Searching journal content for articles similar to Sirak et al. 30 (6): 938_1.

Displaying results 1-10 of 6195

For checked items

view abstracts
download to citation manager

Select this article
Method: Human auditory ossicles as an alternative optimal source of ancient DNA
- Kendra Sirak,
- Daniel Fernandes,
- Olivia Cheronet,
- Eadaoin Harney,
- Matthew Mah,
- Swapan Mallick,
- Nadin Rohland,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Francesca Candilio,
- Ann Marie Lawson,
- Kirsten Mandl,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Juraj Bartík,
- Alfredo Coppa,
- Tumen Dashtseveg,
- Sándor Évinger,
- Zdeněk Farkaš,
- Tamás Hajdu,
- Jamsranjav Bayarsaikhan,
- Lauren McIntyre,
- Vyacheslav Moiseyev,
- Mercedes Okumura,
- Ildikó Pap,
- Michael Pietrusewsky,
- Pál Raczky,
- Alena Šefčáková,
- Andrei Soficaru,
- Tamás Szeniczey,
- Béla Miklós Szőke,
- Dennis Van Gerven,
- Sergey Vasilyev,
- Lynne Bell,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2020 30: 427-436; Published in Advance February 25, 2020, doi:10.1101/gr.260141.119
...in the petrous pyramid that will be destroyed through sampling of ancient DNA highlights the importance of being a careful steward of these elements.As part of a search for alternative optimal sources for ancient DNA that can be used in place of the cochlea, we noted that auditory ossicles have similar...
Select this article
Method: Density separation of petrous bone powders for optimized ancient DNA yields
- Daniel M. Fernandes,
- Kendra A. Sirak,
- Olivia Cheronet,
- Mario Novak,
- Florian Brück,
- Evelyn Zelger,
- Alejandro Llanos-Lizcano,
- Anna Wagner,
- Anna Zettl,
- Kirsten Mandl,
- Kellie Sara Duffet Carlson,
- Victoria Oberreiter,
- Kadir T. Özdoğan,
- Susanna Sawyer,
- Francesco La Pastina,
- Emanuela Borgia,
- Alfredo Coppa,
- Miroslav Dobeš,
- Petr Velemínský,
- David Reich,
- Lynne S. Bell,
- and Ron Pinhasi
Genome Res. April 2023 33: 622-631; Published in Advance April 18, 2023, doi:10.1101/gr.277714.123
...for sampling human petrous bones from the cranial base for ancient DNA analysis. BioTechniques 62: 283–289. doi:10.2144/000114558 ↵Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, et al. 2020. Human auditory ossicles as an alternative optimal...
Select this article
Method: Optimal marker genes for c-separated cell types with SepSolve
- Bartol Borozan,
- Tomislav Prusina,
- Luka Borozan,
- Domagoj Ševerdija,
- Francisca Rojas Ringeling,
- Domagoj Matijević,
- and Stefan Canzar
Genome Res. December 2025 35: 2770-2780; Published in Advance October 9, 2025, doi:10.1101/gr.280637.125
...takes into account expression variation within cell types without including each pair of individual cells in the model, leading to a highly stable set of marker genes that allow to accurately discriminate between cell types and that can be computed to optimality efficiently.A common first step...
Select this article
Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...-bound instances (4.6-fold enrichment; one example is shown in Fig. 2D). A clear example of an ancient RELA-associated TE was MER81, a 114-bp non-autonomous DNA transposon (Bao et al. 2015). MER81 was enriched for RELA binding in all three species (10.9-fold change in human, 10.6-fold change in mouse, and 6.2-fold...
Select this article
Corrigendum: Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. June 2025 35: 1472-1; doi:10.1101/gr.280860.125
...and apologize for any confusion this may have caused.doi: 10.1101/gr.280860.125 Published by Cold Spring Harbor Laboratory Press Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana Jonathan Cahn , James P.B. Lloyd , Ino D. Karemaker , Pascal W.T.C. Jansen , Jahnvi Pflueger...
OPEN ACCESS ARTICLE
Select this article
Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...(c.1181G>C, p.R394T), previously identified as a potential mechanism of resistance to T-DXd, because SLX4 encodes a DNA repair protein that regulates structure-specific endonucleases and seems to play a role in resistance to TOP1 inhibition. Among HER2- cell lines, MCF-7 and ZR-75-1 (HR+) and MDA...
Select this article
Method: A minimally destructive protocol for DNA extraction from ancient teeth
- Éadaoin Harney,
- Olivia Cheronet,
- Daniel M. Fernandes,
- Kendra Sirak,
- Matthew Mah,
- Rebecca Bernardos,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Ann Marie Lawson,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Francesca Candilio,
- Mihai Constantinescu,
- Alfredo Coppa,
- Ion Ciobanu,
- János Dani,
- Zsolt Gallina,
- Francesco Genchi,
- Emese Gyöngyvér Nagy,
- Tamás Hajdu,
- Magdolna Hellebrandt,
- Antónia Horváth,
- Ágnes Király,
- Krisztián Kiss,
- Barbara Kolozsi,
- Péter Kovács,
- Kitti Köhler,
- Michaela Lucci,
- Ildikó Pap,
- Sergiu Popovici,
- Pál Raczky,
- Angela Simalcsik,
- Tamás Szeniczey,
- Sergey Vasilyev,
- Cristian Virag,
- Nadin Rohland,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2021 31: 472-483; Published in Advance February 12, 2021, doi:10.1101/gr.267534.120
...), as an optimal source of ancient DNA (Gamba et al. 2014; Pinhasi et al. 2015, 2019) is one of the driving factors in this revolution, making it possible to access ancient DNA from geographic regions with climatic conditions unfavorable to ancient DNA preservation. However, accessing this optimal source...
Select this article
Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...-Loeffler-Institut, 17493 Greifswald, Germany; 3School of Health Sciences-Biomedical Sciences Program, Missouri State University, Springfield, Missouri 65897, USA A tightly regulated DNA damage response is critical to the overall integrity of the . Here, we combine transcriptomics and proteomics to study DNA damage...
Select this article
Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...sacrificed for this study. Total genomic DNA was extracted using the Qiagen DNeasy blood and tissue kit and quantified on the Qubit DNA quantification system (Thermo Fisher Scientific) using Qubit broad range assay reagents, following the manufacturer's protocol. DNA concentration across all samples...
OPEN ACCESS ARTICLE
Select this article
Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...affinities following from differences in RNA Polymerase II kinetics owing to local GC content.Alternative splicing occurs predominantly cotranscriptionally and thus takes place in close proximity to the DNA from which the transcript originated (Reimer et al. 2021). Beyond being impacted by transcription...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Sirak et al. 30 (6): 938_1.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: