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Article ; Online: Author Correction: Shallow shotgun sequencing reduces technical variation in microbiome analysis.

La Reau, Alex J / Strom, Noah B / Filvaroff, Ellen / Mavrommatis, Konstantinos / Ward, Tonya L / Knights, Dan

2024 Volume 14, Issue 1, Page(s) 6116

Language	English
Publishing date	2024-03-13
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-56475-7
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Article ; Online: Shallow shotgun sequencing reduces technical variation in microbiome analysis.

La Reau, Alex J / Strom, Noah B / Filvaroff, Ellen / Mavrommatis, Konstantinos / Ward, Tonya L / Knights, Dan

Scientific reports

2023 Volume 13, Issue 1, Page(s) 7668

Abstract: The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual ... ...

Abstract	The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive alternative for small studies, but can be cost-prohibitive for biomarker discovery in large populations. Shallow or moderate-depth shotgun metagenomics may serve as a viable alternative to 16S sequencing for large-scale and/or dense longitudinal studies, but only if resolution and reproducibility are comparable. Here we applied both 16S and shallow shotgun stool microbiome sequencing to a cohort of 5 subjects sampled twice daily and weekly, with technical replication at the DNA extraction and the library preparation/sequencing steps, for a total of 80 16S samples and 80 shallow shotgun sequencing samples. We found that shallow shotgun sequencing produced lower technical variation and higher taxonomic resolution than 16S sequencing, at a much lower cost than deep shotgun sequencing. These findings suggest that shallow shotgun sequencing provides a more specific and more reproducible alternative to 16S sequencing for large-scale microbiome studies where costs prohibit deep shotgun sequencing and where bacterial species are expected to have good coverage in whole-genome reference databases.
MeSH term(s)	Humans ; Reproducibility of Results ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Bacteria/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Metagenomics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-05-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-33489-1
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Article: Two genomes are better than one: history, genetics, and biotechnological applications of fungal heterokaryons.

Strom, Noah B / Bushley, Kathryn E

Fungal biology and biotechnology

2016 Volume 3, Page(s) 4

Abstract: Heterokaryosis is an integral part of the parasexual cycle used by predominantly asexual fungi to introduce and maintain genetic variation in populations. Research into fungal heterokaryons began in 1912 and continues to the present day. Heterokaryosis ... ...

Abstract	Heterokaryosis is an integral part of the parasexual cycle used by predominantly asexual fungi to introduce and maintain genetic variation in populations. Research into fungal heterokaryons began in 1912 and continues to the present day. Heterokaryosis may play a role in the ability of fungi to respond to their environment, including the adaptation of arbuscular mycorrhizal fungi to different plant hosts. The parasexual cycle has enabled advances in fungal genetics, including gene mapping and tests of complementation, dominance, and vegetative compatibility in predominantly asexual fungi. Knowledge of vegetative compatibility groups has facilitated population genetic studies and enabled the design of innovative methods of biocontrol. The vegetative incompatibility response has the potential to be used as a model system to study biological aspects of some human diseases, including neurodegenerative diseases and cancer. By combining distinct traits through the formation of artificial heterokaryons, fungal strains with superior properties for antibiotic and enzyme production, fermentation, biocontrol, and bioremediation have been produced. Future biotechnological applications may include site-specific biocontrol or bioremediation and the production of novel pharmaceuticals.
Language	English
Publishing date	2016-05-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2806612-1
ISSN	2054-3085
ISSN	2054-3085
DOI	10.1186/s40694-016-0022-x
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Article: In Vitro Screening of a Culturable Soybean Cyst Nematode Cyst Mycobiome for Potential Biological Control Agents and Biopesticides.

Haarith, Deepak / Kim, Dong-Gyu / Strom, Noah B / Chen, Senyu / Bushley, Kathryn E

Phytopathology

2020 Volume 110, Issue 8, Page(s) 1388–1397

Abstract: Fungal biological control of soybean cyst nematodes (SCN) is an important component of integrated pest management for soybean. However, very few fungal biological control agents are available in the market. In this study, we have screened fungi ... ...

