Giovanni Palla - Publications, H-index & Citations

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Giovanni Palla

biohub

20H-index

63Paper Count

3.7KCitation Count

Published Papers 10

Publication Date

TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution

Science

IF45.8

2026-05-07

PREAI

James D. Pearce; Sara E. Simmonds; Gita Mahmoudabadi; Lakshmi Krishnan; Giovanni Palla; Ana-Maria Istrate; Alexander Tarashansky; Benjamin Nelson; Omar Valenzuela; Donghui Li; Stephen R. Quake; Theofanis Karaletsos

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Nicheformer: a foundation model for single-cell and spatial omics

Nature Methods

IF32.1

2025-10-30

OAAI

Alejandro Tejada-Lapuerta; Anna C. Schaar; Robert Gutgesell; Giovanni Palla; Lennard Halle; Mariia Minaeva; Larsen Vornholz; Leander Dony; Francesca Drummer; Till Richter; Mojtaba Bahrami; Fabian J. Theis

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Defining and benchmarking open problems in single-cell analysis

Nature Biotechnology

IF41.7

2025-07-01

OAAI

Malte D. Luecken; Scott Gigante; Daniel B. Burkhardt; Robrecht Cannoodt; Daniel C. Strobl; Nikolay S. Markov; Luke Zappia; Giovanni Palla; Wesley Lewis; Daniel Dimitrov; Michael E. Vinyard; D. S. Magruder; Michaela F. Mueller; Alma Andersson; Emma Dann; Qian Qin; Dominik J. Otto; Michal Klein; Olga Borisovna Botvinnik; Louise Deconinck; Kai Waldrant; Sai Nirmayi Yasa; Artur Szałata; Andrew Benz; Zhijian Li; Jonathan M. Bloom; Angela Oliveira Pisco; Julio Saez-Rodriguez; Drausin Wulsin; Luca Pinello; Yvan Saeys; Fabian J. Theis; Smita Krishnaswamy

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SpatialData: an open and universal data framework for spatial omics

NATURE METHODS

IF32.1

2024-03-20

OAAI

Marconato, Luca; Palla, Giovanni; Yamauchi, Kevin A.; Virshup, Isaac; Heidari, Elyas; Treis, Tim; Vierdag, Wouter-Michiel; Toth, Marcella; Stockhaus, Sonja; Shrestha, Rahul B.; Rombaut, Benjamin; Pollaris, Lotte; Lehner, Laurens; Voehringer, Harald; Kats, Ilia; Saeys, Yvan; Saka, Sinem K.; Huber, Wolfgang; Gerstung, Moritz; Moore, Josh; Theis, Fabian J.; Stegle, Oliver

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Multimodal characterization of murine gastruloid development

CELL STEM CELL

IF20.4

2023-06-01

OAAI

Suppinger, Simon; Zinner, Marietta; Aizarani, Nadim; Lukonin, Ilya; Ortiz, Raphael; Azzi, Chiara; Stadler, Michael B.; Vianello, Stefano; Palla, Giovanni; Kohler, Hubertus; Mayran, Alexandre; Lutolf, Matthias P.; Liberali, Prisca

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GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks

MOLECULAR SYSTEMS BIOLOGY

IF7.7

2023-04-19

OAAI

Kamal, Aryan; Arnold, Christian; Claringbould, Annique; Moussa, Rim; Servaas, Nila H.; Kholmatov, Maksim; Daga, Neha; Nogina, Daria; Mueller-Dott, Sophia; Reyes-Palomares, Armando; Palla, Giovanni; Sigalova, Olga; Bunina, Daria; Pabst, Caroline; Zaugg, Judith B.

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The scverse project provides a computational ecosystem for single-cell omics data analysis

NATURE BIOTECHNOLOGY

IF41.7

2023-04-10

PREAI

Virshup, Isaac; Bredikhin, Danila; Heumos, Lukas; Palla, Giovanni; Sturm, Gregor; Gayoso, Adam; Kats, Ilia; Koutrouli, Mikaela; Berger, Bonnie; Pe'er, Dana; Regev, Aviv; Teichmann, Sarah; Finotello, Francesca; Wolf, F. Alexander; Yosef, Nir; Stegle, Oliver; Theis, Fabian; Angerer, Philipp; Bergen, Volker; Boyeau, Pierre D.; Buettner, Maren; Eraslan, Gokcen; Fischer, David; Frank, Max C.; Hong, Justin; Klein, Michal; Lange, Marius; Lopez, Romain; Lotfollahi, Mohammad; Luecken, Malte; Ramirez, Fidel A.; Regier, Jeffrey; Rybakov, Sergei; Schaar, Anna; Valiollah Pour Amiri, Valeh; Weiler, Philipp J.; Xing, Galen

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Spatial components of molecular tissue biology

NATURE BIOTECHNOLOGY

IF41.7

2022-02-07

138

PREAI

Palla, Giovanni; Fischer, David S.; Regev, Aviv; Theis, Fabian J.

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Squidpy: a scalable framework for spatial omics analysis

NATURE METHODS

IF32.1

2022-01-31

293

OAAI

Palla, Giovanni; Spitzer, Hannah; Klein, Michal; Fischer, David; Schaar, Anna Christina; Kuemmerle, Louis Benedikt; Rybakov, Sergei; Ibarra, Ignacio L.; Holmberg, Olle; Virshup, Isaac; Lotfollahi, Mohammad; Richter, Sabrina; Theis, Fabian J.

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Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

CELL REPORTS

IF6.9

2019-12-01

OAAI

Berest, Ivan; Arnold, Christian; Reyes-Palomares, Armando; Palla, Giovanni; Rasmussen, Kasper Dindler; Giles, Holly; Bruch, Peter-Martin; Huber, Wolfgang; Dietrich, Sascha; Helin, Kristian; Zaugg, Judith B.

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Research Directions