LIVIVO - Search results -

Search results

Result 1 - 10 of total 37

Search options

Article ; Online: Computational Approaches for Understanding Sequence Variation Effects on the 3D Genome Architecture.

Avdeyev, Pavel / Zhou, Jian

Annual review of biomedical data science

2022 Volume 5, Page(s) 183–204

Abstract: Decoding how genomic sequence and its variations affect 3D genome architecture is indispensable for understanding the genetic architecture of various traits and diseases. The 3D genome organization can be significantly altered by genome variations and in ...

Abstract	Decoding how genomic sequence and its variations affect 3D genome architecture is indispensable for understanding the genetic architecture of various traits and diseases. The 3D genome organization can be significantly altered by genome variations and in turn impact the function of the genomic sequence. Techniques for measuring the 3D genome architecture across spatial scales have opened up new possibilities for understanding how the 3D genome depends upon the genomic sequence and how it can be altered by sequence variations. Computational methods have become instrumental in analyzing and modeling the sequence effects on 3D genome architecture, and recent development in deep learning sequence models have opened up new opportunities for studying the interplay between sequence variations and the 3D genome. In this review, we focus on computational approaches for both the detection and modeling of sequence variation effects on the 3D genome, and we discuss the opportunities presented by these approaches.
MeSH term(s)	Chromatin ; Genome/genetics ; Genomics
Chemical Substances	Chromatin
Language	English
Publishing date	2022-05-10
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2574-3414
ISSN (online)	2574-3414
DOI	10.1146/annurev-biodatasci-102521-012018
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: TruEst: a better estimator of evolutionary distance under the INFER model.

Zabelkin, Alexey / Avdeyev, Pavel / Alexeev, Nikita

Journal of mathematical biology

2023 Volume 87, Issue 2, Page(s) 25

Abstract: Genome rearrangements are evolutionary events that shuffle genomic architectures. The number of genome rearrangements that happened between two genomes is often used as the evolutionary distance between these species. This number is often estimated as ... ...

Abstract	Genome rearrangements are evolutionary events that shuffle genomic architectures. The number of genome rearrangements that happened between two genomes is often used as the evolutionary distance between these species. This number is often estimated as the minimum number of genome rearrangements required to transform one genome into another which are only reliable for closely-related genomes. These estimations often underestimate the evolutionary distance for genomes that have substantially evolved from each other, and advanced statistical methods can be used to improve accuracy. Several statistical estimators have been developed, under various evolutionary models, of which the most complete one, INFER, takes into account different degrees of genome fragility. We present TruEst-an efficient tool that estimates the evolutionary distance between the genomes under the INFER model of genome rearrangements. We apply our method to both simulated and real data. It shows high accuracy on the simulated data. On the real datasets of mammal genomes the method found several pairs of genomes for which the estimated distances are in high consistency with the previous ancestral reconstruction studies.
MeSH term(s)	Animals ; Evolution, Molecular ; Biological Evolution ; Genomics/methods ; Genome ; Gene Rearrangement ; Mammals/genetics ; Algorithms ; Phylogeny ; Models, Genetic
Language	English
Publishing date	2023-07-10
Publishing country	Germany
Document type	Journal Article
ZDB-ID	187101-8
ISSN	1432-1416 ; 0303-6812
ISSN (online)	1432-1416
ISSN	0303-6812
DOI	10.1007/s00285-023-01955-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1495: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Dirichlet Diffusion Score Model for Biological Sequence Generation.

Avdeyev, Pavel / Shi, Chenlai / Tan, Yuhao / Dudnyk, Kseniia / Zhou, Jian

ArXiv

2023

Abstract: Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many ... ...

Abstract	Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences.
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Evaluation of the effectiveness and safety of photodynamic therapy in the treatment of precancerous diseases of the cervix (neoplasia) associated with the human papillomavirus: A systematic review.

Shanazarov, Nasrulla / Bariyeva, Gulzada / Avdeyev, Andrey / Albayev, Rustam / Kisikova, Saule / Zinchenko, Sergey / Galiev, Ilfat

Photodiagnosis and photodynamic therapy

2023 Volume 45, Page(s) 103925

Abstract: This study provides an overview of the effectiveness and safety of PDT for the treatment of HPV-associated precancerous cervical conditions and contains recent findings from relevant research studies. A comprehensive literature search of MEDLINE/PubMed, ... ...

