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Book ; Online ; E-Book: Bioinformatics with Python Cookbook

Antao, Tiago

Use Modern Python Libraries and Applications to Solve Real-World Computational Biology Problems

2022

Abstract: Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data, and this book will show you how to manage these tasks using Python. This updated third edition of the ... ...

Author's details	Tiago Antao
Abstract	Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data, and this book will show you how to manage these tasks using Python. This updated third edition of the Bioinformatics with Python Cookbook begins with a quick overview of the various tools and libraries in the Python ecosystem that will help you convert, analyze, and visualize biological datasets. Next, you'll cover key techniques for next-generation sequencing, single-cell analysis, genomics, metagenomics, population genetics, phylogenetics, and proteomics with the help of real-world examples. You'll learn how to work with important pipeline systems, such as Galaxy servers and Snakemake, and understand the various modules in Python for functional and asynchronous programming. This book will also help you explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks, including Dask and Spark. In addition to this, you'll explore the application of machine learning algorithms in bioinformatics. By the end of this bioinformatics Python book, you'll be equipped with the knowledge you need to implement the latest programming techniques and frameworks, empowering you to deal with bioinformatics data on every scale.
Keywords	Bioinformatics ; Python (Computer program language)
Subject code	170
Language	English
Size	1 online resource (360 pages)
Edition	Third edition.
Publisher	Packt Publishing
Publishing place	Birmingham, England
Document type	Book ; Online ; E-Book
Note	Includes index.
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
ISBN	1-5231-5143-9 ; 1-80324-772-X ; 1-80323-642-6 ; 978-1-5231-5143-1 ; 978-1-80324-772-4 ; 978-1-80323-642-1
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Evolutionary parasitology applied to control and elimination policies.

Antao, Tiago

Trends in parasitology

2011 Volume 27, Issue 6, Page(s) 233–234

MeSH term(s)	Biological Evolution ; Drug Resistance ; Humans ; Malaria/drug therapy ; Malaria/immunology ; Malaria/prevention & control ; Parasitology
Language	English
Publishing date	2011-06
Publishing country	England
Document type	Comment ; Letter
ZDB-ID	2036227-4
ISSN	1471-5007 ; 1471-4922
ISSN (online)	1471-5007
ISSN	1471-4922
DOI	10.1016/j.pt.2011.03.004
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Article ; Online: interPopula: a Python API to access the HapMap Project dataset.

Antao, Tiago

BMC bioinformatics

2010 Volume 11 Suppl 12, Page(s) S10

Abstract: Background: The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not ... ...

Abstract	Background: The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided. Results: interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided. Conclusions: interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.
MeSH term(s)	Databases, Nucleic Acid ; Humans ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Population Groups/genetics ; Software ; Systems Integration
Language	English
Publishing date	2010-12-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-11-S12-S10
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Article ; Online: interPopula

Antao Tiago

BMC Bioinformatics, Vol 11, Iss Suppl 12, p S

a Python API to access the HapMap Project dataset

2010 Volume 10

Abstract: Abstract Background The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not ...

Abstract	Abstract Background The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided. Results interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided. Conclusions interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2010-12-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Niche partitioning of microbial communities in riverine floodplains.

Peipoch, Marc / Miller, Scott R / Antao, Tiago R / Valett, H Maurice

Scientific reports

2019 Volume 9, Issue 1, Page(s) 16384

Abstract: Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of ...

Abstract	Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H': 2.8-4.1) nor β (Sørensen: 0.3-0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.
MeSH term(s)	Biodiversity ; Biofilms ; Carbon/analysis ; Ecosystem ; Microbiota ; Montana ; Nitrogen/analysis ; Phosphorus/analysis ; Rivers/chemistry ; Rivers/microbiology ; Wetlands
Chemical Substances	Phosphorus (27YLU75U4W) ; Carbon (7440-44-0) ; Nitrogen (N762921K75)
Language	English
Publishing date	2019-11-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-52865-4
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Article ; Online ; Research data: (with research data) Intermittent breeding and constraints on litter size: consequences for effective population size per generation (Ne ) and per reproductive cycle (Nb ).

Waples, Robin S / Antao, Tiago

Evolution; international journal of organic evolution

2014 Volume 68, Issue 6, Page(s) 1722–1734

Abstract: In iteroparous species, it is easier to estimate Nb (effective number of breeders in one reproductive cycle) than Ne (effective population size per generation). Nb can be used as a proxy for Ne and also can provide crucial insights into eco-evolutionary ... ...

Abstract	In iteroparous species, it is easier to estimate Nb (effective number of breeders in one reproductive cycle) than Ne (effective population size per generation). Nb can be used as a proxy for Ne and also can provide crucial insights into eco-evolutionary processes that occur during reproduction. We used analytical and numerical methods to evaluate effects of intermittent breeding and litter/clutch size on inbreeding Nb and Ne . Fixed or random litter sizes ≥ 3 have little effect on either effective-size parameter; however, in species (e.g., many large mammals) in which females can produce only one offspring per cycle, female Nb = ∞ and overall Nb = 4Nb (male) . Intermittent breeding reduces the pool of female breeders, which reduces both female and overall Nb reductions are larger in high-fecundity species with high juvenile mortality and increase when multiple reproductive cycles are skipped. Simulated data for six model species showed that both intermittent breeding and litter-size constraints increase Ne , but only slightly. We show how to quantitatively account for these effects, which are important to consider when (1) using Nb to estimate Ne , or (2) drawing inferences about male reproductive success based on estimates of female Nb .
MeSH term(s)	Animals ; Breeding ; Clutch Size/genetics ; Female ; Fertility/genetics ; Litter Size/genetics ; Male ; Models, Genetic ; Population/genetics ; Reproduction/genetics
Language	English
Publishing date	2014-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2036375-8
ISSN	1558-5646 ; 0014-3820 ; 0014-3820
ISSN (online)	1558-5646
ISSN	0014-3820
DOI	10.1111/evo.12384
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Article ; Online: Follicular Helper T Cells Are Major Human Immunodeficiency Virus-2 Reservoirs and Support Productive Infection.

Godinho-Santos, Ana / Foxall, Russell B / Antão, Ana V / Tavares, Bárbara / Ferreira, Tiago / Serra-Caetano, Ana / Matoso, Paula / Sousa, Ana E

The Journal of infectious diseases

2019 Volume 221, Issue 1, Page(s) 122–126

Abstract: Follicular helper T cells (Tfh), CD4 lymphocytes critical for efficient antibody responses, have been shown to be key human immunodeficiency virus (HIV)-1 reservoirs. Human immunodeficiency virus-2 infection represents a unique naturally occurring model ... ...

Abstract	Follicular helper T cells (Tfh), CD4 lymphocytes critical for efficient antibody responses, have been shown to be key human immunodeficiency virus (HIV)-1 reservoirs. Human immunodeficiency virus-2 infection represents a unique naturally occurring model for investigating Tfh role in HIV/acquired immune deficiency syndrome, given its slow rate of CD4 decline, low to undetectable viremia, and high neutralizing antibody titers throughout the disease course. In this study, we investigated, for the first time, Tfh susceptibility to HIV-2 infection by combining in vitro infection of tonsillar Tfh with the ex vivo study of circulating Tfh from HIV-2-infected patients. We reveal that Tfh support productive HIV-2 infection and are preferential viral targets in HIV-2-infected individuals.
MeSH term(s)	DNA, Viral/metabolism ; Female ; HIV Infections/immunology ; HIV Infections/virology ; HIV-1/physiology ; HIV-2/physiology ; Humans ; Middle Aged ; Palatine Tonsil/immunology ; Palatine Tonsil/pathology ; Primary Cell Culture ; RNA, Messenger/metabolism ; Receptors, CCR5/metabolism ; Receptors, CXCR4/metabolism ; T-Lymphocytes, Helper-Inducer/metabolism ; T-Lymphocytes, Helper-Inducer/virology ; Viral Tropism ; gag Gene Products, Human Immunodeficiency Virus/genetics
Chemical Substances	CCR5 protein, human ; CXCR4 protein, human ; DNA, Viral ; RNA, Messenger ; Receptors, CCR5 ; Receptors, CXCR4 ; gag Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2019-09-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiz431
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Article ; Online: Policy options for deploying anti-malarial drugs in endemic countries: a population genetics approach.

Antao, Tiago / Hastings, Ian

Malaria journal

2012 Volume 11, Page(s) 422

Abstract: Background: Anti-malarial drugs are constantly exposed to the threat of evolving drug resistance so good stewardship of existing therapy is an essential component of public health policy. However, the widespread availability of numerous different drugs ... ...

Abstract	Background: Anti-malarial drugs are constantly exposed to the threat of evolving drug resistance so good stewardship of existing therapy is an essential component of public health policy. However, the widespread availability of numerous different drugs through informal providers could undermine official drug deployment policies. A policy of multiple first-line therapy (MFT) is compared with the conventional policy of sequential drug deployment, i.e., where one drug is used until resistance evolves and then replaced by the next drug in the sequence. Methods: Population genetic models of drug resistance are used to make the comparison; this methodology explicitly tracks the genetics of drug resistance (including, importantly, recombination in the sexual stage, intrahost dynamics, and direction of linkage disequilibrium). Results: A policy of MFT outlasts sequential application providing drug usages are low to moderate, and appears not to drive widespread multi-drug resistance. Inadequate dosing is an even more potent driver of drug resistance than the MFT/sequential policy decision. Conclusions: The provision of MFT as a deliberate policy can be encouraged provided overall treatment rates are low or moderate (less than around half of malaria infections are treated) and the ad hoc provision of MFT through the private sector may be tolerated. This must be fully supported by education to ensure people take adequate doses of each of the drugs.
MeSH term(s)	Antimalarials/administration & dosage ; Antimalarials/therapeutic use ; Drug Resistance/genetics ; Drug Resistance, Multiple/genetics ; Drug Therapy, Combination ; Endemic Diseases ; Epistasis, Genetic ; Genetics, Population ; Health Policy ; Humans ; Linkage Disequilibrium ; Malaria/drug therapy ; Malaria/epidemiology ; Malaria/parasitology ; Models, Genetic ; Plasmodium/drug effects ; Plasmodium/genetics
Chemical Substances	Antimalarials
Language	English
Publishing date	2012-12-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2091229-8
ISSN	1475-2875 ; 1475-2875
ISSN (online)	1475-2875
ISSN	1475-2875
DOI	10.1186/1475-2875-11-422
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Article ; Online: Niche partitioning of microbial communities in riverine floodplains

Marc Peipoch / Scott R. Miller / Tiago R. Antao / H. Maurice Valett

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 13

Abstract: Abstract Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the ... ...

Abstract	Abstract Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H’: 2.8–4.1) nor β (Sørensen: 0.3–0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
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Article ; Online: ogaraK: a population genetics simulator for malaria.

Antao, Tiago / Hastings, Ian M

Bioinformatics (Oxford, England)

2011 Volume 27, Issue 9, Page(s) 1335–1336

Abstract: Motivation: The evolution of resistance in Plasmodium falciparum malaria against most available treatments is a major global health threat. Population genetics approaches are commonly used to model the spread of drug resistance. Due to uncommon features ...

Abstract	Motivation: The evolution of resistance in Plasmodium falciparum malaria against most available treatments is a major global health threat. Population genetics approaches are commonly used to model the spread of drug resistance. Due to uncommon features in malaria biology, existing forward-time population genetics simulators cannot suitably model Plasmodium falciparum malaria. Results: Here we present ogaraK, a population genetics simulator for modelling the spread of drug-resistant malaria. OgaraK is designed to make malaria simulation computationally tractable as it models infections, not individual parasites. OgaraK is also able to model the life cycle of the parasite which includes both haploid and diploid phases and sexual and asexual reproduction. We also allow for the simulation of different inbreeding levels, an important difference between high and low transmission areas and a fundamental factor influencing the outcome of strategies to control or eliminate malaria. Availability: OgaraK is available as free software (GPL) from the address http://popgen.eu/soft/ogaraK.
MeSH term(s)	Computer Simulation ; Drug Resistance/genetics ; Genes, Protozoan ; Genetics, Population/methods ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/parasitology ; Plasmodium falciparum/drug effects ; Plasmodium falciparum/genetics ; Software
Language	English
Publishing date	2011-05-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btr139
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