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  • February 21, 2017
  • 09:00 PM
  • 235 views

Redrawing Ratite Relationships

by Jente Ottenburghs in Evolutionary Stories

Scientists have sequenced the DNA of two extinct birds: the moa and the elephantbird. Comparison with their living relatives led to some surprising findings.... Read more »

Maderspacher F. (2017) Evolution: Flight of the Ratites. Current biology : CB, 27(3). PMID: 28171755  

Yonezawa T, Segawa T, Mori H, Campos PF, Hongoh Y, Endo H, Akiyoshi A, Kohno N, Nishida S, Wu J.... (2017) Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites. Current biology : CB, 27(1), 68-77. PMID: 27989673  

  • February 8, 2017
  • 05:36 AM
  • 282 views

Sex, alcohol, and structural variants in fission yeast

by Christophe Dessimoz in Open Reading Frame

Our latest study just came out (Jeffares et al., Nature Comm 2017). In it, we carefully catalogued high-confidence structural variants among all known strains of the fission yeast population, and assessed their impact on spore viability, winemaking and other traits. This post gives a summary and the story behind the paper.

Structural variants (SVs) measure genetic variation beyond single nucleotide changes …

Next generation sequencing is enabling the study of genomic diversity on unprec........ Read more »

Jeffares, D., Jolly, C., Hoti, M., Speed, D., Shaw, L., Rallis, C., Balloux, F., Dessimoz, C., Bähler, J., & Sedlazeck, F. (2017) Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature Communications, 14061. DOI: 10.1038/ncomms14061  

Jeffares, D., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, F., Iqbal, Z., Lau, W., Cheng, T.... (2015) The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nature Genetics, 47(3), 235-241. DOI: 10.1038/ng.3215  

  • January 2, 2017
  • 04:06 AM
  • 374 views

This Month in Blastocystis Research (DEC 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

2016 is coming to an end, and in the last post of the year, I highlight three of the most important articles on Blastocystis published in 2016.... Read more »

Scanlan PD, Knight R, Song SJ, Ackermann G, & Cotter PD. (2016) Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 95-97. PMID: 27545648  

Kurt Ö, Doğruman Al F, & Tanyüksel M. (2016) Eradication of Blastocystis in humans: Really necessary for all?. Parasitology international, 65(6 Pt B), 797-801. PMID: 26780545  

  • December 30, 2016
  • 06:30 PM
  • 355 views

This Month in Blastocystis Research (DEC 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

2016 is coming to an end, and in the last post of the year, I highlight three of the most important articles on Blastocystis published in 2016.... Read more »

Scanlan PD, Knight R, Song SJ, Ackermann G, & Cotter PD. (2016) Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 95-97. PMID: 27545648  

Kurt Ö, Doğruman Al F, & Tanyüksel M. (2016) Eradication of Blastocystis in humans: Really necessary for all?. Parasitology international, 65(6 Pt B), 797-801. PMID: 26780545  

  • December 14, 2016
  • 07:43 AM
  • 356 views

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

by Christian de Guttry in genome ecology evolution etc

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons About 450 mya bony vertebrates radiated into Lobe-finned fish, from which tetrapods appeared later, and Ray-finned fish, which include Teleost (Fig.1). Nowadays they make up to 96 percent of … Continue reading →... Read more »

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J.... (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature genetics, 48(4), 427-37. PMID: 26950095  

  • December 8, 2016
  • 03:14 PM
  • 255 views

ExAC presents a catalogue of human protein-coding genetic variation

by Kamil S. Jaron in genome ecology evolution etc

Exploration of variability of human genomes represents a key step in the holy grail of human genetics – to link genotypes with phenotypes, it also provides insights to human evolution and history. For this purpose Exome Aggregation Consortium (ExAC) have … Continue reading →... Read more »

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB.... (2016) Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285-91. PMID: 27535533  

  • December 8, 2016
  • 09:14 AM
  • 383 views

What are Hierarchical Orthologous Groups (HOGs)?

by Christophe Dessimoz in Open Reading Frame


One central concept in the OMA project and other
work we do to infer relationships between genes is that of Hierarchical
Orthologous Groups, or “HOGs” for the initiated.

We’ve written several papers on aspects pertaining to HOGs—how to infer
them,
how to evaluate them, they being
increasingly adopted by orthology
resources, etc.—but there is
still a great deal of confusion as to what HOGs are and why they matter.