Abstract	This study provides an overview of the effectiveness and safety of PDT for the treatment of HPV-associated precancerous cervical conditions and contains recent findings from relevant research studies. A comprehensive literature search of MEDLINE/PubMed, Cochrane Central Library, and Google Scholar was conducted, including analytic epidemiological studies, and 11 papers were included. The narrative synthesis approach was used to summarize the results of the included studies. Studies were critically appraised using The Joanna Briggs Institute (JBI) tool for assessing the risk of bias. The results of the study demonstrate that CRR for HPV remission ranges from 66.7 % to 92.73 %, whereas for CIN1 it fluctuates from 57.1 % to 83.3 %. The frequency of recurrence of the disease ranged from 3.3 % to 8.9 % during the follow-up period of up to 2 years. Adverse events were observed in 8 (66 %) studies and the most common were cervical stenosis, abdominal pain, vaginal pain, and focal edema. Five types of topical and intravenous applications along with lasers of various wavelengths and intensities were mostly used. However, all studies demonstrated relatively similar results. According to the results, PDT has demonstrated favorable outcomes, but no impressive effect on the treatment of CIN. It should be emphasized, that the effectiveness of PDT for the treatment of HPV-associated CIN may vary depending on some variables, including the kind of PDT agent used, the dosage, duration and frequency of PDT administration, the severity and location of the lesions, and the host immunological response.
MeSH term(s)	Female ; Humans ; Cervix Uteri ; Human Papillomavirus Viruses ; Papillomavirus Infections/drug therapy ; Photochemotherapy/methods ; Photosensitizing Agents/adverse effects ; Photosensitizing Agents/therapeutic use ; Precancerous Conditions/drug therapy ; Uterine Cervical Dysplasia/therapy ; Uterine Cervical Neoplasms/therapy
Chemical Substances	Photosensitizing Agents
Language	English
Publishing date	2023-12-07
Publishing country	Netherlands
Document type	Journal Article ; Systematic Review
ZDB-ID	2149918-4
ISSN	1873-1597 ; 1572-1000
ISSN (online)	1873-1597
ISSN	1572-1000
DOI	10.1016/j.pdpdt.2023.103925
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Details ▾
- Full text online
- Order with fees

Book ; Online: Dirichlet Diffusion Score Model for Biological Sequence Generation

Avdeyev, Pavel / Shi, Chenlai / Tan, Yuhao / Dudnyk, Kseniia / Zhou, Jian

2023

Abstract	Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences. Comment: ICML 2023
Keywords	Computer Science - Machine Learning ; Quantitative Biology - Genomics ; Quantitative Biology - Quantitative Methods
Subject code	004
Publishing date	2023-05-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model.

Avdeyev, Pavel / Jiang, Shuai / Alekseyev, Max A

Evolutionary bioinformatics online

2019 Volume 15, Page(s) 1176934318820534

Abstract: Reconstruction of the median genome consisting of linear chromosomes from three given genomes is known to be intractable. There exist efficient methods for solving a relaxed version of this problem, where the median genome is allowed to have circular ... ...

Abstract	Reconstruction of the median genome consisting of linear chromosomes from three given genomes is known to be intractable. There exist efficient methods for solving a relaxed version of this problem, where the median genome is allowed to have circular chromosomes. We propose a method for construction of an approximate solution to the original problem from a solution to the relaxed problem and prove a bound on its approximation error. Our method also provides insights into the combinatorial structure of genome transformations with respect to appearance of circular chromosomes.
Language	English
Publishing date	2019-06-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2227610-5
ISSN	1176-9343
ISSN	1176-9343
DOI	10.1177/1176934318820534
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A unified ILP framework for core ancestral genome reconstruction problems.

Avdeyev, Pavel / Alexeev, Nikita / Rong, Yongwu / Alekseyev, Max A

Bioinformatics (Oxford, England)

2020 Volume 36, Issue 10, Page(s) 2993–3003

Abstract: Motivation: One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, ...

Abstract	Motivation: One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole-genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of preduplicated ancestral genomes, referred to as the genome halving problem. Generalization of WGDs to whole-genome multiplication events leads to the genome aliquoting problem. Results: In this study, we propose polynomial-size integer linear programming (ILP) formulations for the aforementioned problems. We further obtain such formulations for the restricted and conserved versions of the median and halving problems, which have been recently introduced to improve biological relevance of the solutions. Extensive evaluation of solutions to the different ILP problems demonstrates their good accuracy. Furthermore, since the ILP formulations for the conserved versions have linear size, they provide a novel practical approach to ancestral genome reconstruction, which combines the advantages of homology- and rearrangements-based methods. Availability and implementation: Code and data are available in https://github.com/AvdeevPavel/ILP-WGD-reconstructor. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Biological Evolution ; Evolution, Molecular ; Genome ; Genomics ; Phylogeny ; Programming, Linear
Language	English
Publishing date	2020-02-11
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa100
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2374: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Features of the growth and development of young pigs of various breeding

Tretyakova Olga / Degtyar Anna / Avdeyev Alexander / Ovchinnikov Dmitry / Morozyuk Irina

E3S Web of Conferences, Vol 273, p

2021 Volume 02012

Abstract: The indicators of growth and development, fattening and meat qualities of pigs of the breeding center “Lozovoe” CJSC “Plemzavod-Yubileyny” of the Tyumen region were evaluated. The indicators that characterize the growth and development of young animals ... ...

