Maria Chikina - Publications, H-index & Citations

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Maria Chikina

university of pittsburgh

35H-index

166Paper Count

6.3KCitation Count

Published Papers 50

Publication Date

A scalable approach to investigating sequence-to-function predictions from personal genomes

Nature Methods

IF32.1

2026-06-08

OAAI

Anna E. Spiro; Xinming Tu; Yilun Sheng; Alexander Sasse; Rezwan Hosseini; Maria Chikina; Sara Mostafavi

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MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution

EVOLUTION

IF2.6

2026-01-01

PREAI

Selberg, Avery G.; Clark, Nathan; Nekrutenko, Anton; Chikina, Maria; Kosakovsky pond, Sergei L.

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Epigenetic priming in memory B cells versus naive B cells results in differential induction genes related to T-B interactions

JOURNAL OF IMMUNOLOGY

IF3.4

2025-11-01

PREAI

Callahan, Derrick; Smita, Shuchi; Shlomchik, Mark J.; Chikina, Maria

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Ultra-fast variant effect prediction using biophysical transcription factor binding models

NUCLEIC ACIDS RESEARCH

IF13.1

2025-10-14

PREAI

Hosseini, Rezwan; Balci, Ali Tugrul; Kostka, Dennis; Clark, Nathan; Chikina, Maria

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Best holdout assessment is sufficient for cancer transcriptomic model selection

PATTERNS

IF7.4

2024-12-01

PREAI

Crawford, Jake; Chikina, Maria; Greene, Casey S.

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RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution

MOLECULAR BIOLOGY AND EVOLUTION

IF5.3

2024-10-15

OAAI

Redlich, Ruby; Kowalczyk, Amanda; Tene, Michael; Sestili, Heather H.; Foley, Kathleen; Saputra, Elysia; Clark, Nathan; Chikina, Maria; Meyer, Wynn K.; Pfenning, Andreas R.

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Unlocking gene regulation with sequence-to-function models

NATURE METHODS

IF32.1

2024-08-09

PREAI

Sasse, Alexander; Chikina, Maria; Mostafavi, Sara

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Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods

GENOME BIOLOGY

IF9.4

2024-07-01

OAAI

Hu, Mengying; Chikina, Maria

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Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures

CELL GENOMICS

IF9

2024-06-01

OAAI

Nair, Venugopalan D.; Pincas, Hanna; Smith, Gregory R.; Zaslavsky, Elena; Ge, Yongchao; Amper, Mary Anne S.; Vasoya, Mital; Chikina, Maria; Sun, Yifei; Raja, Archana Natarajan; Mao, Weiguang; Gay, Nicole R.; Esser, Karyn A.; Smith, Kevin S.; Zhao, Bingqing; Wiel, Laurens; Singh, Aditya; Lindholm, Malene E.; Amar, David; Montgomery, Stephen; Snyder, Michael P.; Walsh, Martin J.; Sealfon, Stuart C.

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Evolutionary rate covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

ELIFE

IF0

2024-02-28

OAAI

Little, Jordan; Chikina, Maria; Clark, Nathan L.

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Memory B cell subsets have divergent developmental origins that are coupled to distinct imprinted epigenetic states

NATURE IMMUNOLOGY

IF27.6

2024-01-10

PREAI

Callahan, Derrick; Smita, Shuchi; Joachim, Stephen; Hoehn, Kenneth; Kleinstein, Steven; Weisel, Florian; Chikina, Maria; Shlomchik, Mark

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Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings

NATURE GENETICS

IF31.8

2023-11-30

OAAI

Sasse, Alexander; Ng, Bernard; Spiro, Anna E.; Tasaki, Shinya; Bennett, David A.; Gaiteri, Christopher; De Jager, Philip L.; Chikina, Maria; Mostafavi, Sara

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T cell receptor (TCR) landscape of childhood brain tumors

CANCER RESEARCH

IF16.6

2023-04-04

PREAI

Raphael, Itay; Nisnboym, Michal; Raphael, Rebecca A.; Uttam, Shikhar; Pollack, Ian F.; Chikina, Maria; Rajasundaram, Dhivyaa; Kohanbash, Gary

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Homer1 Alternative Splicing Is Regulated by Gonadotropin-Releasing Hormone and Modulates Gonadotropin Gene Expression

MOLECULAR AND CELLULAR BIOLOGY

IF2.7

2023-03-20

OAAI

Wang, Qian; Chikina, Maria D.; Pincas, Hanna; Sealfon, Stuart C.

