Publications by ESRs

Also released on: ZENODO CERN OPEN ACCESS

see published software here


Aleksei Alekhin | Alexandre Blanckaert | Vedran Bozicevic | Fabian Grandke | Andrea Hatlen | Habib Jan | Evdokim Kovach | Om Kulkarni | Jeannine Marquardt | Soumya Ranganathan | Lizzy Sollars | Alexandra Vatsiou | Jasmin Zohren




Alekhin, Aleksei


Talks:

“Bio4j + Statika: Managing module dependencies on the type level”
Free and Open source Software Developers’ European Meeting. Brussels, Belgium. (FOSDEM 2014) (link)

“Bio4j: bigger, faster, leaner.”
2nd International Work-Conference on Bioinformatics and Biomedical Engineering. Granada Spain. (IWBBIO 2014) abstract

"Bio4j bioinformatics data platform"
Bioinformatics Summer School, St. Petersburg, Russia, (BISS 2014) slides

Posters:

“Statika: managing cloud resources, bioinformatics tools and data.”
2nd International Work-Conference on Bioinformatics and Biomedical Engineering. Granada Spain. (IWBBIO 2014) abstract


"Bio4j: the bioinformatics data platform"
"Statika: managing bioinformatics tools and resources in the cloud"
The XII Symposium on Bioinformatics, Sevilla, Spain, (JdBI 2014) all slides

Publications:

Tobes R, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Kovach E, Alekhin A, Pareja E, (2014)
"Gene calling and bacterial genome annotation with BG7" book chapter.
Bacterial Pangenomics: Methods and Protocols. (link) preprint pdf

Alexey Alekhin, Evdokim Kovach, Marina Manrique, Pablo Pareja-Tobes, Eduardo Pareja, Raquel Tobes, Eduardo Pareja-Tobes (2015)
"MG7: Configurable and scalable 16S metagenomics data analysis" bioRxiv preprint

Software:

Generic tools and libraries:
  • Kovach E, Alekhin A. aws-scala-tools — a Scala library for Amazon Web Services
  • Alekhin A, Kovach E. sbt-s3-resolver — AWS S3 based resolver for the sbt build tool
  • Alekhin A, Pareja-Tobes E. nice-sbt-setting — an sbt plugin with common settings for all era7/ohnosequences releases
  • Alekhin A, Pareja-Tobes E. cosas — a Scala library for type-level sets

Statika project — a set of Scala libraries, which allows to declare dependencies between components of any modular system and track their correctness using Scala type system. statika github org contains all our public statika bundles (for bioinformatics tools). bio4j-modules is a statika-based Bio4j module system.

Loquat project is a framework for creating Amazon-based cloud pipelines for massive parallel computations. It is build on top of the Statika bundles system and is used for nearly all bioinformatics pipelines in Era7. It is based on the Nispero project developed by Evdokim Kovach.

MG7 project is configurable and scalable metagenomics analysis system. It is a chain of various Loquat pipelines that run parallel computations using BLAST and Bio4j for metagenomics taxonomic profiling.

Online:

ITN podcast :http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Blanckaert, Alexandre

Talk:

Blanckaert A. & Hermisson J. (2013),"How Dobzhansky-Muller incompatibilities accumulate in presence of gene flow?"
XIV Congress of the European Society for Evolutionary Biology. Lisbon, Portugal. (ESEB 2013) p878 (pdf)

Short talk + poster:

Blanckaert.A & Hermisson J. (2015), "Adaptation, a Limit to Early Speciation?"
19 Evolutionary Biology Meeting, Marseille, France

Online:

ITN podcast : http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Publication:

Roze D Blanckaert A (2014) Epistasis, pleiotropy, and the mutational load in sexual and asexual populations. Evolution, 68: 1558-5646.


