Author: Altuna Akalin

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Preprints

Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction

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Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

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Strategies for analyzing bisulfite sequencing data

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Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

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Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

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Reproducible genomics analysis pipelines with GNU Guix

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Evaluation of colorectal cancer subtypes and cell lines using deep learning

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The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

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

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

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Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program

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Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos

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Identifying tumor cells at the single cell level

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Janggu - Deep learning for genomics

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Multi-omics and deep learning provide a multifaceted view of cancer

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SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution

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Mutations In Disordered Regions Cause Disease By Creating Endocytosis Motifs

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FACT sets a barrier for cell fate reprogramming in C. elegans and Human

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

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Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning

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Parallel genetics of regulatory sequences in vivo

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Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression

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The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators

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A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA

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Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation

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The conserved histone chaperone LIN-53 links lifespan and healthspan regulation in C. elegans

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Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia

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Pdap1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification

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