Author details

Full Name

Maria Chikina

Affiliation

University of Pittsburgh

ORCID

Career Start Year

2005

Papers

H Index

Expertise

CM4AI Collaborator

Nathan Sheffield (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36800413	IL-21R signal reprogramming cooperates with CD40 and BCR signals to select and differentiate germinal center B cells.	Sci Immunol	2023
37577575	MousiPLIER: A Mouse Pathway-Level Information Extractor Model.	bioRxiv	2023
38036778	Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings.	Nat Genet	2023
36993652	Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings.	bioRxiv	2023
37387140	An intrinsically interpretable neural network architecture for sequence-to-function learning.	Bioinformatics	2023
36919946	A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation.	Mol Syst Biol	2023
36747873	An intrinsically interpretable neural network architecture for sequence to function learning.	bioRxiv	2023
35271505	Heterogeneity and clonality of kidney-infiltrating T cells in murine lupus nephritis.	JCI Insight	2022
35736460	A Quantitative Systems Pharmacology Platform Reveals NAFLD Pathophysiological States and Targeting Strategies.	Metabolites	2022
35468973	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
35761387	Widespread redundancy in -omics profiles of cancer mutation states.	Genome Biol	2022
35561207	Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data.	Bioinformatics	2022
36549275	Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature.	Cell Syst	2022
36109816	Re-analysis on the statistical sampling biases of a mask promotion trial in Bangladesh: a statistical replication.	Trials	2022
36342464	Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness.	Elife	2022
36323307	Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection.	Cell Syst	2022
35942160	Earlier detection of SARS-CoV-2 infection by blood RNA signature microfluidics assay.	Clin Transl Discov	2022
35189135	Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold.	J Theor Biol	2022
34937918	Surface phenotypes of naive and memory B cells in mouse and human tissues.	Nat Immunol	2022
34177926	Antibody Responses to SARS-CoV-2 Following an Outbreak Among Marine Recruits With Asymptomatic or Mild Infection.	Front Immunol	2021
33739420	Phylogenetic Permulations: A Statistically Rigorous Approach to Measure Confidence in Associations in a Phylogenetic Context.	Mol Biol Evol	2021
32706809	Modeling strict age-targeted mitigation strategies for COVID-19.	PLoS One	2020
31873725	Causal network perturbations for instance-specific analysis of single cell and disease samples.	Bioinformatics	2020
32043462	Pan-mammalian analysis of molecular constraints underlying extended lifespan.	Elife	2020
32066950	Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis.	Nat Immunol	2020
31077321	Robust Method for Detecting Convergent Shifts in Evolutionary Rates.	Mol Biol Evol	2019
31732168	Liver Is a Generative Site for the B Cell Response to Ehrlichia muris.	Immunity	2019
31350177	Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8<sup>+</sup> T Cell-Derived Interferon-Î³.	Immunity	2019
31192356	RERconverge: an R package for associating evolutionary rates with convergent traits.	Bioinformatics	2019
31249421	Pathway-level information extractor (PLIER) for gene expression data.	Nat Methods	2019
30763317	Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila.	PLoS Genet	2019
30936494	Adaptive plasticity of IL-10<sup>+</sup> and IL-35<sup>+</sup> T<sub>reg</sub> cells cooperatively promotes tumor T cell exhaustion.	Nat Immunol	2019
29873782	Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.	Nucleic Acids Res	2018
29920228	Hepatocyte-Derived Lipocalin 2 Is a Potential Serum Biomarker Reflecting Tumor Burden in Hepatoblastoma.	Am J Pathol	2018
30130253	Kidney-infiltrating T cells in murine lupus nephritis are metabolically and functionally exhausted.	J Clin Invest	2018
30093596	Ancient convergent losses of <i>Paraoxonase 1</i> yield potential risks for modern marine mammals.	Science	2018
28604385	Differential requirements for myeloid leukemia IFN-Î³ conditioning determine graft-versus-leukemia resistance and sensitivity.	J Clin Invest	2017
28246331	Assessing significance in a Markov chain without mixing.	Proc Natl Acad Sci U S A	2017
29035697	Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling.	Elife	2017
28783703	LAG3 limits regulatory T cell proliferation and function in autoimmune diabetes.	Sci Immunol	2017
28552348	Interferon-Î³ Drives T<sub>reg</sub> Fragility to Promote Anti-tumor Immunity.	Cell	2017
26795247	A Temporal Switch in the Germinal Center Determines Differential Output of Memory B and Plasma Cells.	Immunity	2016
26447924	A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.	Cytometry A	2016
27533619	Wnt signaling regulates hepatobiliary repair following cholestatic liver injury in mice.	Hepatology	2016
27329977	Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.	Mol Biol Evol	2016
27466366	Characterization of Gonadotrope Secretoproteome Identifies Neurosecretory Protein VGF-derived Peptide Suppression of Follicle-stimulating Hormone Gene Expression.	J Biol Chem	2016
27097116	Modeling a human hepatocellular carcinoma subset in mice through coexpression of met and point-mutant Î²-catenin.	Hepatology	2016
25266226	Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation.	Bioinformatics	2015
26223639	Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses.	J Virol	2015
25786808	Low-variance RNAs identify Parkinson's disease molecular signature in blood.	Mov Disord	2015