Bozicevic, Vedran


Poster:

Bozicevic V, Wollstein A, Stephan W, (2012) "Local adaptation in cold-resistance phenotypes of European Drosophila melanogaster populations."
University of Munich, Germany. poster

Online:

ITN podcast : http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Grandke, Fabian

Talk:

Grandke, F (2015) "The bioinformatics toolbox for polyploid crops", Plant Breeding Seminar, Giessen, Germany

Software:
http://polyploid.r-forge.r-project.org/ -R/polyploid
https://bitbucket.org/intercrossing/r_polyploid/ - Preliminary code
https://github.com/grafab/pergola - R/pergola

Online:

ITN podcast: __http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts__

Posters:

Grandke F, Ranganathan S, Czech A, Metzler D, de Haan J, (2014), "Bioinformatic tools for polyploid crop data", NBIC 2014, Lunteren, The Netherlands. (NBIC2014) poster

Grandke F, Van Bers N, Czech A, Ranganathan S, Metzler D, (2015), "Fast and Deterministic Linkage Mapping of Polyploids Using an Approximate Calculation of Recombination Frequencies", PAG 2015, San Diego, USA. (PAG2015) poster

Ranganathan S, Grandke F, Metzler D, (2015), "An overview of phasing methods for polyploids", Achievements Meeting, Ghent, Belgium

Publications:

Grandke F, Ranganathan S, Czech A, de Haan JR, Metzler D (2014), "Bioinformatic Tools for Polyploid Crops", Journal of Agricultural Science and Technology B, Volume 4, Number 9, September 2014

Grandke F, Singh P, Heuven HCM , de Haan JR and Metzler D (2016), "Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids: A comparative study in hexaploid chrysanthemum", BMC Genomics, 17:627

Grandke F, Ranganathan S, van Bers N, de Haan JR and Metzler D (2017), "PERGOLA: Fast and Deterministic Linkage Mapping of Polyploids", BMC Bioinformatics, 18:12

Grandke F, Snowdon R, Samans B (2016), "gsrc - an R package for genome structure rearrangement calling", Bioinformatics, btw648

Hatlen, Andrea


Publications:

Ma L, Hatlen A, Kelly LJ, Becher H, Wang W, Kovarik A, Leitch I, & Leitch AR (2015). Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Dependent DNA Methylation (RdDM) Pathway. Genome biology and evolution, evv171.

Verity R, Hatlen A, Marquardt J, and Zohren J (2013). From hybrids to hermaphrodites in population genetics. Genome Biology, 14:301.

Poster:

Hatlen A, Wagner G, Samans B, Nichols R, and Snowdon R (2014). "Using miRNA in Quantitative Trait Analysis - Brassica napus". PAG 2015 (Poster)

Online:

ITN podcast : http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Software:

miRcounts - For calculating miRNA expression from raw small RNA sequence data :
https://github.com/SBCSnicholsLab/miRcounts

Jan, Habib

Publication(s)
Jan HU, Abbadi A, Lücke S, Nichols RA, Snowdon RJ (2016) Genomic Prediction of Testcross Performance in Canola (Brassica napus). PLoS ONE 11(1): e0147769. doi:10.1371/journal.pone.0147769
Bonnet-Garner et al.2013 "Genome organization and epigenetic marks in mouse germinal vesicle oocytes".Int. J. Dev. Biol. 56: 877-887 (2012)
doi: 10.1387/ijdb.120149ab

Poster:

1. Jan H, Snowdon R, and Nichols R, (2014) "Genome-wide prediction in Brassica napus L."47th Population Genetics Group Meeting (PopGroup47). Bath, UK.(PopGroup47) poster
2. Participated in "Nature Live" show in Natural History Museum (NHM) in London on 15/10/2014 and explained about his current research to common audience.

Online:

ITN podcast : http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Kovach, Evdokim


Talk:

Kovach E, Alekhin A, Manrique M, Pareja-Tobes P, Pareja E, Tobes R, Pareja-Tobes E, (2014)
“MG7: A fast horizontally scalable tool based on cloud computing and graph databases for microbial community profiling”
2nd International Work-Conference on Bioinformatics and Biomedical Engineering. Granada, Spain. (IWBBIO 2014) abstract


Publications - Book Chapter:

Tobes R, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Kovach E, Alekhin A, Pareja E, (2014)
“Gene calling and bacterial genome annotation with BG7” accepted for publication. Bacterial Pangenomics: Methods and Protocols. (link) preprint pdf

Poster:

Kovach E, Alekhin A, Manrique M, Pareja-Tobes P, Pareja E, Tobes R, Pareja-Tobes E, (2014)
“Nispero: a cloud-computing based Scala tool specially suited for bioinformatics data processin
2nd International Work-Conference on Bioinformatics and Biomedical Engineering, Granada Spain. (IWBBIO 2014) abstract

Marina Manrique, Pablo Pareja-Tobes, Evdokim Kovach, Alexey Alekhin, Eduardo Pareja, Eduardo Pareja-Tobes, Raquel Tobes, (2014)
"MG7: A scalable fast tool based on cloud computing and graph databases for microbial community profiling"
24th European Congress of Clinical Microbiology and Infectious Diseases. Barcelona, Spain. http://www.eccmid.org abstract accepted.


Software:

Generic tools and libraries:
  • Kovach E, Alekhin A. aws-scala-tools — a Scala library for Amazon Web Services
  • Kovach E. ivy-s3-resolver — an Ivy resolver that supports publishing to S3 objects
  • Alekhin A, Kovach E. sbt-s3-resolver — AWS S3 based resolver for the sbt build tool
  • Alekhin A, Pareja-Tobes E. nice-sbt-setting — an sbt plugin with common settings for all era7/ohnosequences releases
  • Alekhin A, Pareja-Tobes E. typesets — a Scala library for type-level sets
  • Kovach E, Alekhin A, Pareja-Tobes E. learning-scala — advanced, in-depth materials about specific topics that we found important about coding in Scala

Kovach E. Nispero project — a Scala library for declaring stateless computations and scaling them using a combination of services from AWS
Kovach E, Pareja-Tobes E. fastapasta — a tool to split FASTA files and prepare the tasks JSON file for running a lot of Blast processes in Nispero
Kovach E, Pareja-Tobes E. metapasta — a tool for metagenomics analysis using Nispero

Online:

ITN podcast : http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Kulkarni, Om


Publication:

Larrat S, Kulkarni O, Claude J-B, Beugnot R, Blum MGB, Fusillier K, Lupo J, Tremeaux P, Plages A, Marlu A, Duborjal H, Signori-Schmuck A, Francois O, Zarski J-P, Morand P, Leroy V. (2015)
"Ultradeep pyrosequencing of NS3 to predict response to triple therapy with protease inhibitors in previously treated chronic hepatitis C patients."
Journal of Clinical Microbiology, 53:389–397. doi:10.1128/JCM.02547-14.

Poster:

Kulkarni O, François O, Morand P, Blum M, Larrat S. (2013)
"Estimation of genetic diversity in NS3-protease region of Hepatitis C Virus using 454 pyrosequencing."
European Human Genetics Conference 2013 . Paris,France. (ESHG 2013) Poster

Kulkarni O, François O, Morand P, Blum M, Larrat S. (2013)
"Estimation of genetic diversity in NS3-protease region of Hepatitis C Virus using 454 pyrosequencing."
Infectious Disease Genomics and Global Health conference 2013. Cambridge,UK. (IDGGH 2013) Poster

Online:

ITN podcast

Marquardt, Jeannine

Talk:

Marquardt J, Blanckaert A, Ansell SW, Hermisson J, Metzler D, Leitch AR, Nichols RA , Schneider H. (2015) "Hybrid advantage found in bluebells (Hyacinthoides spec.) from a hybrid zone in Nothern Spain"
Popgroup49 Edinburgh, Uk. (website)

Marquardt J, Ansell SW, Leitch AR, Nichols RA , Schneider H. (2015) "Hybridisation in bluebells (Hyacinthoides spec.)"
Annual Student Conference of the Natural History Museum London, UK.

Publication:

Verity R, Hatlen A, Marquardt J, and Zohren J. (2013) From hybrids to hermaphrodites in population genetics. Genome Biology, 14:301.

Poster:

Marquardt J, Metzler D, Schneider H. (2013) "Integrative DNA taxonomy reveals cryptic fern diversity"
Biosyst.EU 2013. Vienna, Austria. (website) poster
Marquardt J, Leitch AR, Nichols RA, Schneider H. (2013) "Hybridisation between the British bluebell (Hyacinthoides non-scripta) and the Spanish bluebell (H. hispanica)"
SMBE 2015. Vienna, Austria. (http://smbe2015.at/, poster)

Online:

ITN podcast : http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Ranganathan, Soumya

Software:

Ranganathan S. https://github.com/soumya1000/polyphase - Code for phasing polyploids and for evaluating Phasing methods.

Online:

ITN podcast:http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Poster:

Grandke F, Ranganathan S, Czech A, Metzler D, de Haan J, (2014), "Bioinformatic tools for polyploid crop data", NBIC 2014,
Lunteren, The Netherlands. (NBIC2014) poster

Grandke F, Van Bers N, Czech A, Ranganathan S, Metzler D, (2015), "Fast and Deterministic Linkage Mapping of Polyploids Using an Approximate Calculation of Recombination Frequencies", PAG 2015, San Diego, USA. (PAG2015) poster

Ranganathan S, Grandke F, Czech A, Metzler D, (2015), "An overview of phasing methods for polyploids", Achievements Meeting, Ghent, Belgium. Poster.

Publication:

Grandke F, Ranganathan S, Czech A, de Haan JR, Metzler D (2014), "Bioinformatic Tools for Polyploid Crops", Journal of Agricultural Science and Technology B, (accepted)

Sollars, Lizzy


Talks:

Sollars ESA, Zohren J, Boshier D, Clark J, Joecker A, Buggs RJA,(2014) "Sequencing the genome of Fraxinus excelsior (European Ash)
International Plant & Animal Genome XXII San Diego, CA, USA. (PAG XXII) Abstract PDF

Sollars, ESA, Kelly, L., Clavijo, B., Swarbreck, D., Zohren, J., Boshier, D., Clark, J., Joecker, A., Ayling, S., Caccamo, M., Buggs, RJA (2015)
The Genome of Fraxinus excelsior (European Ash). International Plant & Animal Genome conference XXIII. San Diego, USA. PDF

Sollars, ESA, Kelly, L., Clavijo, B., Swarbreck, D., Zohren, J., Boshier, D., Lee, S., Clark, J., Joecker, A., Ayling, S., Caccamo, M., Buggs, RJA (2015)
Collaboration on the genome of Fraxinus excelsior (European Ash). DEFRA Ash Dieback Research Oversight Group meeting, London, UK. PDF

Posters:

Zohren J, Sollars ESA, Clark J, Boshier D, Joecker A, and Buggs RJA, (2013)"Sequencing the genome of Fraxinus excelsior (European Ash).
XIV Congress of the European Society for Evolutionary Biology. Lisbon, Portugal. (ESEB 2013) poster

Sollars ESA, Zohren J, Boshier D, Clark J, Joecker A, and Buggs RJA, (2013) "Sequencing the genome of Fraxinus excelsior (European Ash)."
International Plant & Animal Genome XXII, San Diego, CA, USA. (PAG XXII) poster

Sollars ESA, Zohren J, Boshier D, Clark J, Joecker A, and Buggs RJA, (2014) "Sequencing the genome of Fraxinus excelsior (European Ash)."
47th Population Genetics Group Meeting. Bath, UK. (PopGroup47) poster

Sollars ESA, Kelly, L.J., Swarbreck, D., et al (2015) "Genome sequencing of Fraxinus species to identify loci relevant to ash dieback and emerald ash borer"
35th New Phytologist Symposium: The genomes of forest trees: new frontiers of forest biology, Boston, MA, USA. (35th NPS)

Online:

Sollars, E. Tips & Tricks - Helpful videos for users of the CLC workbenches.
ITN podcast: http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts
Sollars, E. CLC bio press release on ash tree genome research. (2013).

Publications:

In review: Sollars, E.S.A., Harper, A.L., Kelly, L.J. et al. Genome sequence and diversity of European ash trees threatened by ash dieback.

In press: Sollars, E.S.A. & Buggs, R.J.A. Emerging genomics of angiosperm trees. Chapter in: Comparative and Evolutionary Genomics of Angiosperm Trees. Editors: Quentin Cronk & Andrew Groover.

Harper, A.L., McKinney, L.V., Nielsen, L.R., Havlickova, L., Li, Y., Trick, M., Fraser, F., Wang, L., Fellgett, A., Sollars, E.S.A. et al (2016) Molecular Markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using associative transcriptomics. Scientific Reports 6, Article no. 19335

Vatsiou, Alexandra


Talk:

"Comparison of Haplotype Methods to detect selection." ( 2013), TIMC, Grenoble, France. ( http://membres-timc.imag.fr/Nicolas.Thierry-Mieg/jc_bcm.html).
"Comparison of Haplotype Methods to detect selection." (2013), Vienna at MABS. (http://www.mabs.at/)

Posters:

Vatsiou, A. Melodelima, C. Bazin, E. Gaggiotti, O. (2013) "Comparison of Haplotype Methods to detectselection."
XIV Congress of the European Society for Evolutionary Biology. Lisbon, Portugal. (ESEB 2013) poster

Vatsiou, A, Melodelima, C, Bazin, E, Gaggiotti O. "Comparison of Haplotype Methods to detect selection."
(2013) MindTheGap IV conference. Vienna, Austria. (website) poster

Online:

ITN podcast : http://intercrossing.wikispaces.com/Student+Led+Conference+%28PI-free%29See+our+videos+%26+podcasts

Publications:

1. Widespread Signals of Convergent Adaptation to High Altitude in Asia and America.
Matthieu Foll, Oscar Gaggiotti, Josephine Daub, Alexandra Vatsiou, Laurent Excoffier
Am J Hum Genet. 2014 Oct 2;95(4):394-407. doi: 10.1016/j.ajhg.2014.09.002. Epub 2014 Sep 25.
PMID: 25262650


2. A comparison of recent methods for the detection of selective sweeps in structured population scenarios.
Alexandra I. Vatsiou, Eric Bazin, Oscar Gaggiotti.
Mol Ecol. 2015 Aug 28. doi: 10.1111/mec.13360. [Epub ahead of print]
PMID:26314386


Zohren, Jasmin


Talks:

Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, and Buggs RJA (2015) "PolyTypeR genotypes polyploid variants at RAD loci revealing introgression among British birch trees."
Population Genetics Group Meeting 49, Edinburgh, UK.

Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, and Buggs RJA (2015) "PolyTypeR genotypes polyploid variants at RAD loci revealing introgression among British birch trees."
London Evolutionary Research Network Conference, London, UK.

Zohren J, Kardailsky I, Nielsen KL, Joecker A, and Buggs RJA (2015) "Assessing allelic configuration models in polyploids based on variant callings."
Bayer CropScience, Ghent, Belgium.

Sollars ESA, Zohren J, Boshier D, Clark J, Joecker A, Buggs RJA,(2014) "Sequencing the genome of Fraxinus excelsior (European Ash)
International Plant & Animal Genome XXII, San Diego, CA, USA. PAG XXII Abstract PDF

Publications:

Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA (2016). Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by RAD markers. Molecular Ecology, 25:2413–2426. doi:10.1111/mec.13644

Verity R, Hatlen A, Marquardt J, and Zohren J (2013). From Hybrids To Hermaphrodites In Population Genetics.. Genome Biology, 14:301. doi:10.1186/gb-2013-14-1-301

Posters:

ESA Sollars, LJ Kelly, D Swarbreck, B Clavijo, G Kaithakottil, J Zohren et al. (2015) "Genome sequencing of Fraxinus species to identify loci relevant to ash dieback and emerald ash borer"
35th New Phytologist Symposium: The genomes of forest trees: new frontiers of forest biology, Boston, MA, USA. (35th NPS)

Zohren J, Kardailsky I, Nielsen KL, Joecker A, and Buggs RJA (2015) "Assessing Allelic Configuration Models in Fixed Ploidy Variant Calling Using R."
International Plant & Animal Genome XXIII, San Diego, CA, USA. PAG XXIII poster

Sollars ESA, Zohren J, Boshier D, Clark J, Joecker A, and Buggs RJA, (2014) "Sequencing The Genome Of Fraxinus excelsior (European Ash)."
International Plant & Animal Genome XXII, San Diego, CA, USA. PAG XXII poster

Sollars ESA, Zohren J, Boshier D, Clark J, Joecker A, and Buggs RJA, (2014) "Sequencing The Genome Of Fraxinus excelsior (European Ash)."
47th Population Genetics Group Meeting, Bath, UK. PopGroup47 poster

Zohren J, Sollars ESA, Clark J, Boshier D, Joecker A, and Buggs RJA, (2013) "Sequencing The Genome Of Fraxinus excelsior (European Ash)."
XIV Congress of the European Society for Evolutionary Biology, Lisbon, Portugal. ESEB 2013 poster
Save