, Peter-Paul A Unger, Casper Marsman, George Elias, Tineke Jorritsma, Marij Streutker, Kevin Bassler, Kristian Haendler, Theo Rispens, Joachim L Schultze, Anja ten Brinke, Marc Beyer, S Marieke van Ham

Get full text

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter by Zachary Landry, Brandon K. Swan, Gerhard J. Herndl, Ramunas Stepanauskas, Stephen J. Giovannoni

Get full text

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells by Iain C. Macaulay, Valentine Svensson, Charlotte Labalette, Lauren Ferreira, Fiona Hamey, Thierry Voet, Sarah A. Teichmann, Ana Cvejic

Get full text

Singling out how genes are regulated during development by Shawn M. Burgess

“…Their findings add another important piece to understanding the dynamic landscape of gene expression and regulation during early vertebrate development and hint at the dramatic changes single-cell genomics is bringing to the field of developmental biology.…”
Get full text

Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments by Gennady Gorin, John J. Vastola, Meichen Fang, Lior Pachter

“…Here the authors explore the distributional differences expected from distinct biophysical models of transcription and show how measurements from single-cell genomics experiments can shed light on the underlying biological processes.…”
Get full text

Molecular mechanisms and treatment responses of pulmonary fibrosis in severe COVID-19 by Emma J. Kooistra, Kilian Dahm, Antonius E. van Herwaarden, Jelle Gerretsen, Melanie Nuesch Germano, Karoline Mauer, Ruben L. Smeets, Sjef van der Velde, Maarten J. W. van den Berg, Johannes G. van der Hoeven, Anna C. Aschenbrenner, Joachim L. Schultze, Thomas Ulas, Matthijs Kox, Peter Pickkers

Get full text

Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease by Theodore S. Kapellos, Kevin Baßler, Wataru Fujii, Christina Nalkurthi, Anna C. Schaar, Lorenzo Bonaguro, Tal Pecht, Izabela Galvao, Shobhit Agrawal, Adem Saglam, Erica Dudkin, Amit Frishberg, Elena de Domenico, Arik Horne, Chantal Donovan, Richard Y. Kim, David Gallego-Ortega, Tessa E. Gillett, Meshal Ansari, Jonas Schulte-Schrepping, Nina Offermann, Ignazio Antignano, Burcu Sivri, Wenying Lu, Mathew S. Eapen, Martina van Uelft, Collins Osei-Sarpong, Maarten van den Berge, Hylke C. Donker, Harry J.M. Groen, Sukhwinder S. Sohal, Johanna Klein, Tina Schreiber, Andreas Feißt, Ali Önder Yildirim, Herbert B. Schiller, Martijn C. Nawijn, Matthias Becker, Kristian Händler, Marc Beyer, Melania Capasso, Thomas Ulas, Jan Hasenauer, Carmen Pizarro, Fabian J. Theis, Philip M. Hansbro, Dirk Skowasch, Joachim L. Schultze

Get full text

A practical solution to pseudoreplication bias in single-cell studies by Kip D. Zimmerman, Mark A. Espeland, Carl D. Langefeld

“…Single cell genomics uses cells from the same individual, or pseudoreplicates, that can introduce biases and inflate type I error rates. …”
Get full text