Natasha Glover, talented postdoc in the lab,........ Read more »

Sonnhammer, E., Gabaldon, T., Sousa da Silva, A., Martin, M., Robinson-Rechavi, M., Boeckmann, B., Thomas, P., Dessimoz, C., & , . (2014) Big data and other challenges in the quest for orthologs. Bioinformatics, 30(21), 2993-2998. DOI: 10.1093/bioinformatics/btu492  

  • December 2, 2016
  • 08:30 PM
  • 375 views

This Month in Blastocystis Research (NOV 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

Lab protocols on Blastocystis culture, cryopreservation, and subtyping are now available in Wiley Online Library.... Read more »

  • November 27, 2016
  • 04:16 PM
  • 339 views

Interview with Tunca Doğan, OMA Visiting Fellow 2016

by Christophe Dessimoz in Open Reading Frame

Note: the “Life in the Lab” series features interviews of interns and visitors. This post is by our second 2016 OMA Visiting Fellow Tunca Doğan, who spent a month with us earlier this year. You can follow Tunca on Twitter at @tuncadogan. —Christophe



Please introduce yourself in a few sentences.

My name is Tunca Doğan. I received my PhD in 2013 with a thesis study in the fields of bioinformatics and computational biology where we developed methods for the clustering........ Read more »

  • November 22, 2016
  • 03:43 AM
  • 364 views

Interview with Rosa Fernández, 2016 OMA Visiting Fellow

by Christophe Dessimoz in Open Reading Frame

Note: We are rebooting our “Life in the Lab” series, which features interviews of interns and visitors. This post is by our inaugural OMA Visiting Fellow Rosa Fernández García, who spent a month with us earlier this year. You can follow Rosa on Twitter at @Rosamygale. —Christophe

 

Please introduce yourself and your research interests.

I received my bachelor’s degree in Biology (major in Zoology) at Complutense University in Madrid, Spain. I got my master’s and PhD at the s........ Read more »

Fernández R, Laumer CE, Vahtera V, Libro S, Kaluziak S, Sharma PP, Pérez-Porro AR, Edgecombe GD, & Giribet G. (2014) Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. Molecular biology and evolution, 31(6), 1500-13. PMID: 24674821  

Novo M, Fernández R, Andrade SC, Marchán DF, Cunha L, & Díaz Cosín DJ. (2016) Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae). Molecular phylogenetics and evolution, 94(Pt B), 473-8. PMID: 26522608  

Sharma, P., Fernandez, R., Esposito, L., Gonzalez-Santillan, E., & Monod, L. (2015) Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal. Proceedings of the Royal Society B: Biological Sciences, 282(1804), 20142953-20142953. DOI: 10.1098/rspb.2014.2953  

  • November 10, 2016
  • 06:14 AM
  • 479 views

This Month in Blatstocystis Research (OCT 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

Highlights of the month include a Special Issue on Blastocystis appearing in Parasitology International, a study of mitochondrial genomes, relationships between gut parasites and gut bacteria, and a announcement of an EMBO anaerobic protist conference next year in the UK.... Read more »

Dogruman-Al F, Stensvold CR, & Yoshikawa H. (2016) Editorial - PAR INT - special issue on Blastocystis. Parasitology international, 65(6 Pt B), 749. PMID: 27742000  

Iebba V, Santangelo F, Totino V, Pantanella F, Monsia A, Di Cristanziano V, Di Cave D, Schippa S, Berrilli F, & D'Alfonso R. (2016) Gut microbiota related to Giardia duodenalis, Entamoeba spp. and Blastocystis hominis infections in humans from Côte d'Ivoire. Journal of infection in developing countries, 10(9), 1035-1041. PMID: 27694739  

  • September 9, 2016
  • 10:24 AM
  • 486 views

C9orf72-SMCR8 complex, analogous to FLCN- FNIP, localizes to lysosomes and regulates mTORC1

by Joana Guedes in BHD Research Blog

The DENN protein module contains a longin domain, a DENN domain and a d-DENN domain. Nookala et al. (2012) identified a DENN module in folliculin (FLCN), the Birt-Hogg-Dube tumour suppressor. The DENN module is believed to be a GEF for Rab-GTPases, although FLCN is believed to act as a GAP for RagC (Tsun et al., 2013) as is its yeast homologue, LST7, in interaction with the yeast FNIP homologue Lst4 (Pacitto et al., 2015). A recent bioinformatic study identified DENN domains in several other ........ Read more »

  • September 9, 2016
  • 10:00 AM
  • 522 views

Predicting protein function: what’s new?

by Iddo Friedberg in Byte Size Biology

Long time readers of this blog (hi mom!) know that I am working with many other people in an effort called CAFA: the Critical Assessment of protein Function Annotation. This is a challenge that many research groups participate in, and its goal is to determine how well we can predict a protein function from its amino-acid sequence. The first CAFA challenge (CAFA1) was held in 2010-2011 and published in 2013. We learned several things from CAFA1. First, that the top ranking function prediction pro........ Read more »

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A.... (2016) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome biology, 17(1), 184. PMID: 27604469  

  • September 2, 2016
  • 10:41 AM
  • 535 views

This Month in Blastocystis Research - AUG

by Christen Rune Stensvold in Blastocystis Parasite Blog

About the factors potentially limiting susceptibility to Blastocystis colonisation/infection.... Read more »

