Publications by authors named "Alexander Bagaev"

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MutAnt: mutation annotation tool predicts deleteriousness of missense mutations and improves mutation calling from transcriptomics.
Aleksandr Sarachakov, Anastasiya Yudina, Viktor Svekolkin, Anna Parfenenkova, Miryam Spektor, Alexander Bagaev

Hum Genet· December 2025

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Identification of therapeutic targets for renal medullary carcinoma via integrated genomic and transcriptomic profiling.
Pavlos Msaouel, Nizar M Tannir, Funda Meric-Bernstam, Jennifer M King, Martin H Voss, Alexander Bagaev

Cell Rep Med· November 2025

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A simple circuit to sustain intact tumor microenvironments for complex drug interrogations.
A Leila Sarvestani, Samantha Ruff, Kirsten Remmert, Martha Teke, Emily Verbus, Alexander Bagaev

bioRxiv· October 2025

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RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation.
Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U Shanthappa, Alexander Bagaev

Sci Rep· August 2025

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AI-driven multimodal algorithm predicts immunotherapy and targeted therapy outcomes in clear cell renal cell carcinoma.
Danil Stupichev, Natalia Miheecheva, Ekaterina Postovalova, Yang Lyu, Akshaya Ramachandran, Alexander Bagaev

Cell Rep Med· August 2025

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Machine learning-based single-sample molecular classifier for cancer grading.
Zoia Antysheva, Nikita Kotlov, Mariia V Guryleva, Ivan Valiev, Viktor Svekolkin, Alexander Bagaev

Front Oncol· July 2025

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Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.
Anastasiya Yudina, Cagdas Tazearslan, Artur Baisangurov, Ekaterina Nuzhdina, Kelley Lauziere, Alexander Bagaev

Commun Med (Lond)· June 2025

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A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities.
Danilo Fiore, Luca Vincenzo Cappelli, Liu Zhaoqi, Nikita Kotlov, Maria Sorokina, Alexander Bagaev

Cell Rep Med· April 2025

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The Breast Cancer Classifier refines molecular breast cancer classification to delineate the HER2-low subtype.
Polina Turova, Vladimir Kushnarev, Oleg Baranov, Anna Butusova, Sofia Menshikova, Alexander Bagaev

NPJ Breast Cancer· February 2025

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A novel case of glial transdifferentiation in renal medullary carcinoma brain metastasis.
Maria A Gubbiotti, Ian E McCutcheon, Priya Rao, Giannicola Genovese, Linghua Wang, Alexander Bagaev

Acta Neuropathol Commun· January 2025

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Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma.
Cody A Ramirez, Michelle Becker-Hapak, Kartik Singhal, David A Russler-Germain, Felix Frenkel, Alexander Bagaev

Blood Adv· August 2024

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Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in patients with cancer.
Daniiar Dyikanov, Aleksandr Zaitsev, Tatiana Vasileva, Iris Wang, Arseniy A Sokolov, Alexander Bagaev

Cancer Cell· May 2024

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Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients.
Andrea J Radtke, Ekaterina Postovalova, Arina Varlamova, Alexander Bagaev, Maria Sorokina

Cancer Cell· March 2024

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Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data.
Nikita Kotlov, Kirill Shaposhnikov, Cagdas Tazearslan, Madison Chasse, Artur Baisangurov, Alexander Bagaev

Commun Biol· March 2024

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Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling.
Aleksandr Sarachakov, Arina Varlamova, Viktor Svekolkin, Margarita Polyakova, Itzel Valencia, Alexander Bagaev

Blood· December 2023

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Immune-depleted tumor microenvironment is associated with poor outcomes and BTK inhibitor resistance in mantle cell lymphoma.
Preetesh Jain, Krystle Nomie, Nikita Kotlov, VitaIy Segodin, Holly Hill, Alexander Bagaev

Blood Cancer J· October 2023

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Longitudinal Molecular Analysis of Tumor Exome and Transcriptome to Evaluate Clonal Evolution and Identify Novel Therapeutic Targets in Thymoma.
Christopher S Nabel, Yin P Hung, Anna Kurilovich, Aleksandra Lopareva, Dora Dias-Santagata, Alexander Bagaev

JCO Precis Oncol· July 2023

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B-Cell Infiltrate in the Tumor Microenvironment Is Associated With Improved Survival in Resected Lung Adenocarcinoma.
Ibiayi Dagogo-Jack, Ivan Valiev, Nikita Kotlov, Anna Belozerova, Aleksandra Lopareva, Alexander Bagaev

JTO Clin Res Rep· July 2023

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B cell-dependent subtypes and treatment-based immune correlates to survival in stage 3 and 4 lung adenocarcinomas.
Susan Raju Paul, Ivan Valiev, Skylar E Korek, Vladimir Zyrin, Diana Shamsutdinova, Alexander Bagaev

FASEB Bioadv· April 2023

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Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression.
Guangchun Han, Qing Deng, Mario L Marques-Piubelli, Enyu Dai, Minghao Dang, Alexander Bagaev

Blood Cancer Discov· September 2022

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Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes.
Aleksandr Zaitsev, Maksim Chelushkin, Daniiar Dyikanov, Ilya Cheremushkin, Boris Shpak, Alexander Bagaev

Cancer Cell· August 2022

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Multiregional single-cell proteogenomic analysis of ccRCC reveals cytokine drivers of intratumor spatial heterogeneity.
Natalia Miheecheva, Ekaterina Postovalova, Yang Lyu, Akshaya Ramachandran, Alexander Bagaev

Cell Rep· August 2022

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Diagnostic Utility of RNA-Seq for Evaluation of PD-L1 Expression in Clear Cell Renal Cell Carcinoma.
Maria Sorokina, Danil Stupichev, Yang Lyu, Akshaya Ramachandran, Natalia Miheecheva, Alexander Bagaev

Clin Genitourin Cancer· December 2021

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Lack of intrafollicular memory CD4 + T cells is predictive of early clinical failure in newly diagnosed follicular lymphoma.
Patrizia Mondello, Angelo Fama, Melissa C Larson, Andrew L Feldman, Jose C Villasboas, Alexander Bagaev

Blood Cancer J· July 2021

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Conserved pan-cancer microenvironment subtypes predict response to immunotherapy.
Alexander Bagaev, Nikita Kotlov, Krystle Nomie, Viktor Svekolkin, Azamat Gafurov

Cancer Cell· June 2021

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