Abstract	Fungal biological control of soybean cyst nematodes (SCN) is an important component of integrated pest management for soybean. However, very few fungal biological control agents are available in the market. In this study, we have screened fungi previously isolated from SCN cysts over 3 years from a long-term crop rotation field experiment for their ability to antagonize SCN using (i) parasitism, (ii) egg hatch inhibition, and (iii) J2 mortality. We evaluated egg parasitism using an in-vitro egg parasitism bioassays and scored parasitism using the egg parasitic index (EPI) and fluorescent microscopy. The ability of these fungi to produce metabolites causing egg hatch inhibition and J2 mortality was assessed in bioassays using filter-sterilized culture filtrates. We identified 10 high-performing isolates each for egg parasitism and toxicity toward SCN eggs and J2s and repeated the tests after storage for 1 year of cryopreservation at -80°C to validate the durability of biocontrol potential of the chosen 20 isolates. Although the parasitic ability changed slightly for the majority of strains after cryopreservation, they still scored 5/10 on EPI scales. There were no differences in the ability of fungi to produce antinemic metabolites after cryopreservation.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
MeSH term(s)	Animals ; Biological Control Agents ; Cysts ; Mycobiome ; Nematoda ; Plant Diseases ; Glycine max
Chemical Substances	Biological Control Agents
Language	English
Publishing date	2020-06-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-01-20-0015-R
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Article ; Online: Eubacterium coprostanoligenes and Methanoculleus identified as potential producers of metabolites that contribute to swine manure foaming.

Strom, Noah / Ma, Yiwei / Bi, Zheting / Andersen, Daniel / Trabue, Steve / Chen, Chi / Hu, Bo

Journal of applied microbiology

2021 Volume 132, Issue 4, Page(s) 2906–2924

Abstract: Aim: Swine manure foaming is a major problem, causing damage to property, livestock, and people. Here, we identified the main chemicals and microbes that contribute to foaming.: Methods and results: Foaming and non-foaming swine manure were sampled ... ...

Abstract	Aim: Swine manure foaming is a major problem, causing damage to property, livestock, and people. Here, we identified the main chemicals and microbes that contribute to foaming. Methods and results: Foaming and non-foaming swine manure were sampled from farms in Iowa and Illinois. Targeted and untargeted metabolomics analyses identified chemical markers that differed between foaming and non-foaming manure and between manure layers. Microbial community analysis and metagenomics were performed on a subset of samples. Foam contained significantly higher levels of total bile acids and long chain fatty acids like palmitic, stearic and oleic acid than the other manure layers. Foam layers also had significantly higher levels of ubiquinone 9 and ubiquinone 10. The slurry layer of foaming samples contained more alanine, isoleucine/leucine, diacylglycerols (DG), phosphtatidylethanolamines, and vitamin K2, while ceramide was significantly increased in the slurry layer of non-foaming samples. Eubacterium coprostanoligenes and Methanoculleus were more abundant in foaming samples, and E. coprostanoligenes was significantly correlated with levels of DG. Genes involved in diacylglycerol biosynthesis and in the biosynthesis of branched-chain hydrophobic amino acids were overrepresented in foaming samples. Conclusions: A mechanism for manure foaming is hypothesized in which proliferation of Methanoculleus leads to excessive production of methane, while production of DG by E. coprostanoligenes and hydrophobic proteins by Methanosphaera stadtmanae facilitates bubble formation and stabilization. Significance and impact of study: While some chemical and biological treatments have been developed to treat swine manure foaming, its causes remain unknown. We identified key microbes and metabolites that correlate with foaming and point to possible roles of other factors like animal feed.
MeSH term(s)	Animals ; Eubacterium/metabolism ; Humans ; Manure/microbiology ; Methane/metabolism ; Methanomicrobiaceae/genetics ; Swine
Chemical Substances	Manure ; Methane (OP0UW79H66)
Language	English
Publishing date	2021-12-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1358023-1
ISSN	1365-2672 ; 1364-5072
ISSN (online)	1365-2672
ISSN	1364-5072
DOI	10.1111/jam.15384
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Article ; Online: Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes.

