Searching journal content for articles similar to Shakhnovich et al. 15 (3): 385.

Displaying results 1-10 of 151

For checked items

view abstracts
download to citation manager

Select this article
Research: Individualized VDJ recombination predisposes the available Ig sequence space
- Andrei Slabodkin,
- Maria Chernigovskaya,
- Ivana Mikocziova,
- Rahmad Akbar,
- Lonneke Scheffer,
- Milena Pavlović,
- Habib Bashour,
- Igor Snapkov,
- Brij Bhushan Mehta,
- Cédric R. Weber,
- Jose Gutierrez-Marcos,
- Ludvig M. Sollid,
- Ingrid Hobæk Haff,
- Geir Kjetil Sandve,
- Philippe A. Robert,
- and Victor Greiff
Genome Res. December 2021 31: 2209-2224; Published in Advance November 23, 2021, doi:10.1101/gr.275373.121
...between individuals. If these rules differed, identical (auto)antigen-specific Ig sequences would be generated with individual-specific probabilities, signifying that the available Ig sequence space is individual specific. We devised a sensitivity-tested distance measure that enables inter...
OPEN ACCESS ARTICLE
Select this article
Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...) into a hypothesized recipient population (P2) where P1 represents a control population assumed to have no genetic contributions from P3. In this model, the ancestral relationships are traced for a single lineage per population resulting in eight unique coalescent histories with only three possible topologies, that is...
OPEN ACCESS ARTICLE
Select this article
Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...into two segments (first and second half, located at telomere and centromere directions, respectively) would capture two distinct phylogenetic histories when comparing them to each other (Supplemental Fig. S19) or to the topology of the full SD spacer (Fig. 5E). To test for significance, we calculated...
OPEN ACCESS ARTICLE
Select this article
Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
..., Boston, Massachusetts 02115, USA; 4Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA Corresponding author: yufeng.wu@uconn.eduAbstractIn a multicellular organism, cell lineages share a common evolutionary history. Knowing this history can facilitate the study...
OPEN ACCESS ARTICLE
Select this article
Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
..., Sichuan 8 University, Chengdu, Sichuan, 610041, China 9 3. Deep Underground Space Medical Center, West China Hospital, Sichuan University, 10 Chengdu, Chengdu, Sichuan, 610041, China 11 12 # These authors contributed equally 13 * Corresponding author 14 E-mail: danxie@scu.edu.cn (DX), liujifeng777@wchscu...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
RESOURCE: Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs
- Julie E. Horvath,
- David W. Weisrock,
- Stephanie L. Embry,
- Isabella Fiorentino,
- James P. Balhoff,
- Peter Kappeler,
- Gregory A. Wray,
- Huntington F. Willard,
- and Anne D. Yoder
Genome Res. March 2008 18: 489-499; Published in Advance February 1, 2008, doi:10.1101/gr.7265208
...Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs Julie E. Horvath 1 , 7 , David W. Weisrock 2 , Stephanie L. Embry 1 , Isabella Fiorentino 2 , James P. Balhoff 3 , Peter...
Select this article
Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
..., with species 198 from identical subfamilies exhibiting comparable divergence patterns. Notably, the genetic 199 distance between Bovinae and Capridae had expanded considerably in recent evolutionary 200 history, potentially related to the expansion of specific TE subfamilies. 201 We constructed dynamic trees...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT
Select this article
Method: Variational inference using approximate likelihood under the coalescent with recombination
- Xinhao Liu,
- Huw A. Ogilvie,
- and Luay Nakhleh
Genome Res. November 2021 31: 2107-2119; Published in Advance August 23, 2021, doi:10.1101/gr.273631.120
...-branches is small, the resulting coalHMM has a state space of coarse coalescent histories that is not enough to capture the detailed coalescent distribution, leading to biased likelihood (Dutheil et al. 2009; Mailund et al. 2011). The quality of the coalHMM itself (i.e., the quality of the transition matrix...
Select this article
Method: Ultrafast genome-wide inference of pairwise coalescence times
- Regev Schweiger and
- Richard Durbin
Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
...extensions infer the coalescence time of two homologous chromosomes at each genomic position. This inference is used in reconstructing demographic histories, detecting selection signatures, studying -wide associations, constructing ancestral recombination graphs, and more. Inference of coalescence times...
OPEN ACCESS ARTICLE
Select this article
Method: Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
- Alex Warwick Vesztrocy,
- Natasha Glover,
- Paul D. Thomas,
- Christophe Dessimoz,
- and Irene Julca
Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124
...of duplications (Supplemental Table S3). These findings highlight the significant role of gene duplication in the evolutionary history of plants, in agreement with previous studies (Jiao et al. 2011; Soltis et al. 2015).Further analysis of the distribution of duplications across the six categories within each...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Shakhnovich et al. 15 (3): 385.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: