netSmooth: Network-smoothing based imputation for single cell RNA-seq

por Ronen, Jonathan, Akalin, Altuna
Publicado 2018

Evaluation of colorectal cancer subtypes and cell lines using deep learning

por Ronen, Jonathan, Hayat, Sikander, Akalin, Altuna
Publicado 2019

Translog, a web browser for studying the expression divergence of homologous genes

por Dong, Xianjun, Akalin, Altuna, Sharma, Yogita, Lenhard, Boris
Publicado 2010

Deep learning for genomics using Janggu

por Kopp, Wolfgang, Monti, Remo, Tamburrini, Annalaura, Ohler, Uwe, Akalin, Altuna
Publicado 2020

Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction

por Baranovskii, Artem, Gündüz, Irem B., Franke, Vedran, Uyar, Bora, Akalin, Altuna
Publicado 2022

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

por Blin, Kai, Dieterich, Christoph, Wurmus, Ricardo, Rajewsky, Nikolaus, Landthaler, Markus, Akalin, Altuna
Publicado 2014

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

por Uyar, Bora, Yusuf, Dilmurat, Wurmus, Ricardo, Rajewsky, Nikolaus, Ohler, Uwe, Akalin, Altuna
Publicado 2017

Identifying tumor cells at the single-cell level using machine learning

por Dohmen, Jan, Baranovskii, Artem, Ronen, Jonathan, Uyar, Bora, Franke, Vedran, Akalin, Altuna
Publicado 2022

HOT or not: examining the basis of high-occupancy target regions

por Wreczycka, Katarzyna, Franke, Vedran, Uyar, Bora, Wurmus, Ricardo, Bulut, Selman, Tursun, Baris, Akalin, Altuna
Publicado 2019

Global identification of functional microRNA-mRNA interactions in Drosophila

por Wessels, Hans-Hermann, Lebedeva, Svetlana, Hirsekorn, Antje, Wurmus, Ricardo, Akalin, Altuna, Mukherjee, Neelanjan, Ohler, Uwe
Publicado 2019

PiGx: reproducible genomics analysis pipelines with GNU Guix

por Wurmus, Ricardo, Uyar, Bora, Osberg, Brendan, Franke, Vedran, Gosdschan, Alexander, Wreczycka, Katarzyna, Ronen, Jonathan, Akalin, Altuna
Publicado 2018

Single-cell analyses of aging, inflammation and senescence

por Uyar, Bora, Palmer, Daniel, Kowald, Axel, Murua Escobar, Hugo, Barrantes, Israel, Möller, Steffen, Akalin, Altuna, Fuellen, Georg
Publicado 2020

Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells

por Kim, Minchul, Franke, Vedran, Brandt, Bettina, Lowenstein, Elijah D., Schöwel, Verena, Spuler, Simone, Akalin, Altuna, Birchmeier, Carmen
Publicado 2020

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

por Akalin, Altuna, Kormaksson, Matthias, Li, Sheng, Garrett-Bakelman, Francine E, Figueroa, Maria E, Melnick, Ari, Mason, Christopher E
Publicado 2012

Transcriptional features of genomic regulatory blocks

por Akalin, Altuna, Fredman, David, Arner, Erik, Dong, Xianjun, Bryne, Jan Christian, Suzuki, Harukazu, Daub, Carsten O, Hayashizaki, Yoshihide, Lenhard, Boris
Publicado 2009

Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions

por Royo, José Luis, Hidalgo, Carmen, Roncero, Yolanda, Seda, María Angeles, Akalin, Altuna, Lenhard, Boris, Casares, Fernando, Gómez-Skarmeta, José Luis
Publicado 2011

Alternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartments

por Ciolli Mattioli, Camilla, Rom, Aviv, Franke, Vedran, Imami, Koshi, Arrey, Gerard, Terne, Mandy, Woehler, Andrew, Akalin, Altuna, Ulitsky, Igor, Chekulaeva, Marina
Publicado 2019

The conserved histone chaperone LIN‐53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans

por Müthel, Stefanie, Uyar, Bora, He, Mei, Krause, Anne, Vitrinel, Burcu, Bulut, Selman, Vasiljevic, Djordje, Marchal, Iris, Kempa, Stefan, Akalin, Altuna, Tursun, Baris
Publicado 2019

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program

por Wyler, Emanuel, Franke, Vedran, Menegatti, Jennifer, Kocks, Christine, Boltengagen, Anastasiya, Praktiknjo, Samantha, Walch-Rückheim, Barbara, Bosse, Jens, Rajewsky, Nikolaus, Grässer, Friedrich, Akalin, Altuna, Landthaler, Markus
Publicado 2019

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation

por Benedum, Johannes, Franke, Vedran, Appel, Lisa-Marie, Walch, Lena, Bruno, Melania, Schneeweiss, Rebecca, Gruber, Juliane, Oberndorfer, Helena, Frank, Emma, Strobl, Xué, Polyansky, Anton, Zagrovic, Bojan, Akalin, Altuna, Slade, Dea
Publicado 2023