About Me

My name is Ekaterina (Katya) Aladyeva. I am a computational scientist at Dr. Harari's lab at The Ohio State University (OSU) Wexner Medical Center.

I have analyzed single-cell and spatial transcriptomics data in multiple projects in immunology and neuroscience. I am mainly interested in the effects of innate immune cells in aging processes and neurodegenerative diseases. Currently, I am working on a pipeline for an atlas-level brain dataset of patients with Alzheimer's disease.

I have really broad experience in computer science, especially in databases and DevOps. Before I joined academia, I worked as a data engineer in a consulting company in Moscow, Russia.

desktop monitor beside computer tower on inside room
desktop monitor beside computer tower on inside room

Education

  • Moscow State University of Instrument Engineering and Computer Systems
    Specialization – Computer science in Economics.
    Specialist degree (Master’s degree equivalent for US).
    2008-2013

Workplaces

  • Biostatistics Analyst, Dr. Harari Lab, Neurology department, The Ohio State University Wexner Medical Center, Columbus, OH, USA
    February 2024 - current

  • Bioinformatics Scientist, Dr. Harari Lab, Psychiatry department, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
    March 2023 – January 2024

  • Visiting Researcher, Dr. Artyomov Lab, Pathology and Immunology Department, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
    November 2018 – March 2023

  • Data Engineer / Data Scientist, Latvian Biomedical Research and Study Center, Latvia, Riga
    September 2017 – March 2019

  • Data Engineer / Data Scientist, CROC Inc., Moscow, Russia
    September 2013 – August 2017

  • Junior Data Scientist, Commercial Bank “Renaissance Credit”
    July 2012 – August 2013

  • Assistant at computation laboratory, Moscow University of Instrument Engineering and Computer Systems, Moscow, Russia
    November 2009 – June 2012

Publications

  • Non-negative matrix factorization and deconvolution as dual simplex problem
    Denis Kleverov, Ekaterina Aladyeva, Alexey Serdyukov, Maxim N. Artyomov
    https://doi.org/10.1101/2024.04.09.588652
    Preprint, BioRxiv, 2024

  • Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+ GZMB− CD8+ memory T cells and accumulation of type 2 memory T cells
    Marina Terekhova, Amanda Swain, Pavla Bohacova, Ekaterina Aladyeva, Laura Arthur, Anwesha Laha, Denis A Mogilenko, Samantha Burdess, Vladimir Sukhov, Denis Kleverov, Barbora Echalar, Petr Tsurinov, Roman Chernyatchik, Kamila Husarcikova, Maxim N Artyomov
    https://doi.org/10.1016/j.immuni.2023.10.013
    Immunity 56 (12), 2836-2854.e9, 2023

  • Microglia-mediated T cell infiltration drives neurodegeneration in tauopathy
    Xiaoying Chen, Maria Firulyova, Melissa Manis, Jasmin Herz, Igor Smirnov, Ekaterina Aladyeva, Chanung Wang, Xin Bao, Mary Beth Finn, Hao Hu, Irina Shchukina, Min Woo Kim, Carla M Yuede, Jonathan Kipnis, Maxim N Artyomov, Jason D Ulrich, David M Holtzman
    https://doi.org/10.1038/s41586-023-05788-0
    Nature 615, 668–677, 2023

  • Caloric restriction in humans reveals immunometabolic regulators of health span
    O Spadaro, Y Youm, I Shchukina, S Ryu, S Sidorov, A Ravussin, K Nguyen, E Aladyeva, AN Predeus, SR Smith, E Ravussin, C Galban, MN Artyomov, VD Dixit
    https://doi.org/10.1126/science.abg7292
    Science 375 (6581), 671-677, 2022

  • Myeloid cell interferon responses correlate with clearance of SARS-CoV-2
    Dhiraj K Singh, Ekaterina Aladyeva, Shibali Das, Bindu Singh, Ekaterina Esaulova, Amanda Swain, Mushtaq Ahmed, Journey Cole, Chivonne Moodley, Smriti Mehra, Larry S Schlesinger, Maxim N Artyomov, Shabaana A Khader, Deepak Kaushal
    https://doi.org/10.1038/s41467-022-28315-7
    Nature communications 13 (1), 1-15, 2022

  • Metformin strongly affects transcriptome of peripheral blood cells in healthy individuals
    Monta Ustinova, Ivars Silamikelis, Ineta Kalnina, Laura Ansone, Vita Rovite, Ilze Elbere, Ilze Radovica-Spalvina, Davids Fridmanis, Jekaterina Aladyeva, Ilze Konrade, Valdis Pirags, Janis Klovins
    https://doi.org/10.1371/journal.pone.0224835
    PloS one 14 (11), e0224835, 2019

Skills

  • Bioinformatics Pipelines: single cell/nuclei RNAseq, spatial transcriptomics (10X Visium), 10X multiome (scRNAseq + scATACseq), bulkRNAseq analysis + deconvolution

  • Bioinformatics Tools: Seurat, SquidPy, scanpy, Cellranger, Spaceranger,
    DoubletFinder, scDblFinder, hdWGCNA, GATK, Bowtie2

  • Reproducibility: Docker, Snakemake, Nextflow, Git

  • Programming Languages: R, Python, Java

  • Cloud Services: AWS S3, AWS ECR, AWS ECS

  • Databases: Oracle Database, DB2, Greenplum, PostgreSQL

  • Big data: Hortonworks Data Platform (Hadoop), Apache NiFi

  • Machine Learning: Rapidminer, PySpark, IBM Watson Content Analytics, Scikit-learn, Pytorch

  • ETL / Data transferring: Informatica PowerCenter, Pentaho Data Integration, Talend Data Integration, Airflow

Contacts

aladyeva.ekaterina+blog@gmail.com

Scientific media