Goodrich, Julia K / Singer-Berk, Moriel / Son, Rachel / Sveden, Abigail / Wood, Jordan / England, Eleina / Cole, Joanne B / Weisburd, Ben / Watts, Nick / Caulkins, Lizz / Dornbos, Peter / Koesterer, Ryan / Zappala, Zachary / Zhang, Haichen / Maloney, Kristin A / Dahl, Andy / Aguilar-Salinas, Carlos A / Atzmon, Gil / Barajas-Olmos, Francisco /

Barzilai, Nir / Blangero, John / Boerwinkle, Eric / Bonnycastle, Lori L / Bottinger, Erwin / Bowden, Donald W / Centeno-Cruz, Federico / Chambers, John C / Chami, Nathalie / Chan, Edmund / Chan, Juliana / Cheng, Ching-Yu / Cho, Yoon Shin / Contreras-Cubas, Cecilia / Córdova, Emilio / Correa, Adolfo / DeFronzo, Ralph A / Duggirala, Ravindranath / Dupuis, Josée / Garay-Sevilla, Ma Eugenia / García-Ortiz, Humberto / Gieger, Christian / Glaser, Benjamin / González-Villalpando, Clicerio / Gonzalez, Ma Elena / Grarup, Niels / Groop, Leif / Gross, Myron / Haiman, Christopher / Han, Sohee / Hanis, Craig L / Hansen, Torben / Heard-Costa, Nancy L / Henderson, Brian E / Hernandez, Juan Manuel Malacara / Hwang, Mi Yeong / Islas-Andrade, Sergio / Jørgensen, Marit E / Kang, Hyun Min / Kim, Bong-Jo / Kim, Young Jin / Koistinen, Heikki A / Kooner, Jaspal Singh / Kuusisto, Johanna / Kwak, Soo-Heon / Laakso, Markku / Lange, Leslie / Lee, Jong-Young / Lee, Juyoung / Lehman, Donna M / Linneberg, Allan / Liu, Jianjun / Loos, Ruth J F / Lyssenko, Valeriya / Ma, Ronald C W / Martínez-Hernández, Angélica / Meigs, James B / Meitinger, Thomas / Mendoza-Caamal, Elvia / Mohlke, Karen L / Morris, Andrew D / Morrison, Alanna C / Ng, Maggie C Y / Nilsson, Peter M / O'Donnell, Christopher J / Orozco, Lorena / Palmer, Colin N A / Park, Kyong Soo / Post, Wendy S / Pedersen, Oluf / Preuss, Michael / Psaty, Bruce M / Reiner, Alexander P / Revilla-Monsalve, Cristina / Rich, Stephen S / Rotter, Jerome I / Saleheen, Danish / Schurmann, Claudia / Sim, Xueling / Sladek, Rob / Small, Kerrin S / So, Wing Yee / Spector, Timothy D / Strauch, Konstantin / Strom, Tim M / Tai, E Shyong / Tam, Claudia H T / Teo, Yik Ying / Thameem, Farook / Tomlinson, Brian / Tracy, Russell P / Tuomi, Tiinamaija / Tuomilehto, Jaakko / Tusié-Luna, Teresa / van Dam, Rob M / Vasan, Ramachandran S / Wilson, James G / Witte, Daniel R / Wong, Tien-Yin / Burtt, Noël P / Zaitlen, Noah / McCarthy, Mark I / Boehnke, Michael / Pollin, Toni I / Flannick, Jason / Mercader, Josep M / O'Donnell-Luria, Anne / Baxter, Samantha / Florez, Jose C / MacArthur, Daniel G / Udler, Miriam S

Nature communications

2021 Volume 12, Issue 1, Page(s) 3505

Abstract: Hundreds of thousands of genetic variants have been reported to cause severe monogenic diseases, but the probability that a variant carrier develops the disease (termed penetrance) is unknown for virtually all of them. Additionally, the clinical utility ... ...

Abstract	Hundreds of thousands of genetic variants have been reported to cause severe monogenic diseases, but the probability that a variant carrier develops the disease (termed penetrance) is unknown for virtually all of them. Additionally, the clinical utility of common polygenetic variation remains uncertain. Using exome sequencing from 77,184 adult individuals (38,618 multi-ancestral individuals from a type 2 diabetes case-control study and 38,566 participants from the UK Biobank, for whom genotype array data were also available), we apply clinical standard-of-care gene variant curation for eight monogenic metabolic conditions. Rare variants causing monogenic diabetes and dyslipidemias display effect sizes significantly larger than the top 1% of the corresponding polygenic scores. Nevertheless, penetrance estimates for monogenic variant carriers average 60% or lower for most conditions. We assess epidemiologic and genetic factors contributing to risk prediction in monogenic variant carriers, demonstrating that inclusion of polygenic variation significantly improves biomarker estimation for two monogenic dyslipidemias.
MeSH term(s)	Adult ; Biological Variation, Population ; Biomarkers/metabolism ; Diabetes Mellitus, Type 2/genetics ; Diabetes Mellitus, Type 2/metabolism ; Dyslipidemias/genetics ; Dyslipidemias/metabolism ; Exome/genetics ; Genetic Predisposition to Disease/genetics ; Genotype ; Humans ; Multifactorial Inheritance ; Penetrance ; Risk Assessment
Chemical Substances	Biomarkers
Language	English
Publishing date	2021-06-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-23556-4
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Article ; Online: Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes

