Publications

LSSI Group members in bold, *equal contribution

2024

Anna Mei , Kevin P Letscher , Sai Reddy (2024)
external page Engineering next-generation chimeric antigen receptor-T cells: recent breakthroughs and remaining challenges in design and screening of novel chimeric antigen receptor variants
Current Opinion in Biotechnology

Edo Kapetanovic, Cédric R. Weber, Marine Bruand, Daniel Pöschl, Jakub Kucharczyk, Elisabeth Hirth, Claudius Dietsche, Riyaz Khan, Bastian Wagner, Olivier Belli, Rodrigo Vazquez-Lombardi, Rocío Castellanos- Rueda, Raphael B. Di Roberto, Kevin Kalinka, Luca Raess, Kevin Ly, Shivam Rai, Petra S. Dittrich, Randall J. Platt, Elisa Oricchio & Sai T. Reddy (2024)
external page Engineered allogeneic T cells decoupling T-cell-receptor and CD3 signalling enhance the antitumour activity of bispecific antibodies
Nature Biomedical Engineering

Margarita Pertseva, Oceane Follonier, Daniele Scarcella, Sai T Reddy (2024)
external page TCR clustering by contrastive learning on antigen specificity
Briefings in Bioinformatics

Kevin P. Letscher & Sai T. Reddy (2024)
external page Multidimensional analysis reveals predictive markers for CAR-T efficacy
Nature Cancer (News & Views)

Roy A. Ehling, Mason Minot, Max D. Overath, Daniel J. Sheward, Jiami Han, Beichen Gao, Joseph M.
Taft, Margarita Pertseva, Cédric R. Weber, Lester Frei, Thomas Bikias, Ben Murrell and Sai T. Reddy (2024)
external page Synthetic coevolution reveals adaptive mutational trajectories of neutralizing antibodies and SARS-CoV-2
BioRxiv

Rocio Castellanos-Rueda, Kai-Ling K. Wang, Juliette L. Forster, Alice Driessen, Jessica A. Frank, Maria Rodriguez Martinez, Sai T. Reddy (2024)
external page Dissecting the role of CAR signaling architectures on T cell activation and persistence using pooled screening and single-cell sequencing
BioRxiv

Edward B. Irvine, Sai T. Reddy (2024)
external page Advancing Antibody Engineering through Synthetic Evolution and Machine Learning
The Journal of Immunology

Mason Minot, Sai T. Reddy (2024)
external page Meta learning addresses noisy and under-labeled data in machine learning-guided antibody engineering
Cell Systems

2023

Lester Frei, Beichen Gao, Jiami Han, Joseph M. Taft, Edward B. Irvine, Cédric R. Weber, Rachita K. Kumar, Benedikt N. Eisinger, Sai T. Reddy (2023)
external page Deep learning-guided selection of antibody therapies with enhanced resistance to current and prospective SARS-CoV-2 Omicron variants
Preprint available on bioRxiv.

Florian Bieberich, Rodrigo Vazquez-Lombardi, Huixin Jin, Kai-Lin Hong, Petra Herzig, Marcel Trefny, Marta Trüb, Heinz Läubli, Didier Lardinois, Kirsten Mertz, Matthias S. Matter, Alfred Zippelius and Sai T. Reddy (2023)
external page Multimodal single-cell profiling of T cell specificity and reactivity in lung cancer
Preprint available on bioRxiv.

Tudor-Stefan Cotet, Andreas Agrafiotis, Victor Kreiner, Raphael Kuhn, Danielle Shlesinger, Marcos Manero-Carranza, Keywan Khodaverdi, Evgenios Kladis, Aurora Desideri Perea, Dylan Maassen-Veeters, Wiona Glänzer, Solène Massery, Lorenzo Guerci, Kai-Lin Hong, Jiami Han, Kostas Stiklioraitis, Vittoria Martinolli D’Arcy, Raphael Dizerens, Samuel Kilchenmann, Lucas Stalder, Leon Nissen, Basil Vogelsanger, Stine Anzböck, Daria Laslo, Sophie Bakker, Melinda Kondorosy, Marco Venerito, Alejandro Sanz Garcıa, Isabelle Feller, Annette Oxenius, Sai T. Reddy, Alexander Yermanos (2023)
external page ePlatypus: an ecosystem for computational analysis of immunogenomics data
Bioinformatics

