Maria Chikina

Also affiliated with Computational Diagnostics (United States)

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

2in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 2 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Widespread redundancy in -omics profiles of cancer mutation states

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.6638832

Top 100%

0DataRank

Top 100%0 citations

Brock C. Christensen, Maria Chikina, Casey S. Greene, J. P. Wickersham Crawford

Papers

Driven by 54 papers — median percentile 0. Top paper: “Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness”.

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

eLife(2022)10.7554/elife.76911

N/A

0.959DataRank · unranked

41 citations

Maria Chikina, Nathan L Clark, Amanda Kowalczyk

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

Cell Genomics(2024)10.1016/j.xgen.2023.100421

N/A

0.928DataRank · unranked

38 citations

Hanna Pinças, Gregory R. Smith, Elena Zaslavsky, Yongchao Ge, Mary Anne S. Amper +75 more

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

Genome biology(2024)10.1186/s13059-024-03292-w

N/A

0.703DataRank · unranked

26 citations

Maria Chikina, Mengying Hu

A single intranasal dose of human parainfluenza virus type 3-vectored vaccine induces effective antibody and memory T cell response in the lungs and protects hamsters against SARS-CoV-2

npj Vaccines(2022)10.1038/s41541-022-00471-3

N/A

0.651DataRank · unranked

13 citations

Sivakumar Periasamy, Kai Huang, Natalia A. Kuzmina, Palaniappan Ramanathan, Michelle Meyer +10 more

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

Molecular Systems Biology(2023)10.15252/msb.202211361

N/A

0.613DataRank · unranked

21 citations

Clare Miller, Venugopalan D. Nair, Yongchao Ge, Mary Anne S. Amper, Antonio Cappuccio +27 more

Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements

Science(2024)10.1126/science.abn3263

N/A

0.542DataRank · unranked

36 citations

Tobias A. Schmid, Julie E. Elie, Xiaomeng Zhang, Amanda Kowalczyk, Ruby Redlich +89 more

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

eLife(2024)10.7554/elife.93333.3

N/A

0.523DataRank · unranked

14 citations

Maria Chikina, Nathan L Clark, Jordan Little

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

Cell Systems(2022)10.1016/j.cels.2022.10.005

N/A

0.464DataRank · unranked

21 citations

Zijun Zhang, Irene Ramos, Venugopalan D. Nair, Alessandra Soares‐Schanoski, Yongchao Ge +27 more

Temporal dynamics of the multi-omic response to endurance exercise training across tissues

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.21.508770

N/A

0.457DataRank · unranked

20 citations

David Amar, Nicole R. Gay, Pierre M. Jean Beltran, Joshua Adkins, José Juan Almagro Armenteros +95 more

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

Molecular Biology and Evolution(2024)10.1093/molbev/msae210

N/A

0.454DataRank · unranked

11 citations

Amanda Kowalczyk, Michael Tene, Heather H. Sestili, Kathleen Foley, Elysia C. Saputra +5 more

The T cell receptor landscape of childhood brain tumors

Science Translational Medicine(2025)10.1126/scitranslmed.adp0675

N/A

0.447DataRank · unranked

7 citations

Zujian Xiong, Chaim T. Sneiderman, Rebecca A. Raphael, Moshe Mash, Lance Schwegman +28 more

A Quantitative Systems Pharmacology Platform Reveals NAFLD Pathophysiological States and Targeting Strategies

Metabolites(2022)10.3390/metabo12060528

N/A

0.402DataRank · unranked

11 citations

Mark T. Miedel, Fen Pei, Johanna K. DiStefano, Richard DeBiasio, Tong Ying Shun +13 more

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.13.620707

N/A

0.366DataRank · unranked

9 citations

Nathan L Clark, Timothy B. Sackton, Spencer V. Muse, Alexander G. Lucaci, Steven Weaver +4 more

Context-dependent Interactors Regulate TDP-43 Dysfunction in ALS/FTLD

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.07.646890

N/A

0.357DataRank · unranked

8 citations

Yuehua Zhu, Bryan Hurtle, Matthew Wright, John Robinson, Jocelyn C. Mauna +14 more

Widespread redundancy in -omics profiles of cancer mutation states

Genome Biology(2022)10.1186/s13059-022-02705-y

N/A

0.345DataRank · unranked

9 citations

Brock C. Christensen, Maria Chikina, Casey S. Greene, Jake Crawford

Widespread redundancy in -omics profiles of cancer mutation states

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.27.466140

N/A

0.241DataRank · unranked

4 citations

Brock C. Christensen, Maria Chikina, Casey S. Greene, Jake Crawford

Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction

Bioinformatics Advances(2024)10.1093/bioadv/vbae004

N/A

0.208DataRank · unranked

3 citations

Maria Chikina, Casey S. Greene, Jake Crawford

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.11.434984

N/A

0.208DataRank · unranked

3 citations

Maria Chikina, Nathan L Clark, Amanda Kowalczyk

Coevolution due to physical interactions is not a major driving force behind evolutionary rate covariation

(2023)10.7554/elife.93333.1

N/A

0.198DataRank · unranked

2 citations

Maria Chikina, Nathan L Clark, Jordan Little

MousiPLIER: A Mouse Pathway-Level Information Extractor Model

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.31.551386

N/A

0.165DataRank · unranked

2 citations

Benjamin J. Heil, Weiguang Mao, Maria Chikina, Casey S. Greene, Elizabeth A. Heller +1 more

A Pathway-Level Information ExtractoR (PLIER) framework to gain mechanistic insights into obesity in Down syndrome

Biocomputing 2025(2024)10.1142/9789819807024_0030

N/A

0.104DataRank · unranked

1 citations

Yuehua Zhu, Lucas A. Gillenwater, Marc Subirana-Granés, Haoyu Zhang, Negar Janani +5 more

Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.26.546586

N/A

0.104DataRank · unranked

1 citations

Maria Chikina, Casey S. Greene, Jake Crawford

MousiPLIER: A Mouse Pathway-Level Information Extractor Model

eneuro(2024)10.1523/eneuro.0313-23.2024

N/A

0.104DataRank · unranked

1 citations

Benjamin J. Heil, Weiguang Mao, Maria Chikina, Casey S. Greene, Elizabeth A. Heller +1 more

Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data

Bioinformatics(2022)10.1093/bioinformatics/btac136

N/A

0DataRank · unranked

3 citations

Maziyar Baran Pouyan, Dennis Kostka, Maria Chikina, Weiguang Mao

Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.22.440839

N/A

0DataRank · unranked

6 citations

Omotola Gbadamosi, Kathryn Kolor, Jahree Sosa, Claudette M. St. Croix, Gregory A. Gibson +5 more

Prediction of local convergent shifts in evolutionary rates with phyloConverge characterizes the phenotypic associations and modularity of regulatory elements

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.02.490345

N/A

0DataRank · unranked

1 citations

Weiguang Mao, Nathan L Clark, Maria Chikina, Elysia C. Saputra

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

Science Immunology(2023)10.1126/sciimmunol.add1823

N/A

0DataRank · unranked

80 citations

Laura Conter, Rebecca A. Elsner, Shuchi Smita, Florian Weisel, Derrick Callahan +4 more

A cautionary tale on proper use of branch-site models to detect convergent positive selection

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.26.465984

N/A

0DataRank · unranked

13 citations

Maria Chikina, Nathan L Clark, Amanda Kowalczyk

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

eLife(2023)10.7554/elife.93333

N/A

0DataRank · unranked

14 citations

Maria Chikina, Nathan L Clark, Jordan Little

An intrinsically interpretable neural network architecture for sequence-to-function learning

Bioinformatics(2023)10.1093/bioinformatics/btad271

N/A

0DataRank · unranked

6 citations

Mark Maher Ebeid, Panayiotis V. Benos, Dennis Kostka, Maria Chikina, Ali Tuğrul Balcı

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.16.532969

N/A

0DataRank · unranked

29 citations

Bernard Ng, Anna Spiro, Shinya Tasaki, David A. Bennett, Chris Gaiteri +4 more

Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.18.562970

N/A

0DataRank · unranked

3 citations

Maria Chikina, Nathan L Clark, Jordan Little

Phylogenetic Permulations: A Statistically Rigorous Approach to Measure Confidence in Associations in a Phylogenetic Context

Molecular Biology and Evolution(2021)10.1093/molbev/msab068

N/A

0DataRank · unranked

37 citations

Amanda Kowalczyk, Luisa Cusick, Nathan L Clark, Maria Chikina, Elysia C. Saputra

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.06.570425

N/A

0DataRank · unranked

2 citations

Amanda Kowalczyk, Michael Tene, Heather H. Sestili, Kathleen Foley, Elysia C. Saputra +5 more

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

Nature Immunology(2024)10.1038/s41590-023-01721-9

N/A

0DataRank · unranked

44 citations

Shuchi Smita, Stephen Joachim, Kenneth B. Hoehn, Steven H. Kleinstein, Florian Weisel +3 more

Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter

Biochemical Journal(2021)10.1042/bcj20210342

N/A

0DataRank · unranked

38 citations

Omotola Gbadamosi, Kathryn Kolor, Jahree Sosa, Livia Andrzejczuk, Gregory A. Gibson +6 more

Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.14.338608

N/A

0DataRank · unranked

3 citations

Amanda Kowalczyk, Luisa Cusick, Nathan L Clark, Maria Chikina, Elysia C. Saputra

DataRemix: a universal data transformation for optimal inference from gene expression datasets

Bioinformatics(2020)10.1093/bioinformatics/btaa745

N/A

0DataRank · unranked

5 citations

Javad Rahimikollu, Ryan Hausler, Maria Chikina, Weiguang Mao

The impact of exercise on gene regulation in association with complex trait genetics

Nature Communications(2024)10.1038/s41467-024-45966-w

N/A

0DataRank · unranked

24 citations

Nicole R. Gay, MoTrPAC Study Group, Joshua N. Adkins, Brent G. Albertson, David Amar +95 more

InstaPrism: an R package for fast implementation of BayesPrism

Bioinformatics(2024)10.1093/bioinformatics/btae440

N/A

0DataRank · unranked

23 citations

Maria Chikina, Mengying Hu

Modeling strict age-targeted mitigation strategies for COVID-19

PLoS ONE(2020)10.1371/journal.pone.0236237

N/A

0DataRank · unranked

50 citations

Wesley Pegden, Maria Chikina

Pan-mammalian analysis of molecular constraints underlying extended lifespan

eLife(2020)10.7554/elife.51089

N/A

0DataRank · unranked

102 citations

Raghavendran Partha, Nathan L Clark, Maria Chikina, Amanda Kowalczyk

A hybrid constrained continuous optimization approach for optimal causal discovery from biological data

Bioinformatics(2024)10.1093/bioinformatics/btae411

N/A

0DataRank · unranked

7 citations

Panayiotis V. Benos, Maria Chikina, Yuehua Zhu

A unified hypothesis-free feature extraction framework for diverse epigenomic data

Bioinformatics Advances(2024)10.1093/bioadv/vbaf013

N/A

0DataRank · unranked

2 citations

Maria Chikina, Ali Tuğrul Balcı

Best holdout assessment is sufficient for cancer transcriptomic model selection

Patterns(2024)10.1016/j.patter.2024.101115

N/A

0DataRank · unranked

1 citations

Maria Chikina, Casey S. Greene, Jake Crawford

Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis

Nature Immunology(2020)10.1038/s41590-020-0598-4

N/A

0DataRank · unranked

272 citations

Steven J. Mullett, Rebecca A. Elsner, Ashley V. Menk, Nikita Trivedi, Wei Luo +12 more

Author Response: Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

(2024)10.7554/elife.93333.2.sa3

N/A

0DataRank · unranked

0 citations

Maria Chikina, Nathan L Clark, Jordan Little

Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

eLife(2024)10.7554/elife.93333.2

N/A

0DataRank · unranked

0 citations

Maria Chikina, Nathan L Clark, Jordan Little

Widespread redundancy in -omics profiles of cancer mutation states

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.6638832

Top 100%

0DataRank

Top 100%0 citations

Brock C. Christensen, Maria Chikina, Casey S. Greene, J. P. Wickersham Crawford

ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies

Genome Research(2025)10.1101/gr.280586.125

N/A

0DataRank · unranked

2 citations

G. Meyer, Aakash Grover, Alex Michael Francette, Raghavendran Partha, Karen M. Arndt +4 more

Additional file 2 of Widespread redundancy in -omics profiles of cancer mutation states

Open MIND(2022)10.6084/m9.figshare.20167988

Top 100%

0DataRank

Top 100%0 citations

Brock C. Christensen, Maria Chikina, Casey S. Greene, Jake Crawford

CLAMP: Curated Latent-variable Analysis with Molecular Priors

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.05.658122

N/A

0DataRank · unranked

1 citations

S. Nandi, Haoyu Zhang, Maria Chikina, Milton Pividori, Marc Subirana-Granés

Prediction of local convergent shifts in evolutionary rates with phyloConverge

Bioinformatics(2025)10.1093/bioinformatics/btaf366

N/A

0DataRank · unranked

0 citations

Weiguang Mao, Guillermo Hoffmann Meyer, Nathan L Clark, Maria Chikina, Elysia C. Saputra

MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution

Evolution(2025)10.1093/evolut/qpaf240

N/A

0DataRank · unranked

0 citations

Nathan L Clark, Anton Nekrutenko, Maria Chikina, Sergei L. Kosakovsky Pond, Avery Selberg

Maria Chikina

Indexed papers

Top data-sharing exemplar

Papers