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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
..., divergence times, and population sizes) is computed by simulating data under the coalescent with recombination using the candidate model, using these data to automatically construct an HMM, and then computing the likelihood by means of the forward algorithm (Chang and Hancock 1966; Baum et al. 1970, 1972...
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Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell sequencing data Hamim Zafar1,2, Nicholas Navin3, Ken Chen2 and Luay Nakhleh1 1Department of Computer Science, Rice University, Houston, Texas 77005, USA; 2Department of Bioinformatics...
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Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
- Salem Malikic,
- Farid Rashidi Mehrabadi,
- Simone Ciccolella,
- Md. Khaledur Rahman,
- Camir Ricketts,
- Ehsan Haghshenas,
- Daniel Seidman,
- Faraz Hach,
- Iman Hajirasouliha,
- and S. Cenk Sahinalp
Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
....sahinalp@nih.govAbstractAvailable computational methods for tumor phylogeny inference via single-cell sequencing (SCS) data typically aim to identify the most likely perfect phylogeny tree satisfying the infinite sites assumption (ISA). However, the limitations of SCS technologies including frequent allele dropout and variable sequence coverage...
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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
...and generating 53 tissue-enriched cis-regulatory elements (CREs), including 1,645 promoter- and 54 enhancer-associated elements. This study establishes a robust computational framework for 55 cross-species TE analysis and provides key insights into the coevolution of KZFPs and TEs, 56 advancing our understanding...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...and Triturus but on a separate chromosome in Pleurodeles.View larger version: In this window In a new window Figure 4. Phylogeny of newt MHC in the context of MHC sequences from other tetrapod taxa. The RAxML-NG maximum likelihood trees were constructed from protein sequences under the JTT+G4 amino...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...likelihood estimation (ape R package) (Paradis and Schliep 2019). This provided us with the scaled likelihoods of ancestral states for each internal node of the tree. Based on this extensive automated annotation, we then reviewed individually the transitions based on literature on rodent phylogeny...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Bio) and Oxford Nanopore Technologies (ONT), has markedly enhanced both the efficiency and accuracy of genomic studies (Sedlazeck et al. 2018). These technological advances have also propelled pan analyses. Initially developed for bacterial studies (Sherman and Salzberg 2020), the pan approach has now gained...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...a maximum-likelihood approach along our time-calibrated phylogeny in the R package phytools (Revell 2012; R Core Team 2014).Transposable element evolutionTo identify transposable elements in the s of the three studied gar species (L. osseus, L. oculatus, A. spatula), Danio rerio, Acipenser ruthenus, Amia...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...of morphologies, vacuolar morphologies dominate cultured samples (Fig. 1B).View larger version: In this window In a new window Figure 1. Phylogenetic relationships and assembly characteristics of Blastocystis. (A) 18S rRNA maximum likelihood (ML) phylogeny of Blastocystis subtypes, with Proteromonas lacertae...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...duplication blocks, with DupMasker annotations illustrated with colored arrows. The diverse organizational differences of each expansion, including expansion size, duplicon content, and copy number, suggest independent expansion. (B) TBC1D3 neutral phylogeny generated by maximum likelihood; 2300 bp...
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