Publications

=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])

**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.

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:** [] -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

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= 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
 * Publication(s) **

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. [] [|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
 * [|nispero.g8] — templates for nispero projects:
 * [|nisperoCLI] — command line interface for nipper

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])

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])

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]) __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/, )

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. .

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]

__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.

__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.

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])

__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])

__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. ( []). "Comparison of Haplotype Methods to detect selection." (2013), Vienna at MABS. ([])

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. Mol Ecol. 2015 Aug 28. doi: 10.1111/mec.13360. [Epub ahead of print] PMID:26314386
 * Alexandra I. Vatsiou**, Eric Bazin, Oscar Gaggiotti.

=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

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

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

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

__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