Aerin Yang, Kevin M. Jude, Ben Lai, Mason Minot, Anna M. Kocyla, Caleb R. Glassman, Daisuke Nishimiya, Yoon Seok Kim, Sai T. Reddy, Aly A. Khan, K. Christopher Garcia (2023)
external page Deploying synthetic coevolution and machinelearning to engineer protein-protein interactions
Science

Darya Palianina, Raphaël B. Di Roberto, Rocío Castellanos-Rueda, Fabrice Schlatter,
Sai T. Reddy, Nina Khanna (2023)
external page A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell transfer applications
Molecular Therapy: Methods & Clinical Development

Andreas Agrafiotis, Daniel Neumeier, Kai-Lin Hong, Tasnia Chowdhury, Roy Ehling, Raphael Kuhn, Ioana Sandu, Victor Kreiner, Tudor-Stefan Cotet, Danielle Shlesinger, Daria Laslo, Stine Anzböck, Dale Starkie, Daniel J. Lightwood, Annette Oxenius, Sai T. Reddy and Alexander Yermanos (2023)
external page Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen specificity
iScience

Andreas Agrafiotis, Raphael Dizerens, Ilena Vincenti, Ingrid Wagner, Raphael Kuhn, Danielle Shlesinger, Marcos Manero‑Carranza, Tudor‑Stefan Cotet, Kai‑Lin Hong, Nicolas Page, Nicolas Fonta, Ghazal Shammas, Alexandre Mariotte, Margot Piccinno, Mario Kreutzfeldt, Benedikt Gruntz, Roy Ehling, Alessandro Genovese, Alessandro Pedrioli, Andreas Dounas, Sören Franzenburg, Hayrettin Tumani, Tania Kümpfel, Vladyslav Kavaka, Lisa Ann Gerdes, Klaus Dornmair, Eduardo Beltrán, Annette Oxenius, Sai T. Reddy, Doron Merkler, Alexander Yermanos (2023)
external page Persistent virus-specific and clonally expanded antibody-secreting cells respond to induced self-antigen in the CNS
Acta Neuropathologica

2022

Mason Minot, Sai T.Reddy (2022)
external page Nucleotide augmentation for machine learning-guided protein engineering
Bioinformatics Advances

Rocío Castellanos-Rueda, Raphaël B. Di Roberto, Florian Bieberich, Fabrice S. Schlatter, Darya Palianina, Oanh T. P. Nguyen, Edo Kapetanovic, Heinz Läubli, Andreas Hierlemann, Nina Khanna & Sai T. Reddy (2022)
external page speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing
Nature Communications

Luke Vistain, Hoang Van Phan, Bijentimala Keisham, Christian Jordi, Mengjie Chen, Sai T. Reddy & Savaş Tay (2022)
external page Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing
Nature Methods

Daniel J Sheward, Changil Kim, Julian Fischbach, Kenta Sato, Sandra Muschiol, Roy A Ehling, Niklas K Björkström, Gunilla B Karlsson Hedestam, Sai T Reddy, Jan Albert, Thomas P Peacock, Ben Murrell (2022)
external page Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies
The Lancet Infectious Diseases

Rodrigo Vazquez-Lombardi, Johanna S. Jung, Fabrice S. Schlatter, Anna Mei, Natalia Rodrigues Mantuano, Florian Bieberich, Kai-Lin Hong, Jakub Kucharczyk, Edo Kapetanovic, Erik Aznauryan, Cédric R. Weber, Alfred Zippelius, Heinz Läubli, Sai T. Reddy (2022)
external page High-throughput T cell receptor engineering by functional screening identifies candidates with enhanced potency and specificity
Immunity

Joseph M. Taft, Cédric R. Weber, Beichen Gao, Roy A. Ehling, Jiami Han, Lester Frei, Sean W. Metcalfe, Max Overath, Alexander Yermanos, William Kelton, Sai T. Reddy (2022)
external page Deep Mutational Learning Predicts ACE2 Binding and Antibody Escape to Combinatorial Mutations in the SARS-CoV-2 Receptor Binding Domain
Cell

