Search Results - "Bayzid, Md Shamsuzzoha"

Statistical binning enables an accurate coalescent-based estimation of the avian tree by Mirarab, Siavash, Bayzid, Md. Shamsuzzoha, Boussau, Bastien, Warnow, Tandy

“…Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although…”
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Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices by Bhattacharjee, Ananya, Bayzid, Md Shamsuzzoha

“…With the rapid growth rate of newly sequenced genomes, species tree inference from genes sampled throughout the whole genome has become a basic task in…”
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Accurate phylogenetic tree reconstruction from quartets: a heuristic approach by Reaz, Rezwana, Bayzid, Md Shamsuzzoha, Rahman, M Sohel

“…Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A 'quartet' is…”
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STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency by Islam, Mazharul, Sarker, Kowshika, Das, Trisha, Reaz, Rezwana, Bayzid, Md Shamsuzzoha

“…Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree…”
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Biological computation and computational biology: survey, challenges, and discussion by Chelly Dagdia, Zaineb, Avdeyev, Pavel, Bayzid, Md. Shamsuzzoha

“…Biological computation involves the design and development of computational techniques inspired by natural biota. On the other hand, computational biology…”
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CHAPAO: Likelihood and hierarchical reference-based representation of biomolecular sequences and applications to compressing multiple sequence alignments by Rahman, Md Ashiqur, Tutul, Abdullah Aman, Abdullah, Sifat Muhammad, Bayzid, Md Shamsuzzoha

“…High-throughput experimental technologies are generating tremendous amounts of genomic data, offering valuable resources to answer important questions and…”
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Evaluation of classification and forecasting methods on time series gene expression data by Tripto, Nafis Irtiza, Kabir, Mohimenul, Bayzid, Md Shamsuzzoha, Rahman, Atif

“…Time series gene expression data is widely used to study different dynamic biological processes. Although gene expression datasets share many of the…”
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Multiobjective Formulation of Multiple Sequence Alignment for Phylogeny Inference by Nayeem, Muhammad Ali, Bayzid, Md. Shamsuzzoha, Rahman, Atif Hasan, Shahriyar, Rifat, Rahman, M. Sohel

“…Multiple sequence alignment (MSA) is a preliminary task for estimating phylogenies. It is used for homology inference among the sequences of a set of species…”
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Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data by Moumi, Nazifa Ahmed, Das, Badhan, Tasnim Promi, Zarin, Bristy, Nishat Anjum, Bayzid, Md Shamsuzzoha

“…Understanding cell differentiation-the process of generation of distinct cell-types-plays a pivotal role in developmental and evolutionary biology…”
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CD-MAWS: An Alignment-Free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets by Anjum, Naser, Nabil, Raian Latif, Rafi, Rakibul Islam, Bayzid, Md. Shamsuzzoha, Rahman, M. Saifur

“…Multiple sequence alignment has been the traditional and well established approach of sequence analysis and comparison, though it is time and memory consuming…”
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Terraces in species tree inference from gene trees by Habib, Mursalin, Roy, Kowshic, Hasan, Saem, Rahman, Atif Hasan, Bayzid, Md. Shamsuzzoha

“…A terrace in a phylogenetic tree space is a region where all trees contain the same set of subtrees, due to certain patterns of missing data among the taxa…”
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Distance-Based Phylogenetic Placement with Statistical Support by Hasan, Navid Bin, Balaban, Metin, Biswas, Avijit, Bayzid, Md Shamsuzzoha, Mirarab, Siavash

“…Phylogenetic identification of unknown sequences by placing them on a tree is routinely attempted in modern ecological studies. Such placements are often…”
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Genome wide association studies on seven yield‐related traits of 183 rice varieties in Bangladesh by Roy, Nilanjan, Kabir, Acramul Haque, Zahan, Nourin, Mouna, Shahba Tasmiya, Chakravarty, Sakshar, Rahman, Atif Hasan, Bayzid, Md. Shamsuzzoha

“…Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated…”
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Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree" by Mirarab, Siavash, Bayzid, Md Shamsuzzoha, Boussau, Bastien, Warnow, Tandy

“…Liu and Edwards argue against the use of weighted statistical binning within a species tree estimation pipeline. However, we show that their mathematical…”
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EGRET: edge aggregated graph attention networks and transfer learning improve protein–protein interaction site prediction by Mahbub, Sazan, Bayzid, Md Shamsuzzoha

“…Abstract Motivation Protein–protein interactions (PPIs) are central to most biological processes. However, reliable identification of PPI sites using…”
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Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees by Bayzid, Md Shamsuzzoha

“…Estimating species trees from multiple genes is complicated and challenging due to . One of the basic approaches to understanding differences between gene…”
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Pair-EGRET: enhancing the prediction of protein–protein interaction sites through graph attention networks and protein language models by Alam, Ramisa, Mahbub, Sazan, Bayzid, Md Shamsuzzoha

“…Abstract Motivation Proteins are responsible for most biological functions, many of which require the interaction of more than one protein molecule. However,…”
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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses by Bayzid, Md Shamsuzzoha, Mirarab, Siavash, Boussau, Bastien, Warnow, Tandy

“…Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across…”
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Gene tree parsimony for incomplete gene trees: addressing true biological loss by Bayzid, Md Shamsuzzoha, Warnow, Tandy

“…Species tree estimation from gene trees can be complicated by gene duplication and loss, and "gene tree parsimony" (GTP) is one approach for estimating species…”
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Align-gram: Rethinking the Skip-gram Model for Protein Sequence Analysis by Ibtehaz, Nabil, Sourav, S. M. Shakhawat Hossain, Bayzid, Md. Shamsuzzoha, Rahman, M. Sohel

“…The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted…”
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