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Involvement of Histone Demethylase LSD1 in Short-Time-Scale Gene Expression Changes during Cell Cycle Progression in Embryonic Stem Cells

MOLECULAR AND CELLULAR BIOLOGY

IF2.7

2023-03-20

OAAI

Nair, Venugopalan D.; Ge, Yongchao; Balasubramaniyan, Natarajan; Kim, Jaeyun; Okawa, Yuya; Chikina, Maria; Troyanskaya, Olga; Sealfon, Stuart C.

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A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation

MOLECULAR SYSTEMS BIOLOGY

IF7.7

2023-03-15

OAAI

Mao, Weiguang; Miller, Clare M.; Nair, Venugopalan D.; Ge, Yongchao; Amper, Mary Anne S.; Cappuccio, Antonio; George, Mary-Catherine; Goforth, Carl W.; Guevara, Kristy; Marjanovic, Nada; Nudelman, German; Pincas, Hanna; Ramos, Irene; Sealfon, Rachel S. G.; Soares-Schanoski, Alessandra; Vangeti, Sindhu; Vasoya, Mital; Weir, Dawn L.; Zaslavsky, Elena; Biobank Team, Seunghee; Kim-Schulze, Seunghee; Gnjatic, Sacha; Merad, Miriam; Letizia, Andrew G.; Troyanskaya, Olga G.; Sealfon, Stuart C.; Chikina, Maria

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IL-21 R signal reprogramming cooperates with CD40 and BCR signals to select and differentiate germinal center B cells

SCIENCE IMMUNOLOGY

IF16.3

2023-02-03

PREAI

Luo, Wei; Conter, Laura; Elsner, Rebecca A.; Smita, Shuchi; Weisel, Florian; Callahan, Derrick; Wu, Shuxian; Chikina, Maria; Shlomchik, Mark

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Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature

CELL SYSTEMS

IF7.7

2022-12-01

OAAI

Cappuccio, Antonio; Chawla, Daniel G.; Chen, Xi; Rubenstein, Aliza B.; Cheng, Wan Sze; Mao, Weiguang; Burke, Thomas W.; Tsalik, Ephraim L.; Petzold, Elizabeth; Henao, Ricardo; McClain, Micah T.; Woods, Christopher W.; Chikina, Maria; Troyanskaya, Olga G.; Sealfon, Stuart C.; Kleinstein, Steven H.; Zaslavsky, Elena

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Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

ELIFE

IF0

2022-11-07

OAAI

Kowalczyk, Amanda; Chikina, Maria; Clark, Nathan

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Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection

CELL SYSTEMS

IF7.7

2022-11-01

OAAI

Sauerwald, Natalie; Zhang, Zijun; Ramos, Irene; Nair, Venugopalan D.; Soares-Schanoski, Alessandra; Ge, Yongchao; Mao, Weiguang; Alshammary, Hala; Gonzalez-Reiche, Ana S.; van de Guchte, Adriana; Goforth, Carl W.; Lizewski, Rhonda A.; Lizewski, Stephen E.; Amper, Mary Anne S.; Vasoya, Mital; Seenarine, Nitish; Guevara, Kristy; Marjanovic, Nada; Miller, Clare M.; Nudelman, German; Schilling, Megan A.; Sealfon, Rachel S. G.; Termini, Michael S.; Vangeti, Sindhu; Weir, Dawn L.; Zaslavsky, Elena; Chikina, Maria; Wu, Ying Nian; Bakel, Harm Van; Letizia, Andrew G.; Sealfon, Stuart C.; Troyanskaya, Olga G.

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Research Directions