Jiami Han, Solène Masserey, Danielle Shlesinger, Raphael Kuhn, Chrysa Papadopoulou, Andreas Agrafiotis, Victor Kreiner, Raphael Dizerens, Kai-Lin Hong, Cédric Weber, Victor Greiff, Annette Oxenius, Sai T Reddy, Alexander Yermanos (2022)
external page Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes
Bioinformatics Advances

Daniel J Sheward, Changil Kim, Julian Fischbach, Sandra Muschiol, Roy A Ehling, Niklas K Björkström, Gunilla B Karlsson Hedestam, Sai T Reddy, Jan Albert, Thomas P Peacock, Ben Murrell (2022)
external page Evasion of neutralising antibodies by omicron sublineage BA.2.75
The Lancet Infectious Diseases

Danielle Shlesinger, Kai-Lin Hong, Ghazal Shammas, Nicolas Page, Ioana Sandu, Andreas Agrafiotis, Victor Kreiner, Nicolas Fonta, Ilena Vincenti, Ingrid Wagner, Margot Piccinno, Alexandre Mariotte, Bogna Klimek, Raphael Dizerens, Marcos Manero-Carranza, Raphael Kuhn, Roy Ehling, Lester Frei, Keywan Khodaverdi, Camilla Panetti, Nicole Joller, Annette Oxenius, Doron Merkler, Sai T. Reddy and Alexander Yermanos (2022)
external page Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity
Genes & Immunity

Cédric R. Weber, Teresa Rubio, Longlong Wang, Wei Zhang, Philippe A. Robert, Rahmad Akbar, Igor Snapkov, Jinghua Wu, Marieke L. Kuijjer, Sonia Tarazona, Ana Conesa, Geir K. Sandve, Xiao Liu, Sai T. Reddy and Victor Greiff (2022)
external page Reference-based comparison of adaptive immune receptor repertoires
Cell Reports Methods

Ilena Vincenti, Nicolas Page, Karin Steinbach, Alexander Yermanos, Sylvain Lemeille, Nicolas Nunez, Mario Kreutzfeldt, Bogna Klimek, Giovanni Di Liberto, Kristof Egervari, Margot Piccinno, Ghazal Shammas, Alexandre Mariotte, Nicolas Fonta, Nicolas Liaudet, Danielle Shlesinger, Anna Rita Liuzzi, Ingrid Wagner, Cynthia Saadi, Christine Stadelmann, Sai Reddy, Burkhard Becher and Doron Merkler (2022)
external page Tissue-resident memory CD8+ T cells cooperate with CD4+ T cells to drive compartmentalized immunopathology in the CNS
Science Translational Medicine

Raphael Kuhn, Ioana Sandu, Andreas Agrafiotis, Kai-Lin Hong, Daniel Neumeier, Doron Merkler, Annette Oxenius, Sai T. Reddy, Alexander Yermanos (2022)
external page Clonally expanded virus-specific CD8 T cells acquire diverse transcriptional phenotypes during acute, chronic, and latent infections
Frontiers in Immunology

Alexander Yermanos, Kai-Lin Hong, Andreas Agrafiotis, Jiami Han, Sarah Nadeau, Cecilia Valenzuela, Asli Azizoglu, Roy Ehling, Beichen Gao, Michael Spahr, Daniel Neumeier, Ching-Hsiang Chang, Andreas Dounas, Ezequiel Petrillo, Ina Nissen, Elodie Burcklen, Mirjam Feldkamp, Christian Beisel, Annette Oxenius, Miodrag Savic, Tanja Stadler, Fabian Rudolf, Sai T. Reddy (2022)
external page DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2
BMC Genomics

Daniel Neumeier, Alexander Yermanos, Andreas Agrafiotis, Lucia Csepregi, Tasnia Chowdhury, Roy A. Ehling, Raphael Kuhn, Tudor-Stefan Cotet, Raphaël Brisset-Di Roberto, Mariangela Di Tacchio, Renan Antonialli, Dale Starkie, Daniel J. Lightwood, Annette Oxenius, and Sai T. Reddy (2022)
external page Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells
Proceedings of the National Academy of Sciences of the United States of America