1 - 50 of 61

Peter F Hickey

The Walter and Eliza Hall Institute of Medical Research

Career Start Year 2010

Number of shared co-authors 1

Kathleen M Fisch

Center for Computational Biology and Bioinformatics, University of California

Career Start Year 2009

Number of shared co-authors 3

Oliver Stegle

Wellcome Sanger Institute

Career Start Year 2008

Number of shared co-authors 6

Yuanfang Guan

University of Michigan ann arbor

Career Start Year 2007

Number of shared co-authors 5

Simon Anders

Heidelberg University

Career Start Year 2006

Number of shared co-authors 2

Joshua W K Ho

The University of Hong Kong

Career Start Year 2006

Number of shared co-authors 1

David L Corcoran

The University of North Carolina at Chapel Hill

Career Start Year 2005

Number of shared co-authors 3

Jessica C Mar

Australian Institute for Bioengineering and Nanotechnology, University of Queensland

Career Start Year 2005

Number of shared co-authors 1

Stephen A Ramsey

Oregon State University

Career Start Year 2004

Number of shared co-authors 0

Shyam Prabhakar

Genome Institute of Singapore (GIS)

Career Start Year 2004

Number of shared co-authors 1

Zhandong Liu

Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital

Career Start Year 2003

Number of shared co-authors 3

Gerald Quon

University of California davis

Career Start Year 2003

Number of shared co-authors 2

Terence P Speed

Walter and Eliza Hall Institute of Medical Research

Career Start Year 2003

Number of shared co-authors 0

Manolis Kellis

Massachusetts Institute of Technology

Career Start Year 2003

Number of shared co-authors 5

Olivier Elemento

Meyer Cancer Center

Career Start Year 2002

Number of shared co-authors 2

Sven Bergmann

University of Lausanne

Career Start Year 2002

Number of shared co-authors 3

Eran Segal

Weizmann Institute of Science

Career Start Year 2001

Number of shared co-authors 2

Jean Yee Hwa Yang

The University of Sydney

Career Start Year 2001

Number of shared co-authors 0

Mikhail G Dozmorov

Virginia Commonwealth University

Career Start Year 2001

Number of shared co-authors 2

Christina Kendziorski

University of Wisconsin-Madison

Career Start Year 1999

Number of shared co-authors 0

Eric E Schadt

Icahn School of Medicine at Mount Sinai

Career Start Year 1998

Number of shared co-authors 10

Mark D Robinson

University of Zurich

Career Start Year 1997

Number of shared co-authors 2

Shannon K McWeeney

Oregon Health & Science University, University of California Berkeley

Career Start Year 1997

Number of shared co-authors 5

Wolfgang Huber

Technische Universitat Munchen

Career Start Year 1995

Number of shared co-authors 2

Gordon K Smyth

The University of Melbourne

Career Start Year 1992

Number of shared co-authors 1

Fabian J Theis

Technical University of Munich

Career Start Year 1992

Number of shared co-authors 4

Wing Hung Wong

Stanford University

Career Start Year 1991

Number of shared co-authors 2

Aviv Regev

Broad Institute of MIT and Harvard

Career Start Year 1987

Number of shared co-authors 7

Nir Yosef

Center for Computational Biology, University of California berkeley

Career Start Year 1986

Number of shared co-authors 2

Yuval Kluger

Yale University School of Medicine

Career Start Year 1984

Number of shared co-authors 0

row(s) 1 - 30 of 30

Stuart C Sealfon

Icahn School of Medicine at Mount Sinai

Co-authored papers 16

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Co-authored papers 9

Elena Zaslavsky

Icahn School of Medicine at Mount Sinai

Co-authored papers 7

Amanda Kowalczyk

Co-authored papers 6

Panayiotis V Benos

University of Florida

Co-authored papers 3

Chris Gaiteri

SUNY Upstate Medical University

Co-authored papers 2

William Horne

Co-authored papers 2

Wynn K Meyer

Co-authored papers 2

Boris M Hartmann

Institute of Veterinary Disease Control

Co-authored papers 2

Curtis Huttenhower

Broad Institute of MIT and Harvard

Co-authored papers 2

Philip L De Jager

Columbia University Medical Center

Co-authored papers 2

Casey S Greene

Dartmouth College Geisel School of Medicine, Princeton University, University of Colorado Anschutz Medical Campus, University of Pennsylvania Perelman School of Medicine

Co-authored papers 2

David A Bennett

Rush University Medical Center

Co-authored papers 2

Garry P Nolan

Stanford University School of Medicine

Co-authored papers 1

Yu Qian

J. Craig Venter Institute

Co-authored papers 1

Cindy Sander

UPMC Hillman Cancer Center