Publications

This list is compiled from my ORCID record, Google Scholar profile, and Europe PMC. For posters, slides, training datasets and other outputs that aren’t indexed as formal publications, see my Other Research Outputs page. Last updated July 2026.

2026

Hunt SE, Lemos D, Pericherla SR, Austine-Orimoloye O, Cibrian Uhalte E, Yates TM, Ansari M, Thompson L, Foreman J, Simpson TI, Ware JS, Wright CF, Freeberg MA, Firth HV. Gene2Phenotype: A Database of Structured Human Monogenic Diseases and Pathomechanisms. J Mol Biol. 2026;438:169768. doi: 10.1016/j.jmb.2026.169768
Yates AD, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, et al., Freeberg MA, Martin FJ, Finn RD. Ensembl 2026. Nucleic Acids Res. 2026;54(D1):D1053-D1060. doi: 10.1093/nar/gkaf1239
Thakur M, Bosc N, Brooksbank C, Ernst C, Freeberg MA, Gurwitz KT, Hermjakob H, Hulcoop DG, Martin MJ, McDonagh EM, Mithani A, O’Boyle NM, Ochoa D, Payne T, Perez-Riverol Y, Sarkans U, Sokolov A, Staudt N, Stephenson JD, Tzampatzopoulou E, Vizcaíno JA, Zdrazil B, McEntyre J. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2025. Nucleic Acids Res. 2026;54(D1):D10-D19. doi: 10.1093/nar/gkaf1078

2025

Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K, and the Human Pangenome Reference Consortium. Highly accurate assembly polishing with DeepPolisher. Genome Res. 2025;35(7):1595-1608. doi: 10.1101/gr.280149.124
D’Altri T, Freeberg MA, Curwin AJ, Alonso A, Freitas AT, Capella-Gutierrez S, Gadelha L, Hagwall A, Hovig E, Kerry G, Kirli K, Kochel K, Kohlbacher O, Korbel JO, Leinonen J, Marciniak B, Oliveira JS, Petersen K, Silva MJ, Stegle O, Valencia A, Viklund J, Guigo R, Parkinson H, Navarro A, Rambla J, Keane TM. The Federated European Genome-Phenome Archive as a global network for sharing human genomics data. Nat Genet. 2025;57(3):481-485. doi: 10.1038/s41588-025-02101-9 (preprint: MetaArXiv, Dec 2024)
Laurie S, Steyaert W, de Boer E, Polavarapu K, Schuermans N, et al., Fernandez-Callejo M, Freeberg M, Garcia-Pelaez J, et al., Solve-RD consortium, Brookes AJ, Evangelista T, Gilissen C, Graessner H, Hoogerbrugge N, Ossowski S, Riess O, Schüle R, Synofzik M, Verloes A, Matalonga L, Brunner HG, Lohmann K, de Voer RM, Töpf A, Vissers LELM, Beltran S, Hoischen A. Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses. Nat Med. 2025;31(2):478-489. doi: 10.1038/s41591-024-03420-w (Publisher Correction: Nat Med. 2025;31(8):2819-2820, doi: 10.1038/s41591-025-03754-z; preprint: medRxiv, Dec 2023)
Dyer SC, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, et al., Freeberg MA, Harrison PW, Martin FJ, Yates AD. Ensembl 2025. Nucleic Acids Res. 2025;53(D1):D948-D957. doi: 10.1093/nar/gkae1071
Thakur M, Brooksbank C, Finn RD, Firth HV, Foreman J, Freeberg M, Gurwitz KT, Harrison M, Hulcoop D, Hunt SE, Leach AR, Levchenko M, Marques D, McDonagh EM, Mithani A, Parkinson H, Perez-Riverol Y, Perova Z, Sarkans U, Tirunagari S, Tzampatzopoulou E, Venkatesan A, Vizcaino JA, Wingfield B, Zdrazil B, McEntyre J. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2024. Nucleic Acids Res. 2025;53(D1):D10-D19. doi: 10.1093/nar/gkae1089