Daniel J Sheward, Changil Kim, Roy A Ehling, Alec Pankow, Xaquin Castro Dopico, Robert Dyrdak, Darren P Martin, Sai T Reddy, Joakim Dillner, Gunilla B Karlsson Hedestam, Jan Albert, Ben Murrell (2022)
external page Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study
The Lancet Infectious Diseases

Erik Aznauryan, Alexander Yermanos, Elvira Kinzina, Anna Devaux, Edo Kapetanovic, Denitsa Milanova, George M.Church, Sai T.Reddy (2022)
external page Discovery and validation of human genomic safe harbor sites for gene and cell therapies
Cell Reports Methods

Tom Z. Yuan, Carolina Lucas, Valter S. Monteiro, Akiko Iwasaki, Marisa L. Yang, Hector F. Nepita, Ana G. Lujan Hernandez, Joseph M. Taft, Lester Frei, Sai T. Reddy, Cédric R. Weber, Kevin P. Malobisky, Rodrigo Mesquita, Aaron K. Sato (2022)
external page A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron
Preprint available on bioRxiv.

2021

Roy A. Ehling, Cédric R. Weber, Derek M. Mason, Simon Friedensohn, Bastian Wagner, Florian Bieberich, Edo Kapetanovic, Rodrigo Vazquez-Lombardi, Raphaël B. Di Roberto, Kai-Lin Hong, Camille Wagner, Michele Pataia, Max D. Overath, Daniel J. Sheward, Ben Murrell, Alexander Yermanos, Andreas P. Cuny, Miodrag Savic, Fabian Rudolf, Sai T. Reddy (2021)
external page SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display
Cell Reports

Kyrin R. Hanning, Mason Minot, Annmaree K. Warrender, William Kelton, Sai T. Reddy (2021)
external page Deep mutational scanning for therapeutic antibody engineering
Trends in pharmacological sciences

Lucia Csepregi, Kenneth B. Hoehn, Daniel Neumeier, Joseph M. Taft, Simon Friedensohn, Cédric R. Weber, Arkadij Kummer, Fabian Sesterhenn, Bruno E. Correia, Sai T. Reddy (2021)
external page The Physiological Landscape and Specificity of Antibody Repertoires
Preprint available on bioRxiv.

Sailan Shui, Pablo Gainza, Leo Scheller, Che Yang, Yoichi Kurumida, Stéphane Rosset,
Sandrine Georgeon, Raphaël B. Di Roberto, Rocío Castellanos-Rueda, Sai T. Reddy &
Bruno E. Correia
external page A rational blueprint for the design of chemically-controlled protein switches
Nature Communications

Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy A. Ehling, Derek M. Mason, Bastian Wagner, Edo Kapetanovic, Raphael Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf and Sai T. Reddy (2021)
external page A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients
Frontiers in Immunology

Margarita Pertseva, Beichen Gao, Daniel Neumeier, Alexander Yermanos and Sai T. Reddy (2021)
external page Applications of Machine and Deep Learning in Adaptive Immunity
Annual Review of Chemical and Biomolecular Engineering

Alexander Yermanos, Andreas Agrafiotis, Raphael Kuhn, Damiano Robbiani, Josephine Yates, Chrysa Papadopoulou, Jiami Han, Ioana Sandu, Cédric Weber, Florian Bieberich, Rodrigo Vazquez-Lombardi, Andreas Dounas, Daniel Neumeier, Annette Oxenius, Sai T Reddy (2021)
external page Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes
NAR Genomics and Bioinformatics

Derek M. Mason, Simon Friedensohn, Cédric R. Weber, Christian Jordi, Bastian Wagner, Simon M. Meng, Roy A. Ehling, Lucia Bonati, Jan Dahinden, Pablo Gainza, Bruno E. Correia & Sai T. Reddy (2021)
external page Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning
Nature Biomedical Engineering

RocíoCastellanos-Rueda, Raphaël B.Di Roberto, Fabrice S.Schlatter, Sai T.Reddy (2021)
external page Leveraging Single-Cell Sequencing for Chimeric Antigen Receptor T Cell Therapies
Trends in Biotechnology

Daniel Neumeier, Alessandro Pedrioli, Alessandro Genovese, Ioana Sandu, Roy Ehling, Kai-Lin Hong, Chrysa Papadopoulou, Andreas Agrafiotis, Raphael Kuhn, Danielle Shlesinger, Damiano Robbiani, Jiami Han, Laura Hauri, Lucia Csepregi, Victor Greiff, Doron Merkler, Sai T. Reddy, Annette Oxenius, Alexander Yermanos (2021)
external page Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single-cell analysis
European Journal of Immunology

2020

Lucia Csepregi, Roy Ehling, Bastian Wagner, Sai T.Reddy (2020)
external page Immune literacy: reading, writing and editing adaptive immunity
iScience

Charlotte U. Zajc, Benjamin Salzer, Joseph M. Taft, Sai T. Reddy, Manfred Lehner, Michael W. Traxlmayr (2020)
external page Driving CARs with alternative navigation tools – the potential of engineered binding scaffolds
The FEBS Journal

Raphaël B. Di Roberto, Rocío Castellanos-Rueda, Samara Frey, David Egli, Rodrigo Vazquez-Lombardi, Edo Kapetanovic, Jakub Kucharczyk, Sai T.Reddy (2020)
external page A functional screening strategy for engineering chimeric antigen receptors with reduced on-target, off-tumour activation
Molecular Therapy

Suzanne P. M. Welten, Alexander Yermanos, Nicolas S. Baumann, Franziska Wagen, Nathalie Oetiker, Ioana Sandu, Alessandro Pedrioli, Jennifer D. Oduro, Sai T. Reddy, Luka Cicin-Sain, Werner Held & Annette Oxenius (2020)
external page Tcf1+ cells are required to maintain the inflationary T cell pool upon MCMV infection
Nature Communications

Riedel R, Addo R, Ferreira-Gomes M, Heinz GA, Heinrich F, Kummer J, Greiff V, Schulz D, Klaeden C, Cornelis R, Menzel U, Kröger S, Stervbo U, Köhler R, Haftmann C, Kühnel S, Lehmann K, Maschmeyer P, McGrath M, Naundorf S, Hahne S, Sercan-Alp Ö, Siracusa F, Stefanowski J, Weber M, Westendorf K, Zimmermann J, Hauser AE, Reddy ST, Durek P, Chang HD, Mashreghi MF, and Radbruch A (2020)
external page Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow
Nature Communications

Yermanos A, Dounas A, Greiff V, Stadler T, Oxenius A, Reddy ST (2020)
external page Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes
Immunogenetics

Yermanos A, Sandu I, Pedrioli A, Borsa M, Wagen F, Oetiker N, Welten SPM, Pallmer K, Reddy ST, Oxenius A (2020)
external page Profiling Virus-Specific Tcf1+ T Cell Repertoires During Acute and Chronic Viral Infection
Frontiers in Immunology

Yermanos A, Kräutler NJ, Pedrioli A, Menzel U, Greiff V, Stadler T, Oxenius A, Reddy ST (2020) 
external page IgM Antibody Repertoire Fingerprints in Mice Are Personalized but Robust to Viral Infection Status
Frontiers in Cellular and Infection Microbiology

Yermanos A, Greiff V, Stadler T, Oxenius A, Reddy ST (2020)
external page The influence of the phylogenetic inference pipeline on murine antibody repertoire sequencing data following viral infection
Preprint available on bioRxiv.

Friedensohn S, Neumeier D, Khan TA, Csepregi L, Parola C, Gorter de Vries A, Erlach L, Mason DM and Reddy ST (2020)
external page Convergent selection in antibody repertoires is revealed by deep learning
Preprint available on bioRxiv.

Weber CR, Akbar R, Yermanos A, Pavlović M, Snapkov I, Sandve GK, Reddy ST and Greiff V (2020) 
external page immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Bioinformatics

Kräutler NJ*, Yermanos A*, Pedrioli A, Welten SPM, Lorgé D, Greczmiel U, Bartsch I, Scheuermann J, Kiefer JD, Eyer K, Menzel U, Greiff V, Neri D, Stadler T, Reddy ST and Oxenius A (2020)
external page Quantitative and Qualitative Analysis of Humoral Immunity Reveals Continued and Personalized Evolution in Chronic Viral Infection
Cell Reports

Fallet B, Hao Y, Florova M, Cornille K, Verge de los Aires A, Girelli Zubani G, Ertuna YI, Greiff V, Menzel U, Hammad K, Merkler D, Reddy ST, Weill JC, Reynaud CA, Pinschewer DD (2020)
external page Chronic Viral Infection Promotes Efficient Germinal Center B Cell Responses
Cell Reports

2019

Smakaj E, Babrak L, Ohlin M, Shugay M, Briney B, Tosoni D, Galli C, Grobelsek V, D’Angelo I, Olson B, Reddy ST, Greiff V, Trück J, Marquez S, Lees W and Miho E (2019)
external page Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences 
Bioinformatics

Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM and Reddy ST (2019)
external page Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells
mAbs

Mason DM, Friedensohn S, Weber CR, Jordi C, Wagner B, Meng SM, Gainza P, Correia BE and Reddy ST (in review)
external page Deep learning enables therapeutic antibody optimization in mammalian cells by deciphering high-dimensional protein sequence space 
Preprint available on bioRxiv.

Miho E, Roskar R, Greiff V and Reddy ST (2019) 
external page The fundamental principles of antibody repertoire architecture revealed by large-scale network analysis 
Nature Communications

Sesterhenn F, Galloux M, Vollers SS, Csepregi L, Yang C, Descamps D, Bonet J, Friedensohn S, Gainza P, Corthésy P, Chen M, Rosset S, Rameix-Welti MA, Éléouët JF, Reddy ST, Graham BS, Riffault S and Correia BE (2019) 
external page Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen 
PLOS Biology

D’Amico L*, Menzel U*, Prummer M, Müller P,  Buchi M, Kashyap A, Haessler U, Yermanos AD, Gébleux R, Briendl M, Hell T, Wolter FI, Beerli RR, Truxova I, Radek Š, Vlajnic T, Grawunder U, Reddy ST and Zippelius A (2019) 
external page A novel anti-HER2 anthracycline-based antibody-drug conjugate induces adaptive anti-tumor immunity and potentiates PD-1 blockade in breast cancer 
Journal for ImmunoTherapy of Cancer

Pesch T, Bonati L, Kelton WJ, Parola C, Ehling RA, Csepregi L, Kitamura D, Reddy ST (2019) 
external page Molecular design, optimization and genomic integration of chimeric B cell receptors in murine B cells 
Frontiers in Immunology

2018

Yermanos AD, Dounas AK, Stadler T, Oxenius A, Reddy ST (2018) 
external page Tracing Antibody Repertoire Evolution by Systems Phylogeny 
Frontiers in Immunology

Parola C, Mason DM, Zingg A, Neumeier D, Reddy ST (2018)
external page Genome Engineering of Hybridomas to Generate Stable Cell Lines for Antibody Expression 
Methods in Molecular Biology - Springer Book Chapter

Friedensohn S*, Lindner JM*, Cornacchione V, Iazeolla M, Miho E, Zingg A, Meng S, Traggiai E, Reddy ST (2018) 
external page Synthetic standards combined with error and bias correction improves the accuracy and quantitative resolution of antibody repertoire sequencing in human and naive memory B cells 
Frontiers in Immunology 

Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST (2018)
external page High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis 
Nucleic Acids Research

Miho E, Yermanos AD, Weber CR, Berger CT, Reddy ST, Greiff V (2018)
external page Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires 
Frontiers in Immunology

2017

Parola C, Neumeier D, Reddy ST (2017)
external page Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering 
Immunology

Greiff V*, Weber CR*, Palme J, Bodenhofer U, Miho E, Menzel U, Reddy ST (2017) 
external page Learning The High-Dimensional Immunogenomic Features That Predict Public And Private Antibody Repertoires 
The Journal of Immunology 

