Publications

You can find a selection and all our publications below. We are big fans of pre-prints, as they accelerate science and make it more accessible, and that is why you might find some of them twice.

Highlighted

Global Environmental Genomics Reveals Vast Uncultivated Protist Diversity and Taxonomic Blind Spots

Miguel F. Romero-Gutiérrez, Arianna I. Krinos, Xyrus Maurer-Alcala, John A. Burns, Ramunas Stepanauskas, Tanja Woyke, Frederik Schulz

openRxiv  ·  26 Mar 2025  ·  doi:10.1101/2025.03.26.645542

Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera

Auden E. Cote-L’Heureux, Elinor G. Sterner, Xyrus X. Maurer-Alcalá, Laura A. Katz

mBio  ·  09 Apr 2025  ·  doi:10.1128/MBIO.03916-24

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2025

Characterizing lineage-specific genes in testate lobose amoebae (Arcellinida)

Angela K. Jiang, Taylor R. Sehein, Rebecca Gawron, Laura A. Katz, Xyrus X. Maurer-Alcalá

Protist  ·  01 Sep 2025  ·  doi:10.1016/J.PROTIS.2025.126115

Genome content reorganization in the non-model ciliate Chilodonella uncinata : insights into nuclear architecture, DNA content, and chromosome fragmentation during macronuclear development

Ragib Ahsan, Xyrus X. Maurer-Alcalá, Laura A. Katz

mSphere  ·  25 Jun 2025  ·  doi:10.1128/MSPHERE.00075-25

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Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera

Auden E. Cote-L’Heureux, Elinor G. Sterner, Xyrus X. Maurer-Alcalá, Laura A. Katz

mBio  ·  09 Apr 2025  ·  doi:10.1128/MBIO.03916-24

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Global Environmental Genomics Reveals Vast Uncultivated Protist Diversity and Taxonomic Blind Spots

Miguel F. Romero-Gutiérrez, Arianna I. Krinos, Xyrus Maurer-Alcala, John A. Burns, Ramunas Stepanauskas, Tanja Woyke, Frederik Schulz

openRxiv  ·  26 Mar 2025  ·  doi:10.1101/2025.03.26.645542

2024

TIdeS: A Comprehensive Framework for Accurate Open Reading Frame Identification and Classification in Eukaryotic Transcriptomes

Xyrus X Maurer-Alcalá, Eunsoo Kim

Genome Biology and Evolution  ·  21 Nov 2024  ·  doi:10.1093/GBE/EVAE252

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Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict

Elinor G Sterner, Auden Cote-L’Heureux, Xyrus X Maurer-Alcalá, Laura A Katz

Genome Biology and Evolution  ·  01 Nov 2024  ·  doi:10.1093/GBE/EVAE239

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Foraminifera as a model of eukaryotic genome dynamism

Caitlin Timmons, Kristine Le, H. B. Rappaport, Elinor G. Sterner, Xyrus X. Maurer-Alcalá, Susan T. Goldstein, Laura A. Katz

mBio  ·  13 Mar 2024  ·  doi:10.1128/MBIO.03379-23

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Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates

Xyrus X. Maurer-Alcalá, Auden Cote-L’Heureux, Sergei L. Kosakovsky Pond, Laura A. Katz

PLOS ONE  ·  25 Jan 2024  ·  doi:10.1371/JOURNAL.PONE.0291688

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2023

Long-Read–Based Genome Assembly Reveals Numerous Endogenous Viral Elements in the Green Algal Bacterivore Cymbomonas tetramitiformis

Yangtsho Gyaltshen, Andrey Rozenberg, Amber Paasch, John A Burns, Sally Warring, Raegan T Larson, Xyrus X Maurer-Alcalá, Joel Dacks, Apurva Narechania, Eunsoo Kim

Genome Biology and Evolution  ·  26 Oct 2023  ·  doi:10.1093/GBE/EVAD194

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2022

Chromatin remodeling is required for sRNA‐guided DNA elimination in Paramecium

Aditi Singh, Xyrus X Maurer‐Alcalá, Therese Solberg, Lilia Häußermann, Silvan Gisler, Michael Ignarski, Estienne C Swart, Mariusz Nowacki

The EMBO Journal  ·  11 Oct 2022  ·  doi:10.15252/EMBJ.2022111839

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Taxon-rich transcriptomics supports higher-level phylogeny and major evolutionary trends in Foraminifera

Roberto Sierra, Florian Mauffrey, Joana Cruz, Maria Holzmann, Andrew J. Gooday, …, Rabindra Thakur, Mattia Greco, Agnes K.M. Weiner, Laura A. Katz, Jan Pawlowski

Molecular Phylogenetics and Evolution  ·  01 Sep 2022  ·  doi:10.1016/J.YMPEV.2022.107546

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A small RNA-guided PRC2 complex eliminates DNA as an extreme form of transposon silencing

Chundi Wang, Therese Solberg, Xyrus X. Maurer-Alcalá‬, Estienne C. Swart, Feng Gao, Mariusz Nowacki

Cell Reports  ·  01 Aug 2022  ·  doi:10.1016/J.CELREP.2022.111263

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Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events

Auden Cote-L’Heureux, Xyrus X. Maurer-Alcalá, Laura A. Katz

PLOS Genetics  ·  22 Jun 2022  ·  doi:10.1371/JOURNAL.PGEN.1010239

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Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements

Sebastian T. Bechara, Lyna E.S. Kabbani, Xyrus X. Maurer-Alcalá, Mariusz Nowacki

RNA  ·  09 Jun 2022  ·  doi:10.1261/RNA.079134.122

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Deciphering phylogenetic relationships in class Karyorelictea (Protista, Ciliophora) based on updated multi-gene information with establishment of a new order Wilbertomorphida n. ord.