Julia K. Goodrich / Moriel Singer-Berk / Rachel Son / Abigail Sveden / Jordan Wood / Eleina England / Joanne B. Cole / Ben Weisburd / Nick Watts / Lizz Caulkins / Peter Dornbos / Ryan Koesterer / Zachary Zappala / Haichen Zhang / Kristin A. Maloney / Andy Dahl / Carlos A. Aguilar-Salinas / Gil Atzmon / Francisco Barajas-Olmos /

Nir Barzilai / John Blangero / Eric Boerwinkle / Lori L. Bonnycastle / Erwin Bottinger / Donald W. Bowden / Federico Centeno-Cruz / John C. Chambers / Nathalie Chami / Edmund Chan / Juliana Chan / Ching-Yu Cheng / Yoon Shin Cho / Cecilia Contreras-Cubas / Emilio Córdova / Adolfo Correa / Ralph A. DeFronzo / Ravindranath Duggirala / Josée Dupuis / Ma Eugenia Garay-Sevilla / Humberto García-Ortiz / Christian Gieger / Benjamin Glaser / Clicerio González-Villalpando / Ma Elena Gonzalez / Niels Grarup / Leif Groop / Myron Gross / Christopher Haiman / Sohee Han / Craig L. Hanis / Torben Hansen / Nancy L. Heard-Costa / Brian E. Henderson / Juan Manuel Malacara Hernandez / Mi Yeong Hwang / Sergio Islas-Andrade / Marit E. Jørgensen / Hyun Min Kang / Bong-Jo Kim / Young Jin Kim / Heikki A. Koistinen / Jaspal Singh Kooner / Johanna Kuusisto / Soo-Heon Kwak / Markku Laakso / Leslie Lange / Jong-Young Lee / Juyoung Lee / Donna M. Lehman / Allan Linneberg / Jianjun Liu / Ruth J. F. Loos / Valeriya Lyssenko / Ronald C. W. Ma / Angélica Martínez-Hernández / James B. Meigs / Thomas Meitinger / Elvia Mendoza-Caamal / Karen L. Mohlke / Andrew D. Morris / Alanna C. Morrison / Maggie C. Y. Ng / Peter M. Nilsson / Christopher J. O’Donnell / Lorena Orozco / Colin N. A. Palmer / Kyong Soo Park / Wendy S. Post / Oluf Pedersen / Michael Preuss / Bruce M. Psaty / Alexander P. Reiner / Cristina Revilla-Monsalve / Stephen S. Rich / Jerome I. Rotter / Danish Saleheen / Claudia Schurmann / Xueling Sim / Rob Sladek / Kerrin S. Small / Wing Yee So / Timothy D. Spector / Konstantin Strauch / Tim M. Strom / E. Shyong Tai / Claudia H. T. Tam / Yik Ying Teo / Farook Thameem / Brian Tomlinson / Russell P. Tracy / Tiinamaija Tuomi / Jaakko Tuomilehto / Teresa Tusié-Luna / Rob M. van Dam / Ramachandran S. Vasan / James G. Wilson / Daniel R. Witte / Tien-Yin Wong / AMP-T2D-GENES Consortia / Noël P. Burtt / Noah Zaitlen / Mark I. McCarthy / Michael Boehnke / Toni I. Pollin / Jason Flannick / Josep M. Mercader / Anne O’Donnell-Luria / Samantha Baxter / Jose C. Florez / Daniel G. MacArthur / Miriam S. Udler

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 15

Abstract: Penetrance of variants in monogenic disease and clinical utility of common polygenic variation has not been well explored on a large-scale. Here, the authors use exome sequencing data from 77,184 individuals to generate penetrance estimates and assess ... ...

Abstract	Penetrance of variants in monogenic disease and clinical utility of common polygenic variation has not been well explored on a large-scale. Here, the authors use exome sequencing data from 77,184 individuals to generate penetrance estimates and assess the utility of polygenic variation in risk prediction of monogenic variants.
Keywords	Science ; Q
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Chiropractic treatment of hand and wrist pain in older people: systematic protocol development Part 2: cohort natural-history treatment trial.