Yermanos A, Greiff V, Krautler NJ, Menzel U, Dounas A, Miho E, Oxenius A, Stadler T, Reddy ST (2017)
external page Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim) 
Bioinformatics

Reddy ST (2017) 
external page The patterns of T-cell target recognition 
Nature

Greiff V*, Menzel U*, Miho E, Weber CR, Riedel R, Cook S, Valai A, Lopes T, Radbruch A, Winkler TH, Reddy ST (2017)
external page Systems analysis reveals high genetic and antigen-driven predetermination of antibody repertoires throughout B-cell development 
Cell Reports 

Kelton W, Waindok A, Pogson M, Parola C, Reddy ST (2017)
external page Reprogramming MHC specificity by CRISPR-Cas9-assisted cassette exchange 
Scientific Reports 

2016

Friedensohn S, Khan TA, Reddy ST (2016) 
external page Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires 
Trends in Biotechnology

Pogson M*, Parola C*, Kelton WJ, Heuberger P, Reddy ST (2016)  
external page Immunogenomic engineering of a plug-and-(dis)play hybridoma platform 
Nature Communications 

Kelton WJ, Pesch T, Matile S, Reddy ST (2016)  
external page Surveying the delivery methods of CRISPR/Cas9 for ex vivo mammalian cell engineering 
Chimia

Waldmeier L, Hellmann I, Gutknecht CK, Wolter FI, Cook SC, Reddy ST, Grawunder U, Beerli R (2016)  
external page Transpo-mAb display: Transposition-mediated B cell display and functional screening of full-length IgG antibody libraries 
mAbs 

Khan TA, Friedensohn S, Gorter de Vries AR, Straszewski J, Ruscheweyh H-J, Reddy ST (2016)  
external page Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting 
Science Advances 

2015

Müller P, Kreuzaler M, Khan TA, Thomsen DS, Martin K, Glatz K, Savic S, Harbeck N, Nitz U, Gluz O, Bergwelt-Baildon M, Kreipe H, Reddy ST, Christgen M, Zippelius A (2015) 
external page Trastuzumab emtansine (T-DM1) renders HER2+ breast cancer highly susceptible to CTLA-4/PD-1 blockade 
Science Translational Medicine

Also see commentary: external page Is all cancer therapy immunotherapy?  

Glanville J, D’Angelo S, Khan TA, Reddy ST, Naranjo L, Ferrara F, Bradbury ARM (2015) 
external page Deep sequencing in library selection projects: what insight does it bring? 
Current Opinion in Structural Biology 

Greiff V, Miho E, Menzel U, Reddy ST (2015) 
external page Bioinformatic and statistical analysis of adaptive immune repertoires 
Trends in Immunology

Pogson M, Kelton W, Reddy ST (2015) 
external page Microscale technologies for high-throughput analysis of immune cells 
Microscale Technologies for Cell Engineering - Springer Book Chapter

Greiff V, Bhat P, Cook S, Menzel U, Kang W, Reddy ST (2015) 
external page A bioinformatic framework for immune repertoire diversityprofiling enables detection of immunological status 
Genome Medicine

Berger CT*, Greiff V*, Mehling M, Fritz S, Meier MA, Hoenger G, Conen A, Recher M, Battegay, Reddy ST, Hess C (2015) 
external page Influenza vaccine response profiles are affected by vaccine preparation and preexisting immunity, but not HIV infection 
Human Vaccines and Immunotherapeutics

2014

Schanz M, Liechti T, Zagordi O, Miho E, Reddy ST, Günthard HF, Trkola A, Huber M (2014) 
external page High-throughput sequencing of human immunoglobulin variable regions with subtype identification 
PLOS ONE

Greiff V*, Menzel U*, Haessler U, Cook SC, Friedensohn S, Khan TA, Pogson M, Hellmann I, Reddy ST (2014) 
external page Quantitative assessment of the robustness of next-generation sequencing of antibody variable repertoires from immunized mice 
BMC Immunology

Lavinder JJ, Hoi KH, Reddy ST, Wine Y, Georgiou G (2014) 
external page Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire 
PLOS ONE

Menzel U*, Greiff V*, Khan TA, Haessler U, Hellmann I, Friedensohn S, Cook SC, Pogson M, Reddy ST (2014) 
external page Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing 
PLOS ONE