2024

Rujano MA, Boiten JW, Ohmann C, Canham S, Contrino S, David R, Ewbank J, Filippone C, Connellan C, Custers I, van Nuland R, Mayrhofer MT, Holub P, Álvarez EG, Bacry E, Hughes N, Freeberg MA, Schaffhauser B, Wagener H, Sánchez-Pla A, Bertolini G, Panagiotopoulou M. Sharing sensitive data in life sciences: an overview of centralized and federated approaches. Brief Bioinform. 2024;25(4):bbae262. doi: 10.1093/bib/bbae262
Johansson LF, Laurie S, Spalding D, Gibson S, Ruvolo D, Thomas C, Piscia D, de Andrade F, Been G, Bijlsma M, Brunner H, Cimerman S, Dizjikan FY, Ellwanger K, Fernandez M, Freeberg M, van de Geijn GJ, Kanninga R, Maddi V, Mehtarizadeh M, Neerincx P, Ossowski S, Rath A, Roelofs-Prins D, Stok-Benjamins M, van der Velde KJ, Veal C, van der Vries G, Wadsley M, Warren G, Zurek B, Keane T, Graessner H, Beltran S, Swertz MA, Brookes AJ, Solve-RD consortium. An interconnected data infrastructure to support large-scale rare disease research. Gigascience. 2024;13:giae058. doi: 10.1093/gigascience/giae058 (preprint: medRxiv, Dec 2023)

2023

Denommé-Pichon AS, Matalonga L, de Boer E, Jackson A, Benetti E, et al., Solve-RD DITF-ITHACA, Solve-RD SNV-indel Working Group, Solve-RD Consortia, Orphanomix Group, Vitobello A, Vissers LELM, Faivre L. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing. Genet Med. 2023;25(4):100018. doi: 10.1016/j.gim.2023.100018
Corvò A, Matalonga L, Spalding D, Senf A, Laurie S, Picó-Amador D, Fernandez-Callejo M, Paramonov I, Romero AF, Garcia-Rios E, Ciges JI, Mohan A, Thomas C, Silva Valencia AF, Halmagyi C, Freeberg MA, Töpf A, Horvath R, Saunders G, Gut I, Keane T, Piscia D, Beltran S. Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases. Cell Genom. 2023;3(2):100246. doi: 10.1016/j.xgen.2022.100246
Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh EM, Orchard S, Papatheodorou I, Velankar S, Vizcaino JA, Witham R, Zdrazil B, McEntyre J. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2022. Nucleic Acids Res. 2023;51(D1):D9-D17. doi: 10.1093/nar/gkac1098

2022

Freeberg MA, Fromont LA, D’Altri T, Romero AF, Ciges JI, Jene A, Kerry G, Moldes M, Ariosa R, Bahena S, Barrowdale D, Barbero MC, Fernandez-Orth D, Garcia-Linares C, Garcia-Rios E, Haziza F, Juhasz B, Llobet OM, Milla G, Mohan A, Rueda M, Sankar A, Shaju D, Shimpi A, Singh B, Thomas C, de la Torre S, Uyan U, Vasallo C, Flicek P, Guigo R, Navarro A, Parkinson H, Keane T, Rambla J. The European Genome-phenome Archive in 2021. Nucleic Acids Res. 2022;50(D1):D980-D987. doi: 10.1093/nar/gkab1059

2021

Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, et al., Freeberg MA, et al., Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom. 2021;1(2):100029. doi: 10.1016/j.xgen.2021.100029
Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M, Burdett T, Clissold H, Donnelly S, Dyke SOM, Freeberg MA, Haendel MA, Hata C, Holub P, Jeanson F, Jene A, Kawashima M, Kawashima S, Konopko M, Kyomugisha I, Li H, Linden M, Rodriguez LL, Morita M, Mulder N, Muller J, Nagaie S, Nasir J, Ogishima S, Ota Wang V, Paglione LD, Pandya RN, Parkinson H, Philippakis AA, Prasser F, Rambla J, Reinold K, Rushton GA, Saltzman A, Saunders G, Sofia HJ, Spalding JD, Swertz MA, Tulchinsky I, van Enckevort EJ, Varma S, Voisin C, Yamamoto N, Yamasaki C, Zass L, Guidry Auvil JM, Nyrönen TH, Courtot M. The Data Use Ontology to streamline responsible access to human biomedical datasets. Cell Genom. 2021;1(2):100028. doi: 10.1016/j.xgen.2021.100028

