Publications

Submitted
Herman JL, Aştefănoaei MS, Gratie D-E, Rich C, Novák A, Anderson JWJ, Lyngsø R, Hein J. RNA structure prediction in the presence of alignment uncertainty. Submitted.
Herman JL, Novák A, Challis CJ, Schmidler SC, Hein J. StatAlign 3: Bayesian alignment and phylogenetics with protein structures. (under review). Submitted.Abstract

StatAlign is a Markov chain Monte Carlo (MCMC)-based software package for performing joint inference of multiple sequence alignments and phylogenetic trees within a Bayesian framework. In this note we describe significant improvements to the software, including new types of MCMC samplers, and a facility for adding additional layers to the basic evolutionary model.

We have used this new model extension framework to develop a plugin for alignment and phylogenetic inference under a joint probabilistic model of sequence and structural evolution, allowing protein structural information to be used in statistical inference of alignments and trees.
Availability:
The latest version of StatAlign, including example datasets, and the plugins described in this note, is available for download from http://statalign.github.io

2016
Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman JL, Kaper F, Fan J-B, Zhang K, Chun J, et al. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nature Methods [Internet]. 2016;13 :241-244. Publisher's VersionAbstract

The transcriptional state of a cell reflects a variety of biological factors, from cell-type-specific features to transient processes such as the cell cycle, all of which may be of interest. However, identifying such aspects from noisy single-cell RNA-seq data remains challenging. We developed pathway and gene set overdispersion analysis (PAGODA) to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.

2015
Christensen AB, Herman JL, Elphick MR, Kober KM, Janies D, Linchangco G, Semmens DC, Bailly X, Vinogradov SN, Hoogewijs D. Phylogeny of Echinoderm Hemoglobins. PLoS ONE [Internet]. 2015;10 :e0129668. Publisher's VersionAbstract

Background

Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and α-globin/β-globin tetramer hemoglobin, and several minor groups. In contrast, very little is known about hemoglobins in echinoderms, a phylum of exclusively marine organisms closely related to vertebrates, beyond the presence of coelomic hemoglobins in sea cucumbers and brittle stars. We identified about 50 hemoglobins in sea urchin, starfish and sea cucumber genomes and transcriptomes, and used Bayesian inference to carry out a molecular phylogenetic analysis of their relationship to vertebrate sequences, specifically, to assess the hypothesis that the neuroglobin and cytoglobin lineages are also present in echinoderms.

Results

The genome of the sea urchin Strongylocentrotus purpuratus encodes several hemoglobins, including a unique chimeric 14-domain globin, 2 androglobin isoforms and a unique single androglobin domain protein. Other strongylocentrotid genomes appear to have similar repertoires of globin genes. We carried out molecular phylogenetic analyses of 52 hemoglobins identified in sea urchin, brittle star and sea cucumber genomes and transcriptomes, using different multiple sequence alignment methods coupled with Bayesian and maximum likelihood approaches. The results demonstrate that there are two major globin lineages in echinoderms, which are related to the vertebrate neuroglobin and cytoglobin lineages. Furthermore, the brittle star and sea cucumber coelomic hemoglobins appear to have evolved independently from the cytoglobin lineage, similar to the evolution of erythroid oxygen binding globins in cyclostomes and vertebrates.

Conclusion

The presence of echinoderm globins related to the vertebrate neuroglobin and cytoglobin lineages suggests that the split between neuroglobins and cytoglobins occurred in the deuterostome ancestor shared by echinoderms and vertebrates.

Herman JL, Szabó A, Miklós I, Hein J. Approximate statistical alignment by iterative sampling of substitution matrices. arXiv preprint arXiv:1501.04986. 2015.Abstract

We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorithm. This procedure provides an efficient and simple method by which to generate alternative alignments according to their expected accuracy, and allows appropriate parameters for substitution matrices to be selected in an automated fashion. In the cases considered here, the sampled alignments with the highest likelihood have an accuracy consistently higher than alignments generated using the standard BLOSUM62 matrix.

Herman JL, Novák A, Lyngsø R, Szabó A, Miklós I, Hein J. Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinformatics [Internet]. 2015;16 :108. Publisher's VersionAbstract

Background

A standard procedure in many areas of bioinformatics is to use a single multiple sequence alignment (MSA) as the basis for various types of analysis. However, downstream results may be highly sensitive to the alignment used, and neglecting the uncertainty in the alignment can lead to significant bias in the resulting inference. In recent years, a number of approaches have been developed for probabilistic sampling of alignments, rather than simply generating a single optimum. However, this type of probabilistic information is currently not widely used in the context of downstream inference, since most existing algorithms are set up to make use of a single alignment.

Results

In this work we present a framework for representing a set of sampled alignments as a directed acyclic graph (DAG) whose nodes are alignment columns; each path through this DAG then represents a valid alignment. Since the probabilities of individual columns can be estimated from empirical frequencies, this approach enables sample-based estimation of posterior alignment probabilities. Moreover, due to conditional independencies between columns, the graph structure encodes a much larger set of alignments than the original set of sampled MSAs, such that the effective sample size is greatly increased.

Conclusions

The alignment DAG provides a natural way to represent a distribution in the space of MSAs, and allows for existing algorithms to be efficiently scaled up to operate on large sets of alignments. As an example, we show how this can be used to compute marginal probabilities for tree topologies, averaging over a very large number of MSAs. This framework can also be used to generate a statistically meaningful summary alignment; example applications show that this summary alignment is consistently more accurate than the majority of the alignment samples, leading to improvements in downstream tree inference.

Implementations of the methods described in this article are available at http://​statalign.​github.​io/​WeaveAlign.

2014
Herman JL, Challis CJ, Novák A, Hein J, Schmidler SC. Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Molecular Biology and Evolution [Internet]. 2014;31 (9) :2251-2266. Publisher's VersionAbstract

For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence–structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set.

2012
Herman JL. Missing patterns and mutually unobservable landmarks, in New Statistics and Modern Natural Sciences (LASR 2012). Leeds University Press ; 2012.
2011
Herman JL, Bouremoum S, Keys KL, Miao H, Hein J. Metabolic random fields: stochastic models for the loss and gain of reactions in metabolic networks related by a phylogeny. 2011.
Herman JL, Hein J. Statistical alignment of multiple protein structures under a dynamics-based model of structural evolution, in Next Generation Statistics in Biosciences (LASR 2011). Leeds University Press ; 2011.