Khan TA, Reddy ST (2014) 
external page Immunological principles regulating immunomodulation with biomaterials
Acta Biomaterials

Haessler U, Reddy ST (2014) 
external page Using Next-Generation Sequencing for Discovery of High-Frequency Monoclonal Antibodies in the Variable Gene Repertoires from Immunized Mice 
Methods in Molecular Biology

Publications before ETH Zurich

Ippolito GC, Hoi KH, Reddy ST, Carroll SM, Ge X, Rogosch T, Zemlin M, Shultz LD, Ellington AD, VandenBerg CL, Georgoiu G (2012) 
external page Antibody repertoires in humanized NOD-scid-IL2Gnull mice and humab B cells reveals human-like diversification and tolerance checkpoints in mice 
PLOS ONE

Reddy ST, Georgiou G (2011) 
external page Systems analysis of adaptive immunity by utilization of high-throughput technologies 
Current Opinion in Biotechnology

Thomas SN, van der Vlies AJ, O’neil CP, Reddy ST, Yu SS, Giorgio TD, Swartz MA, Hubbell JA (2010)
external page Engineering complement activation on polypropylene sulfide nanoparticles
Biomaterials

Reddy ST, Ge X, Miklos A, Hughes R, Kang SH, Hoi KH, Chrysostomou C, Smith SH, Iverson BL, Tucker PW, Ellington AD, Georgiou G (2010)
external page Monoclonal antibodies isolated without screening by analyzing the variable gene repertoire of plasma cells 
Nature Biotechnology

Jung ST, Reddy ST, Kang TH, Borrok MJ, Sandie I, Tucker PW, Georgiou G (2010)
external page Aglycosylated IgG variants expressed in E. coli that selectively bind FcγR1 potentiate tumor cell killing by monocyte-dendritic cells 
Proceedings of National Academy of Sciences of the United States of America

Mercanzini A, Reddy ST, Velluto D, Colin P, Maillard A, Bensadoun JC, Hubbell JA, Renaud P (2010)
external page Controlled release nanoparticle embedded coatings reduce the tissue reaction to neuroprostheses 
Journal of Controlled Release

Lim HY, Rutkowski JM, Helft J, Reddy ST, Swartz MA, Randolph GJ, Angeli V (2009)
external page Hypercholesterolemic mice exhibit lymphatic vessel dysfunction and degeneration 
The American Journal of Pathology

Swartz MA, Hubbell JA, Reddy ST (2008)  
external page Lymphatic drainage function and its immunological implications: From dendritic cell homing to vaccine design 
Seminars in Immunology

Reddy ST, van der Vlies AJ, Simeoni E, Angeli V, Randolph GJ, L.K. Lee LK, Swartz MA, Hubbell JA (2007) 
external page Exploiting lymphatic transport and complement activation in nanoparticle vaccines 
Nature Biotechnology 

Reddy ST, Swartz MA, Hubbell JA (2006)
external page Targeting dendritic cells with biomaterials: developing the next generation of vaccines 
Trends in Immunology

Reddy ST, Rehor A, Schmoekel HG, Hubbell JA, Swartz MA (2006)
external page In vivo targeting of dendritic cells in lymph nodes with poly(propylene sulfide) nanoparticles 
Journal of Controlled Release

Reddy ST, Berk DA, Jain RK, Swartz MA (2006) 
external page A sensitive in vivo model for quantifying interstitial convective transport of injected macromolecules and nanoparticles 
Journal of Applied Physiology

Reddy ST, Kelton WJ, Parola C, Mason DM, Pogson M, Mammalian cell line for protein production and library generation, WO2017174329A1 (Priority: April 4, 2016, Pending).
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Reddy ST, Ge X, Boutz D, Ellington AD, Marcotte EM, Lavinder J, Georgiou, G, Rapid isolation of monoclonal antibodies from animals, WO2011146514 A2 (Priority: 2010, Pending).
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Georgiou G, Jung ST, Reddy ST, Immunoglobulin Fc polypeptides, US8679493 B2 (Priority: 2009, Granted: 2014).
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