Search Results - "Lahdesmaki, Harri"

LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation by Halla-aho, Viivi, Lähdesmäki, Harri

“…Abstract Motivation DNA methylation is an important epigenetic modification, which has multiple functions. DNA methylation and its connections to diseases have…”
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ChromDMM: a Dirichlet-multinomial mixture model for clustering heterogeneous epigenetic data by Osmala, Maria, Eraslan, Gökçen, Lähdesmäki, Harri

“…Abstract Motivation Research on epigenetic modifications and other chromatin features at genomic regulatory elements elucidates essential biological mechanisms…”
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mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion by Jokinen, Emmi, Heinonen, Markus, Lähdesmäki, Harri

“…Abstract Motivation Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes…”
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EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings by Korpela, Dani, Jokinen, Emmi, Dumitrescu, Alexandru, Huuhtanen, Jani, Mustjoki, Satu, Lähdesmäki, Harri

“…Abstract Motivation T cells play an essential role in adaptive immune system to fight pathogens and cancer but may also give rise to autoimmune diseases. The…”
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Learning conditional variational autoencoders with missing covariates by Ramchandran, Siddharth, Tikhonov, Gleb, Lönnroth, Otto, Tiikkainen, Pekka, Lähdesmäki, Harri

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lgpr: an interpretable non-parametric method for inferring covariate effects from longitudinal data by Timonen, Juho, Mannerström, Henrik, Vehtari, Aki, Lähdesmäki, Harri

“…Abstract Motivation Longitudinal study designs are indispensable for studying disease progression. Inferring covariate effects from longitudinal data, however,…”
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TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs by Jokinen, Emmi, Dumitrescu, Alexandru, Huuhtanen, Jani, Gligorijević, Vladimir, Mustjoki, Satu, Bonneau, Richard, Heinonen, Markus, Lähdesmäki, Harri

“…Abstract Motivation T cells use T cell receptors (TCRs) to recognize small parts of antigens, called epitopes, presented by major histocompatibility complexes…”
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TSignal: a transformer model for signal peptide prediction by Dumitrescu, Alexandru, Jokinen, Emmi, Paatero, Anja, Kellosalo, Juho, Paavilainen, Ville O, Lähdesmäki, Harri

“…Abstract Motivation Signal peptides (SPs) are short amino acid segments present at the N-terminus of newly synthesized proteins that facilitate protein…”
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BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data by Kaehaerae, Juhani, Laehdesmaeki, Harri

“…Transcription factors (TFs) are a class of DNA-binding proteins that have a central role in regulating gene expression. To reveal mechanisms of transcriptional…”
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Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics by Äijö, Tarmo, Lähdesmäki, Harri

“…Motivation: Regulation of gene expression is fundamental to the operation of a cell. Revealing the structure and dynamics of a gene regulatory network (GRN) is…”
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MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis by Rautio, Sini, Lähdesmäki, Harri

“…Transcription factors (TFs) are proteins that bind to DNA and regulate gene expression. To understand details of gene regulation, characterizing TF binding…”
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PairGP: Gaussian process modeling of longitudinal data from paired multi-condition studies by Vantini, Michele, Mannerström, Henrik, Rautio, Sini, Ahlfors, Helena, Stockinger, Brigitta, Lähdesmäki, Harri

“…High-throughput technologies produce gene expression time-series data that need fast and specialized algorithms to be processed. While current methods already…”
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Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation by Äijö, Tarmo, Butty, Vincent, Chen, Zhi, Salo, Verna, Tripathi, Subhash, Burge, Christopher B, Lahesmaa, Riitta, Lähdesmäki, Harri

“…Gene expression profiling using RNA-seq is a powerful technique for screening RNA species' landscapes and their dynamics in an unbiased way. While several…”
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The effect of music performance on the transcriptome of professional musicians by Kanduri, Chakravarthi, Kuusi, Tuire, Ahvenainen, Minna, Philips, Anju K., Lähdesmäki, Harri, Järvelä, Irma

“…Music performance by professional musicians involves a wide-spectrum of cognitive and multi-sensory motor skills, whose biological basis is unknown. Several…”
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LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs by Äijö, Tarmo, Yue, Xiaojing, Rao, Anjana, Lähdesmäki, Harri

“…5-methylcytosine (5mC) is a widely studied epigenetic modification of DNA. The ten-eleven translocation (TET) dioxygenases oxidize 5mC into oxidized…”
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Learning the structure of dynamic Bayesian networks from time series and steady state measurements by Lähdesmäki, Harri, Shmulevich, Ilya

“…Dynamic Bayesian networks (DBN) are a class of graphical models that has become a standard tool for modeling various stochastic time-varying phenomena. In many…”
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Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks by Intosalmi, Jukka, Nousiainen, Kari, Ahlfors, Helena, Lähdesmäki, Harri

“…Mechanistic models based on ordinary differential equations provide powerful and accurate means to describe the dynamics of molecular machinery which…”
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snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions by Nousiainen, Kari, Kanduri, Kartiek, Ricaño-Ponce, Isis, Wijmenga, Cisca, Lahesmaa, Riitta, Kumar, Vinod, Lähdesmäki, Harri

“…Abstract Motivation Co-localization of trait associated SNPs for specific transcription-factor binding sites or regulatory regions in the genome can yield…”
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A subpopulation model to analyze heterogeneous cell differentiation dynamics by Chan, Yat Hin, Intosalmi, Jukka, Rautio, Sini, Lähdesmäki, Harri

“…Cell differentiation is steered by extracellular signals that activate a cell type specific transcriptional program. Molecular mechanisms that drive the…”
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Notch signaling regulates the differentiation of neural crest from human pluripotent stem cells by Noisa, Parinya, Lund, Carina, Kanduri, Kartiek, Lund, Riikka, Lähdesmäki, Harri, Lahesmaa, Riitta, Lundin, Karolina, Chokechuwattanalert, Hataiwan, Otonkoski, Timo, Tuuri, Timo, Raivio, Taneli

“…Neural crest cells are specified at the border between the neural plate and the epiderm. They are capable of differentiating into various somatic cell types,…”
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