Searching journal content for articles similar to Rabinowicz and Scahidanandam 12 (7): 1015.

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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...1, Raony Cardenas1, Thyago Cardoso1, Luis F. Paulin2, Philippe Sanio2, Joseph Mafofo1, Haiguo Wu1, Val Zvereff1, Albarah El-Khani1, Fahed Al Marzooqi1, Tiago R. Magalhães1, Fritz J. Sedlazeck2,3,4 and Javier Quilez1 1M42, Abu Dhabi, United Arab Emirates; 2Human Genome Sequencing Center, Baylor...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...the reference, such as disease- and trait-associated variants or engineered sequences. Recent work has applied synthetic regulatory genomics to characterized dozens of deletions, inversions, and rearrangements of DNase I hypersensitive sites (DHSs). Here, we use the state-of-the-art model Enformer to predict...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...Katharine M. Jenike1, Lucía Campos-Domínguez2, Marilou Boddé3, José Cerca4,6, Christina N. Hodson5, Michael C. Schatz1 and Kamil S. Jaron3 1Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA; 2Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
..., China, and the United States (n = 72) in the largest comparative genomics study to date. We applied rigorous filters to exclude mixed infections and analyzed a data set from 141 isolates from the zoonotic groups IIa (n = 119) and IId (n = 22). Based on 28,047 high-quality, biallelic genomic SNPs, we...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
..., transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate...
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Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
- Etienne Routhier,
- Edgard Pierre,
- Ghazaleh Khodabandelou,
- and Julien Mozziconacci
Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
...(Ostrov et al. 2019) that could reach even the scale of the human . In the field of genomic engineering, the first step is to design the DNA sequence of interest, either resulting from very few edits of the wild-type sequence, or from a more extensive rewriting, or even from the introduction of DNA...
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Research: High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
- Michael J. Johnston,
- Ana Nikolic,
- Nicoletta Ninkovic,
- Paul Guilhamon,
- Florence M.G. Cavalli,
- Steven Seaman,
- Franz J. Zemp,
- John Lee,
- Aly Abdelkareem,
- Katrina Ellestad,
- Alex Murison,
- Michelle M. Kushida,
- Fiona J. Coutinho,
- Yussanne Ma,
- Andrew J. Mungall,
- Richard Moore,
- Marco A. Marra,
- Michael D. Taylor,
- Peter B. Dirks,
- Trevor J. Pugh,
- Sorana Morrissy,
- Bradley St Croix,
- Douglas J. Mahoney,
- Mathieu Lupien,
- and Marco Gallo
Genome Res. August 2019 29: 1211-1222; Published in Advance June 27, 2019, doi:10.1101/gr.246520.118
...separated by SV status. SV-associated loops tend to connect genomic loci separated by a much larger apparent distance, although this is unlikely the true molecular distance following chromosomal rearrangement. P-values calculated by Wilcoxon rank-sum test. (C) Hi-C contact maps assuming a standard...
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Method: Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies
- Paul Geeleher,
- Zhenyu Zhang,
- Fan Wang,
- Robert F. Gruener,
- Aritro Nath,
- Gladys Morrison,
- Steven Bhutra,
- Robert L. Grossman,
- and R. Stephanie Huang
Genome Res. October 2017 27: 1743-1751; Published in Advance August 28, 2017, doi:10.1101/gr.221077.117
...cell lines and mouse models. However, these platforms suffer from serious limitations, including small sample sizes. Here, we have developed a novel computational method that allows us to impute drug response in very large clinical cancer genomics data sets, such as The Cancer Genome Atlas (TCGA...
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Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
.... neoformans for human virulence. Genome sequencing and phylogenetic analysis of 387 isolates, representing the global VNI and African VNB lineages, highlighted a deep, nonrecombining split in VNB (herein, VNBI and VNBII). VNBII was enriched for clinical samples relative to VNBI, while phenotypic profiling...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...The population genomics of rhesus macaques (Macaca mulatta) based on whole- sequences Cheng Xue,1 Muthuswamy Raveendran,1 R. Alan Harris,1,2 Gloria L. Fawcett,1,19 Xiaoming Liu,3 Simon White,1 Mahmoud Dahdouli,1,20 David Rio Deiros,1 Jennifer E. Below,3 William Salerno,1 Laura Cox,4 Guoping Fan,5...
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