Hulbert, James R / Osterbauer, Paul / Davis, P Thomas / Printon, Richard / Goessl, Casey / Strom, Noah

Journal of chiropractic medicine

2009 Volume 6, Issue 1, Page(s) 32–41

Abstract: ... b) the variety of hand-wrist conditions presented by older patients; (c) the accommodations ...

Abstract	Objectives: This study examines (a) the feasibility of continued research with an older population; (b) the variety of hand-wrist conditions presented by older patients; (c) the accommodations to standard chiropractic treatment for older patients; and (d) the validity, reliability, responsiveness of measures, and preliminary estimates of outcome of treatment for general hand-wrist pain. Methods: A cohort of 55 volunteers, first evaluated over a 5-week natural-history baseline period, was offered 5-week chiropractic treatment and then interviewed at 6 months posttreatment. Descriptive and preliminary inferential analyses are reported. Start values for power analysis are offered. Results: The project recruited a sample of 55 and retained 47 (85%) participants over 8 months, indicating feasibility of a larger project. Participants provided strong self-reported, albeit preliminary, evidence of benefit. Mean values and SDs of pain and strength measures are provided for future power calculations. Conclusions: Clinical research with older participants presenting with hand-wrist pain and dysfunction is feasible. Validity, reliability, and responsiveness of self-reports are demonstrated. The research presents preliminary evidence of the benefit of chiropractic treatment for older patients presenting with hand-wrist symptoms.
Language	English
Publishing date	2009-08-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2365038-2
ISSN	1556-3715 ; 1556-3707
ISSN (online)	1556-3715
ISSN	1556-3707
DOI	10.1016/j.jcme.2007.02.011
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Article ; Online: Leveraging population admixture to characterize the heritability of complex traits.

Zaitlen, Noah / Pasaniuc, Bogdan / Sankararaman, Sriram / Bhatia, Gaurav / Zhang, Jianqi / Gusev, Alexander / Young, Taylor / Tandon, Arti / Pollack, Samuela / Vilhjálmsson, Bjarni J / Assimes, Themistocles L / Berndt, Sonja I / Blot, William J / Chanock, Stephen / Franceschini, Nora / Goodman, Phyllis G / He, Jing / Hennis, Anselm J M / Hsing, Ann /

Nature genetics

2014 Volume 46, Issue 12, Page(s) 1356–1362

Abstract: Despite recent progress on estimating the heritability explained by genotyped SNPs (h(2)g), a large gap between h(2)g and estimates of total narrow-sense heritability (h(2)) remains. Explanations for this gap include rare variants or upward bias in ... ...

Abstract	Despite recent progress on estimating the heritability explained by genotyped SNPs (h(2)g), a large gap between h(2)g and estimates of total narrow-sense heritability (h(2)) remains. Explanations for this gap include rare variants or upward bias in family-based estimates of h(2) due to shared environment or epistasis. We estimate h(2) from unrelated individuals in admixed populations by first estimating the heritability explained by local ancestry (h(2)γ). We show that h(2)γ = 2FSTCθ(1 - θ)h(2), where FSTC measures frequency differences between populations at causal loci and θ is the genome-wide ancestry proportion. Our approach is not susceptible to biases caused by epistasis or shared environment. We applied this approach to the analysis of 13 phenotypes in 21,497 African-American individuals from 3 cohorts. For height and body mass index (BMI), we obtained h(2) estimates of 0.55 ± 0.09 and 0.23 ± 0.06, respectively, which are larger than estimates of h(2)g in these and other data but smaller than family-based estimates of h(2).
MeSH term(s)	Black or African American/genetics ; Aged ; Black People ; Body Mass Index ; Cardiovascular Diseases/genetics ; Case-Control Studies ; Chromosome Mapping ; Cohort Studies ; Computer Simulation ; Epistasis, Genetic ; Female ; Genetics, Population/methods ; Genome-Wide Association Study ; Genotype ; Humans ; Male ; Middle Aged ; Models, Genetic ; Models, Statistical ; Multifactorial Inheritance ; Phenotype ; Polymorphism, Single Nucleotide ; Prostatic Neoplasms/genetics ; Quantitative Trait, Heritable ; Reproducibility of Results ; United States
Language	English
Publishing date	2014-11-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/ng.3139
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