Author

A. Kowalczyk

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 7 Cell Biology· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 7 Organism:mouse· 5 Research Focus:cell type annotation· 4 Organism:human· 4 Research Focus:chromatin & epigenetic regulation· 3 Assay:whole-genome sequencing· 3 Research Focus:differential expression· 2 Approach:experimental assay· 2

Frequent Co-Authors

M. Chikina· 7 shared N. Clark· 4 shared N. L. Clark· 3 shared R. Partha· 3 shared A. Ashkenazy-Titelman· 1 shared A. Bendelac· 1 shared A. Bow· 1 shared A. Morgun· 1 shared

Activity by Year

2018-2024 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 11 mutual co-author links

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7 shared papersEvolutionary Biology

M. Chikina

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Author profile →

9 papers

Recent·Most cited

DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS

E. M. Appleton, K. Hong, C. Rodriguez-Caycedo, Y. Tanaka, A. Ashkenazy-Titelman, K. Bhide, C. Rasmussen-Ivey, X. Ambriz-Pena, N. Korover, H. Bai, A. Quieroz, J. Nelson, G. Rathod, G. Knox, M. Morgan, , E. Hysolli

This paper reports the first derivation of elephant induced pluripotent stem cells (emiPSCs) using a modified reprogramming protocol that inhibits TP53 expansion genes.

bioRxiv · Mar 5, 2024Cell Biology

GATA4 regionalizes intestinal metabolism and barrier function to prevent immunopathology

Z. M. Earley, W. Lisicka, J. J. Sifakis, R. A. Gamboa, A. Kowalczyk, J. Barlow, D. G. Shaw, V. Discepolo, I. L. Tan, S. Gona, J. Ernest, P. Matzinger, L. B. Barreiro, A. Morgun, A. Bendelac, , B. Jabri

Epithelial GATA4 regulates intestinal regionalization of bacterial colonization, metabolic pathways, and tissue immunity.

bioRxiv · Oct 28, 2021 · PreprintImmunology

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

A. Kowalczyk, M. Chikina, N. L. Clark

The paper warns against misinterpreting branch-site models in comparative genomics, showing how failing to distinguish phylogeny-wide from branch-specific positive selection leads to false inferences and proposes a 'drop-out' test to address this issue.

bioRxiv · Oct 26, 2021 · PreprintEvolutionary Biology

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

A. Kowalczyk, O. Gbadamosi, K. Kolor, J. Sosa, C. St Croix, G. Gibson, M. Chikina, E. Aizenman, N. Clark, K. Kiselyov

The paper uses evolutionary rate covariation to predict the mitochondrial localization of SLC30A9, which is confirmed experimentally as a zinc exporter.

bioRxiv · Apr 22, 2021Evolutionary Biology

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

A. Kowalczyk, M. Chikina, N. Clark

The paper identifies coding and noncoding sequences that evolve differently in hairless mammals, revealing distinct evolutionary patterns between protein-coding genes and regulatory elements.

bioRxiv · Mar 11, 2021Evolutionary Biology

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

E. Saputra, A. Kowalczyk, L. Cusick, N. Clark, M. Chikina

This paper introduces phylogenetic permulations to calculate accurate p-values for phylogenetic analyses, improving statistical confidence in phenotype-genetic element associations.

bioRxiv · Oct 14, 2020Evolutionary Biology

Cancer control is a key functionality underlying evolution of extended lifespan in mammals

A. Kowalczyk, R. Partha, N. Clark, M. Chikina

The paper uses comparative genomics to link evolutionary constraint on cancer-related pathways with extended lifespan in mammals, supporting the role of cancer control in longevity.

bioRxiv · Apr 23, 2019 · PreprintEvolutionary Biology

Robust methods for detecting convergent shifts in evolutionary rates

R. Partha, A. Kowalczyk, N. L. Clark, M. Chikina

The paper improves a method for detecting convergent evolutionary rate shifts by addressing statistical limitations through data transformation and weighted regression.

bioRxiv · Oct 30, 2018Evolutionary Biology

RERconverge: an R package for associating evolutionary rates with convergent traits

A. Kowalczyk, W. K. Meyer, R. Partha, W. Mao, N. L. Clark, M. Chikina

RERconverge associates evolutionary rates with convergent traits across phylogenies, supporting binary and continuous traits with visualization and enrichment tools.

bioRxiv · Oct 23, 2018Evolutionary Biology