Mingzhen Ma, Yuqing Li, Xyrus X. Maurer-Alcalá, Yurui Wang, Ying Yan

Molecular Phylogenetics and Evolution  ·  01 Apr 2022  ·  doi:10.1016/J.YMPEV.2022.107406

How Ciliated Protists Survive by Cysts: Some Key Points During Encystment and Excystment

Yuqing Li, Yurui Wang, Shijing Zhang, Xyrus X. Maurer-Alcalá, Ying Yan

Frontiers in Microbiology  ·  17 Feb 2022  ·  doi:10.3389/FMICB.2022.785502

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2020

Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion

Susan A Smith, Xyrus X Maurer-Alcalá, Ying Yan, Laura A Katz, Luciana F Santoferrara, George B McManus

Genome Biology and Evolution  ·  01 Sep 2020  ·  doi:10.1093/GBE/EVAA185

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Programmed genome rearrangements in ciliates

Iwona Rzeszutek, Xyrus X. Maurer-Alcalá, Mariusz Nowacki

Cellular and Molecular Life Sciences  ·  27 May 2020  ·  doi:10.1007/S00018-020-03555-2

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De novo Sequencing, Assembly, and Annotation of the Transcriptome for the Free‐Living Testate Amoeba Arcella intermedia

Giulia M. Ribeiro, Alfredo L. Porfírio‐Sousa, Xyrus X. Maurer‐Alcalá, Laura A. Katz, Daniel J.G. Lahr

Journal of Eukaryotic Microbiology  ·  12 Feb 2020  ·  doi:10.1111/JEU.12788

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2019

Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates

Ying Yan, Xyrus X. Maurer-Alcalá, Rob Knight, Sergei L. Kosakovsky Pond, Laura A. Katz

mBio  ·  24 Dec 2019  ·  doi:10.1128/MBIO.02524-19

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Evolutionary origins and impacts of genome architecture in ciliates

Xyrus X. Maurer‐Alcalá, Mariusz Nowacki

Annals of the New York Academy of Sciences  ·  10 May 2019  ·  doi:10.1111/NYAS.14108

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PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes

Mario A Cerón-Romero, Xyrus X Maurer-Alcalá, Jean-David Grattepanche, Ying Yan, Miguel M Fonseca, L A Katz

Molecular Biology and Evolution  ·  07 May 2019  ·  doi:10.1093/MOLBEV/MSZ103

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2018

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘Omics

Xyrus X Maurer-Alcalá, Ying Yan, Olivia A Pilling, Rob Knight, Laura A Katz

Genome Biology and Evolution  ·  26 Jun 2018  ·  doi:10.1093/GBE/EVY133

Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics)

Xyrus X. Maurer-Alcalá, Rob Knight, Laura A. Katz

mBio  ·  07 Mar 2018  ·  doi:10.1128/MBIO.01836-17

2017

Nuclear Features of the Heterotrich Ciliate Blepharisma americanum: Genomic Amplification, Life Cycle, and Nuclear Inclusion

Megan M. Wancura, Ying Yan, Laura A. Katz, Xyrus X. Maurer‐Alcalá

Journal of Eukaryotic Microbiology  ·  07 Jun 2017  ·  doi:10.1111/JEU.12422

2016

Phylogenomics of ‘Discosea’: A new molecular phylogenetic perspective on Amoebozoa with flat body forms

Yonas I. Tekle, O. Roger Anderson, Laura A. Katz, Xyrus X. Maurer-Alcalá, Mario Alberto Cerón Romero, Robert Molestina

Molecular Phylogenetics and Evolution  ·  01 Jun 2016  ·  doi:10.1016/J.YMPEV.2016.03.029

Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the CiliateChilodonella uncinata

Xyrus X. Maurer-Alcalá, Laura A. Katz

Genome Biology and Evolution  ·  29 Apr 2016  ·  doi:10.1093/GBE/EVW099

2015

An epigenetic toolkit allows for diverse genome architectures in eukaryotes

Xyrus X Maurer-Alcalá, Laura A Katz

Current Opinion in Genetics & Development  ·  01 Dec 2015  ·  doi:10.1016/J.GDE.2015.10.005

2014

Characterization of the Life Cycle and Heteromeric Nature of the Macronucleus of the Ciliate Chilodonella uncinata Using Fluorescence Microscopy

Laure Bellec, Xyrus X. Maurer‐Alcala, Laura A. Katz

Journal of Eukaryotic Microbiology  ·  29 Apr 2014  ·  doi:10.1111/JEU.12109