Blessmann, J., Ali, I., Ton Nu, P., Dinh, B., Ngo Viet, T., Le Van, A., Clark, C., & Tannich, E. (2003) Longitudinal Study of Intestinal Entamoeba histolytica Infections in Asymptomatic Adult Carriers. Journal of Clinical Microbiology, 41(10), 4745-4750. DOI: 10.1128/JCM.41.10.4745-4750.2003  

Scanlan PD, Stensvold CR, Rajilić-Stojanović M, Heilig HG, De Vos WM, O'Toole PW, & Cotter PD. (2014) The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. FEMS microbiology ecology, 90(1), 326-30. PMID: 25077936  

  • August 12, 2016
  • 05:10 AM
  • 492 views

Simulation study suggests that mutations induce conformational changes in FLCN - possible cause of Birt-Hogg-Dubé syndrome

by Joana Guedes in BHD Research Blog

Germline mutations of the folliculin gene are normally responsible for Birt–Hogg–Dubé (BHD) syndrome. The 3D structure of the C-terminal domain of folliculin (FLCN), folliculin-CT, has been previously determined (Nookala et al., 2012). FLCN is a tumor suppressor and a guanine nucleotide exchange factor (GEF) for Rab35. GEF activity of FLCN towards its GTPase might be essential for cellular processes. Most of the reported FLCN mutations lead to the BHD phenotype (Lim et al., 20........ Read more »

  • August 1, 2016
  • 07:36 PM
  • 639 views

This Month in Blastocystis Research - Interactive Edition

by Christen Rune Stensvold in Blastocystis Parasite Blog

What are your thoughts on Blastocystis carriage and age? Please comment!... Read more »

  • July 13, 2016
  • 10:57 AM
  • 668 views

The Genetic Architecture of Complex Disease

by Daniel Koboldt in Massgenomics

It’s no secret that while genome-wide association studies (GWAS) have implicated thousands of genetic loci in human phenotypes, the variants uncovered collectively explain only a fraction of the observed variance between individuals. The reasons for this “missing heritability” are a subject of vigorous debate in the scientific community. One possible explanation is that rare (low-frequency) variants […]... Read more »

Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, Ma C, Fontanillas P, Moutsianas L, McCarthy DJ.... (2016) The genetic architecture of type 2 diabetes. Nature. PMID: 27398621  

  • June 15, 2016
  • 09:37 AM
  • 572 views

Video Tip of the Week: UCSC Genome Browser Exon-only Mode

by Mary in OpenHelix

The team at UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “multi-region” option.  When it was first launched, I did a tip on how to use that, with some of the things that I noticed […]... Read more »

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A.... (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Research, 44(D1). DOI: 10.1093/nar/gkv1275  

  • June 13, 2016
  • 08:30 PM
  • 674 views

This Month in Blastocystis Research (MAY 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

The May entry of "This Month in Blastocystis Research" focusses especially on the increasing interest in Blastocystis in a gut microbiota context. ... Read more »

Andersen LO, Bonde I, Nielsen HB, & Stensvold CR. (2015) A retrospective metagenomics approach to studying Blastocystis. FEMS microbiology ecology, 91(7). PMID: 26130823  

Stensvold CR, & Clark CG. (2016) Current status of Blastocystis: A personal view. Parasitology international. PMID: 27247124  

O'Brien Andersen L, Karim AB, Roager HM, Vigsnæs LK, Krogfelt KA, Licht TR, & Stensvold CR. (2016) Associations between common intestinal parasites and bacteria in humans as revealed by qPCR. European journal of clinical microbiology . PMID: 27230509  

Ramírez JD, Sánchez A, Hernández C, Flórez C, Bernal MC, Giraldo JC, Reyes P, López MC, García L, Cooper PJ.... (2016) Geographic distribution of human Blastocystis subtypes in South America. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 32-5. PMID: 27034056  

  • June 12, 2016
  • 10:35 PM
  • 839 views

Seeing Through the Skin

by Aurametrix team in Olfactics and Diagnostics

​Human skin emits light (albeit the glow is extremely weak) and a wide variety of small molecules that may be sometimes "sniffed" by dogs or even other humans. These chemicals tell a story about our health and wellness, things we eat and drink, touch and breathe. Mosquitoes use such emissions to assess our "attractiveness" from indicators such as Indoles (unpleasantly smelling but healthy "inner soil" biomarker) or carbon dioxide (amount of which correlates with the size of the person........ Read more »

Gao W, Emaminejad S, Nyein HY, Challa S, Chen K, Peck A, Fahad HM, Ota H, Shiraki H, Kiriya D.... (2016) Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis. Nature, 529(7587), 509-14. PMID: 26819044  

Yokota T, Zalar P, Kaltenbrunner M, Jinno H, Matsuhisa N, Kitanosako H, Tachibana Y, Yukita W, Koizumi M, & Someya T. (2016) Ultraflexible organic photonic skin. Science advances, 2(4). PMID: 27152354  

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