2020

Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I. Guidelines for reporting single-cell RNA-seq experiments. Nat Biotechnol. 2020;38(12):1384-1386. doi: 10.1038/s41587-020-00744-z
Fuller GG, Han T, Freeberg MA, Moresco JJ, Ghanbari Niaki A, Roach NP, Yates JR, Myong S, Kim JK. RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. Elife. 2020;9:e48480. doi: 10.7554/elife.48480 (preprint: bioRxiv, May 2019)

2018

Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J, Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018;15(7):475-476. doi: 10.1038/s41592-018-0046-7 (preprint: bioRxiv, Oct 2017)
Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B. Community-Driven Data Analysis Training for Biology. Cell Syst. 2018;6(6):752-758. doi: 10.1016/j.cels.2018.05.012 (preprint: bioRxiv, Nov 2017)

2017

Malhotra S, Freeberg MA, Winans SJ, Taylor J, Beemon KL. A Novel Long Non-Coding RNA in the hTERT Promoter Region Regulates hTERT Expression. Noncoding RNA. 2017;4(1):E1. doi: 10.3390/ncrna4010001
Jin M, Fuller GG, Han T, Yao Y, Alessi AF, Freeberg MA, Roach NP, Moresco JJ, Karnovsky A, Baba M, Yates JR, Gitler AD, Inoki K, Klionsky DJ, Kim JK. Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress. Cell Rep. 2017;20(4):895-908. doi: 10.1016/j.celrep.2017.06.082
Hong S, Freeberg MA, Han T, Kamath A, Yao Y, Fukuda T, Suzuki T, Kim JK, Inoki K. LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs. Elife. 2017;6:e25237. doi: 10.7554/elife.25237
Weiser NE, Yang DX, Feng S, Kalinava N, Brown KC, Khanikar J, Freeberg MA, Snyder MJ, Csankovszki G, Chan RC, Gu SG, Montgomery TA, Jacobsen SE, Kim JK. MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality. Dev Cell. 2017;41(4):408-423. doi: 10.1016/j.devcel.2017.04.023

2016

Turaga N, Freeberg MA, Baker D, Chilton J, Galaxy Team, Nekrutenko A, Taylor J. A guide and best practices for R/Bioconductor tool integration in Galaxy. F1000Research. 2016;5:1345 [version 1]. doi: 10.12688/f1000research.9821.1
Freeberg MA, Kim JK. Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Bioinformatic Analysis. Methods Mol Biol. 2016;1361:91-104. doi: 10.1007/978-1-4939-3079-1_6

2015

Alessi AF, Khivansara V, Han T, Freeberg MA, Moresco JJ, Tu PG, Montoye E, Yates JR, Karp X, Kim JK. Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1. Proc Natl Acad Sci U S A. 2015;112(52):E7213-22. doi: 10.1073/pnas.1509499112 (Correction to Supporting Information: PNAS. 2016;113(7):E942, doi: 10.1073/pnas.1600214113)

2014

Jin M, He D, Backues SK, Freeberg MA, Liu X, Kim JK, Klionsky DJ. Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation. Curr Biol. 2014;24(12):1314-1322. doi: 10.1016/j.cub.2014.04.048

2013

Freeberg MA, Han T, Moresco JJ, Kong A, Yang YC, Lu ZJ, Yates JR, Kim JK. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol. 2013;14(2):R13. doi: 10.1186/gb-2013-14-2-r13
Billi AC, Freeberg MA, Day AM, Chun SY, Khivansara V, Kim JK. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genet. 2013;9(3):e1003392. doi: 10.1371/journal.pgen.1003392

2012

Billi AC, Freeberg MA, Kim JK. piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Genome Biol. 2012;13(7):164. doi: 10.1186/gb-2012-13-7-164
Billi AC, Alessi AF, Khivansara V, Han T, Freeberg M, Mitani S, Kim JK. The Caenorhabditis elegans HEN1 ortholog, HENN-1, methylates and stabilizes select subclasses of germline small RNAs. PLoS Genet. 2012;8(4):e1002617. doi: 10.1371/journal.pgen.1002617

Preprints (not yet published in a journal)

Lariviere D, Mei H, Freeberg M, Taylor J, Nekrutenko A. Understanding trivial challenges of microbial genomics: An assembly example. bioRxiv. 2018. doi: 10.1101/347625