Recent Publications

Implementation and validation of single-cell genomics experiments in neuroscience

Dec 3, 2024

Nature neuroscience

Marco Colonna, Genevieve Konopka, Shane A Liddelow, Tomasz Nowakowski, Rajeshwar Awatramani, Helen S Bateup, Cathryn R Cadwell, Emre Caglayan, Jerry L Chen, Jesse Gillis, Martin Kampmann, Fenna Krienen, Samuel E Marsh, Michelle Monje, Michael R O'Dea, Rickie Patani, Alex A Pollen, Francisco J Quintana, Marissa Scavuzzo, Matthew Schmitz, Steven A Sloan, Paul J Tesar, Jessica Tollkuhn, Maria Antonietta Tosches, Madeleine E Urbanek, Jonathan M Werner, Omer A Bayraktar, Ozgun Gokce, Naomi Habib

Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue

Dec 2, 2024

PLoS biology

Jonathan M Werner, Jesse Gillis

The co-chaperone DNAJA2 buffers proteasomal degradation of cytosolic proteins with missense mutations

Dec 2, 2024

Journal of cell science

Heather A Baker, Jonathan P Bernardini, Veronika Csizmók, Angel Madero, Shriya Kamat, Hailey Eng, Jessica Lacoste, Faith Au Yeung, Sophie Comyn, Elizabeth Hui, Gaetano Calabrese, Brian Raught, Mikko Taipale, Thibault Mayor

Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning

Nov 28, 2024

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Zhuohan Yu, Yuning Yang, Xingjian Chen, Ka-Chun Wong, Zhaolei Zhang, Yuming Zhao, Xiangtao Li

Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors

Nov 28, 2024

bioRxiv : the preprint server for biology

Ilya E Vorontsov, Ivan Kozin, Sergey Abramov, Alexandr Boytsov, Arttu Jolma, Mihai Albu, Giovanna Ambrosini, Katerina Faltejskova, Antoni J Gralak, Nikita Gryzunov, Sachi Inukai, Semyon Kolmykov, Pavel Kravchenko, Judith F Kribelbauer-Swietek, Kaitlin U Laverty, Vladimir Nozdrin, Zain M Patel, Dmitry Penzar, Marie-Luise Plescher, Sara E Pour, Rozita Razavi, Ally W H Yang, Ivan Yevshin, Arsenii Zinkevich, Matthew T Weirauch, Philipp Bucher, Bart Deplancke, Oriol Fornes, Jan Grau, Ivo Grosse, Fedor A Kolpakov, Codebook/GRECO-BIT Consortium, Vsevolod J Makeev, Timothy R Hughes, Ivan V Kulakovskiy

Extensive binding of uncharacterized human transcription factors to genomic dark matter

Nov 28, 2024

bioRxiv : the preprint server for biology

Rozita Razavi, Ali Fathi, Isaac Yellan, Alexander Brechalov, Kaitlin U Laverty, Arttu Jolma, Aldo Hernandez-Corchado, Hong Zheng, Ally W H Yang, Mihai Albu, Marjan Barazandeh, Chun Hu, Ilya E Vorontsov, Zain M Patel, Codebook Consortium, Ivan V Kulakovskiy, Philipp Bucher, Quaid Morris, Hamed S Najafabadi, Timothy R Hughes

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

Nov 28, 2024

bioRxiv : the preprint server for biology

Arttu Jolma, Aldo Hernandez-Corchado, Ally W H Yang, Ali Fathi, Kaitlin U Laverty, Alexander Brechalov, Rozita Razavi, Mihai Albu, Hong Zheng, Codebook Consortium, Ivan V Kulakovskiy, Hamed S Najafabadi, Timothy R Hughes

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

Nov 28, 2024

bioRxiv : the preprint server for biology

Antoni J Gralak, Katerina Faltejskova, Ally W H Yang, Clemence Steiner, Julie Russeil, Nadia Grenningloh, Sachi Inukai, Mustafa Demir, Riccardo Dainese, Cooper Owen, Eugenia Pankevich, Codebook/GRECO-BIT Consortium, Timothy R Hughes, Ivan V Kulakovskiy, Judith F Kribelbauer-Swietek, Guido van Mierlo, Bart Deplancke

Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors

Nov 28, 2024

bioRxiv : the preprint server for biology

Arttu Jolma, Kaitlin U Laverty, Ali Fathi, Ally W H Yang, Isaac Yellan, Ilya E Vorontsov, Sachi Inukai, Judith F Kribelbauer-Swietek, Antoni J Gralak, Rozita Razavi, Mihai Albu, Alexander Brechalov, Zain M Patel, Vladimir Nozdrin, Georgy Meshcheryakov, Ivan Kozin, Sergey Abramov, Alexandr Boytsov, Codebook Consortium, Oriol Fornes, Vsevolod J Makeev, Jan Grau, Ivo Grosse, Philipp Bucher, Bart Deplancke, Ivan V Kulakovskiy, Timothy R Hughes

Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes

Nov 28, 2024

Nature communications

Amos A Lim, Delaram Pouyabahar, Mishal Ashraf, Kate Huang, Michelle Lohbihler, Brandon M Murareanu, Matthew L Chang, Maggie Kwan, Faisal J Alibhai, Thinh Tran, Amine Mazine, Michael A Laflamme, Gary D Bader, Zachary Laksman, Stephanie Protze