Publications by authors named "Pinar Pir"

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Distinct deregulation trends of transcriptional protein complexes in aging naive T cells.
Emel Kökrek, Pınar Pir

J Leukoc Biol· March 2025

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Optimized network based natural language processing approach to reveal disease comorbidities in COVID-19.
Emre Taylan Duman, Gizem Tuna, Enes Ak, Gülben Avsar, Pinar Pir

Sci Rep· January 2024

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SUMA: a lightweight machine learning model-powered shared nearest neighbour-based clustering application interface for scRNA-Seq data.
Hamza Umut Karakurt, Pınar Pir

Turk J Biol· December 2023

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An integrated study to decipher immunosuppressive cellular communication in the PDAC environment.
Gülben Avşar, Pınar Pir

NPJ Syst Biol Appl· November 2023

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A comparative performance evaluation of imputation methods in spatially resolved transcriptomics data.
Gülben Avşar, Pınar Pir

Mol Omics· February 2023

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In silico analysis of metabolic effects of bipolar disorder on prefrontal cortex identified altered GABA, glutamate-glutamine cycle, energy metabolism and amino acid synthesis pathways.
Hamza Umut Karakurt, Pınar Pir

Integr Biol (Camb)· October 2022

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Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data.
Müberra Fatma Cesur, Tunahan Çakır, Pınar Pir

mSystems· June 2022

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MODOMICS: a database of RNA modification pathways. 2021 update.
Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Pınar Pir

Nucleic Acids Res· January 2022

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Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer.
Dilara Uzuner, Yunus Akkoç, Nesibe Peker, Pınar Pir, Devrim Gözüaçık

Sci Rep· August 2021

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A mark of disease: how mRNA modifications shape genetic and acquired pathologies.
Eliana Destefanis, Gülben Avşar, Paula Groza, Antonia Romitelli, Serena Torrini, Pınar Pir

RNA· April 2021

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Comparison of visualization tools for single-cell RNAseq data.
Batuhan Cakir, Martin Prete, Ni Huang, Stijn van Dongen, Pinar Pir

NAR Genom Bioinform· September 2020

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Next-Generation Genome-Scale Models Incorporating Multilevel 'Omics Data: From Yeast to Human.
Tunahan Çakır, Emel Kökrek, Gülben Avşar, Ecehan Abdik, Pınar Pir

Methods Mol Biol· June 2020

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Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epithelial cells with metabolic and protein-protein interaction networks.
Hamza Umut Karakurt, Pınar Pİr

Turk J Biol· June 2020

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Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Michael F Jantsch, Alessandro Quattrone, Mary O'Connell, Mark Helm, Michaela Frye, Pinar Pir

RNA Biol· November 2018

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PTEN Regulates PI(3,4)P Signaling Downstream of Class I PI3K.
Mouhannad Malek, Anna Kielkowska, Tamara Chessa, Karen E Anderson, David Barneda, Pınar Pir

Mol Cell· November 2017

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Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine.
Pınar Pir, Nicolas Le Novère

Methods Mol Biol· October 2016

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Toward Community Standards and Software for Whole-Cell Modeling.
Dagmar Waltemath, Jonathan R Karr, Frank T Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Pinar Pir

IEEE Trans Biomed Eng· October 2016

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Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis.
Douglas B Kell, Neil Swainston, Pınar Pir, Stephen G Oliver

Trends Biotechnol· April 2015

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Yeast cells with impaired drug resistance accumulate glycerol and glucose.
Duygu Dikicioglu, Sebnem Oc, Bharat M Rash, Warwick B Dunn, Pınar Pir

Mol Biosyst· January 2014

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Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids.
Annette A Alcasabas, Michaela de Clare, Pınar Pir, Stephen G Oliver

BMC Genomics· October 2013

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A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.
Kieran Smallbone, Hanan L Messiha, Kathleen M Carroll, Catherine L Winder, Naglis Malys, Pınar Pir

FEBS Lett· September 2013

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Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory.
Duygu Dikicioglu, Pınar Pir, Stephen G Oliver

Biotechnol J· September 2013

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Yeast-based automated high-throughput screens to identify anti-parasitic lead compounds.
Elizabeth Bilsland, Andrew Sparkes, Kevin Williams, Harry J Moss, Michaela de Clare, Pinar Pir

Open Biol· February 2013

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A prototrophic deletion mutant collection for yeast metabolomics and systems biology.
Michael Mülleder, Floriana Capuano, Pınar Pir, Stefan Christen, Uwe Sauer

Nat Biotechnol· December 2012

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The genetic control of growth rate: a systems biology study in yeast.
Pınar Pir, Alex Gutteridge, Jian Wu, Bharat Rash, Douglas B Kell

BMC Syst Biol· January 2012

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