Abstract	The indicators of growth and development, fattening and meat qualities of pigs of the breeding center “Lozovoe” CJSC “Plemzavod-Yubileyny” of the Tyumen region were evaluated. The indicators that characterize the growth and development of young animals were taken into account: live weight, age, average daily growth. When the live weight of 100 kg was reached, an ultrasound device was used to evaluate the thickness of bacon, the depth of muscles and the yield of lean meat, which are in the database of breeding records for 2011-2020. To characterize the meat qualities, 1144 Landrace piglets were slaughtered, 275 - large white breed, 129 - Pietren breed, 339 hybrids (LxKB), 159 hybrids (LxD), 460 hybrids obtained from boars of foreign selection. A comparative analysis of commercial hybrids of various variants of crossing pigs of domestic and foreign selection is carried out. Processing of the research results was carried out in the laboratory of Molecular diagnostics and Biotechnology of the Don State Agrarian University. The influence of the breed is established.
Keywords	Environmental sciences ; GE1-350
Subject code	630
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes.

Bernot, James P / Avdeyev, Pavel / Zamyatin, Anton / Dreyer, Niklas / Alexeev, Nikita / Pérez-Losada, Marcos / Crandall, Keith A

GigaScience

2022 Volume 11

Abstract: Background: The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles ... ...

Abstract	Background: The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles also cause hundreds of millions of dollars of losses annually due to biofouling. However, genomic resources for crustaceans, and barnacles in particular, are lacking. Results: Using 62× Pacific Biosciences coverage, 189× Illumina whole-genome sequencing coverage, 203× HiC coverage, and 69× CHi-C coverage, we produced a chromosome-level genome assembly of the gooseneck barnacle Pollicipes pollicipes. The P. pollicipes genome is 770 Mb long and its assembly is one of the most contiguous and complete crustacean genomes available, with a scaffold N50 of 47 Mb and 90.5% of the BUSCO Arthropoda gene set. Using the genome annotation produced here along with transcriptomes of 13 other barnacle species, we completed phylogenomic analyses on a nearly 2 million amino acid alignment. Contrary to previous studies, our phylogenies suggest that the Pollicipedomorpha is monophyletic and sister to the Balanomorpha, which alters our understanding of barnacle larval evolution and suggests homoplasy in a number of naupliar characters. We also compared transcriptomes of P. pollicipes nauplius larvae and adults and found that nearly one-half of the genes in the genome are differentially expressed, highlighting the vastly different transcriptomes of larvae and adult gooseneck barnacles. Annotation of the genes with KEGG and GO terms reveals that these stages exhibit many differences including cuticle binding, chitin binding, microtubule motor activity, and membrane adhesion. Conclusion: This study provides high-quality genomic resources for a key group of crustaceans. This is especially valuable given the roles P. pollicipes plays in European fisheries, as a sentinel species for coastal ecosystems, and as a model for studying barnacle adhesion as well as its key position in the barnacle tree of life. A combination of genomic, phylogenetic, and transcriptomic analyses here provides valuable insights into the evolution and development of barnacles.
MeSH term(s)	Animals ; Chromosomes ; Ecosystem ; Phylogeny ; Thoracica/genetics ; Thoracica/metabolism ; Transcriptome
Language	English
Publishing date	2022-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giac021
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Implicit Transpositions in DCJ Scenarios.

Avdeyev, Pavel / Jiang, Shuai / Alekseyev, Max A

Frontiers in genetics

2017 Volume 8, Page(s) 212

Abstract: Genome rearrangements are large-scale evolutionary events that shuffle genomic architectures. The minimal number of such events between two genomes is often used in phylogenomic studies to measure the evolutionary distance between the genomes. Double-Cut- ...

Abstract	Genome rearrangements are large-scale evolutionary events that shuffle genomic architectures. The minimal number of such events between two genomes is often used in phylogenomic studies to measure the evolutionary distance between the genomes. Double-Cut-and-Join (DCJ) operations represent a convenient model of most common genome rearrangements (reversals, translocations, fissions, and fusions), while other genome rearrangements, such as transpositions, can be modeled by pairs of DCJs. Since the DCJ model does not directly account for transpositions, their impact on DCJ scenarios is unclear. In the present work, we study implicit appearance of transpositions (as pairs of DCJs) in DCJ scenarios. We consider shortest DCJ scenarios satisfying the maximum parsimony assumption, as well as more general DCJ scenarios based on some realistic but less restrictive assumptions. In both cases, we derive a uniform lower bound for the rate of implicit transpositions, which depends only on the genomes but not a particular DCJ scenario between them. Our results imply that implicit appearance of transpositions in DCJ scenarios may be unavoidable or even abundant for some pairs of genomes. We estimate that for mammalian genomes implicit transpositions constitute at least 6% of genome rearrangements.
Language	English
Publishing date	2017-12-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2017.00212
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito