We provide the skills, knowledge and expertise that are needed to manage, process and study data from large scale multi-omics experiments. Our extensive knowledge in computer science, statistics, artificial intelligence, bioinformatics and genetics allows for faster data analysis and discovery of patterns present in the data.

Our process and services

  1. We process the raw data using our own pipelines optimized for speed and versatility (e.g. RNA-seq, Whole genome bisulfite sequencing, etc.).
  2. Perform quality control of the data
  3. Apply the latest academia-standard statistical tools and techniques to answer the research questions
  4. Build and evaluate artificial intelligence (AI) algorithms to elucidate potential diagnostic markers and quantify their accuracy
  5. Integrate the findings with publically available data to aid biological interpretation (e.g. gene set enrichment analysis)
  6. Deliver the data analysis report including concise, stylish figures, ready for inclusion to the mauscript
  7. Contribute to writing grant proposals and research manuscripts

Summary of widespread differential methylation around authopagy lysosomal pathway genes in human appendix and prefrontal cortex neurons of healthy and Parkinson’s disease patients.

The team

The core of our company is comprised of scientists that provide bioinformatics consulting services. We are aided by a network of skilled software engineers, programmers,

Juozas Gordevičius, PhD



With BSc, MSc and PhD in computer science Juozas has all the knowledge and skill required to train complex AI models. He spent 10 years in biomedical research as a bioinformatics scientist. Advancing our knowledge towards understanding of human disease and accurate diagnostis is Juozas’ goal.

Selected publications

  • Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing. Gordevičius J, Narmontė M, Gibas P, Kvederavičiūtė K, Tomkutė V, Paluoja P, Krjutškov K, Salumets A, Kriukienė E. Clin Epigenetics. 2020 Oct 20;12(1):153. doi: 10.1186/s13148-020-00938-x. PMID: 33081811.

  • Epigenomic analysis of Parkinson’s disease neurons identifies Tet2 loss as neuroprotective. Marshall LL, Killinger BA, Ensink E, Li P, Li KX, Cui W, Lubben N, Weiland M, Wang X, Gordevicius J, Coetzee GA, Ma J, Jovinge S, Labrie V. Nat Neurosci. 2020 Oct;23(10):1203-1214. doi: 10.1038/s41593-020-0690-y. PMID: 32807949.

  • Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether- directed sequencing. Gibas P, Narmontė M, Staševskij Z, Gordevičius J, Klimašauskas S, Kriukienė E. PLoS Biol. 2020 Apr 10;18(4):e3000684. doi: 10.1371/journal.pbio.3000684. PMID: 32275660.

  • Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease. Oh G, Koncevičius K, Ebrahimi S, Carlucci M, Groot DE, Nair A, Zhang A, Kriščiūnas A, Oh ES, Labrie V, Wong AHC, Gordevičius J, Jia P, Susic M, Petronis A. Genome Biol. 2019 Jan 3;20(1):2. doi: 10.1186/s13059-018-1608-9. PMID: 30606238.

  • Cell-Free DNA Modification Dynamics in Abiraterone Acetate-Treated Prostate Cancer Patients. Gordevičius J, Kriščiūnas A, Groot DE, Yip SM, Susic M, Kwan A, Kustra R, Joshua AM, Chi KN, Petronis A, Oh G. Clin Cancer Res. 2018 Jul 15;24(14):3317-3324. doi: 10.1158/1078-0432.CCR-18-0101. PMID: 29615462.

  • Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging. Oh G, Ebrahimi S, Carlucci M, Zhang A, Nair A, Groot DE, Labrie V, Jia P, Oh ES, Jeremian RH, Susic M, Shrestha TC, Ralph MR, Gordevičius J, Koncevičius K, Petronis A. Nat Commun. 2018 Feb 13;9(1):644. doi: 10.1038/s41467-018-03073-7. PMID: 29440637.

  • Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. Staševskij Z, Gibas P, Gordevičius J, Kriukienė E, Klimašauskas S. Mol Cell. 2017 Feb 2;65(3):554-564.e6.doi: 10.1016/j.molcel.2016.12.012. PMID: 28111014.

  • Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Labrie V, Buske OJ, Oh E, Jeremian R, Ptak C, Gasiūnas G, Maleckas A, Petereit R, Žvirbliene A, Adamonis K, Kriukienė E, Koncevičius K, Gordevičius J, Nair A, Zhang A, Ebrahimi S, Oh G, Šikšnys V, Kupčinskas L, Brudno M, Petronis A. Nat Struct Mol Biol. 2016 Jun;23(6):566-73. doi: 10.1038/nsmb.3227. PMID: 27159559.

  • DNA unmethylome profiling by covalent capture of CpG sites. Kriukienė E, Labrie V, Khare T, Urbanavičiūtė G, Lapinaitė A, Koncevičius K, Li D, Wang T, Pai S, Ptak C, Gordevičius J, Wang SC, Petronis A, Klimašauskas S. Nat Commun. 2013;4:2190. doi: 10.1038/ncomms3190. PMID: 23877302.

  • Epigenetic markers of prostate cancer in plasma circulating DNA. Cortese R, Kwan A, Lalonde E, Bryzgunova O, Bondar A, Wu Y, Gordevicius J, Park M, Oh G, Kaminsky Z, Tverkuviene J, Laurinavicius A, Jankevicius F, Sendorek DH, Haider S, Wang SC, Jarmalaite S, Laktionov P, Boutros PC, Petronis A. Hum Mol Genet. 2012 Aug 15;21(16):3619-31. doi: 10.1093/hmg/dds192. PMID: 22619380.

Povilas Gibas



Povilas is the guru of next generation sequencing data analyses and beautiful graphs!

Selected publications

  • Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing. Gordevičius J, Narmontė M, Gibas P, Kvederavičiūtė K, Tomkutė V, Paluoja P, Krjutškov K, Salumets A, Kriukienė E. Clin Epigenetics. 2020 Oct 20;12(1):153. doi: 10.1186/s13148-020-00938-x. PMID: 33081811.

  • A Bisulfite-free Approach for Base-Resolution Analysis of Genomic 5-Carboxylcytosine. Ličytė J, Gibas P, Skardžiūtė K, Stankevičius V, Rukšėnaitė A, Kriukienė E. Cell Rep. 2020 Sep 15;32(11):108155. doi:10.1016/j.celrep.2020.108155. PMID: 32937122.

  • Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether- directed sequencing. Gibas P, Narmontė M, Staševskij Z, Gordevičius J, Klimašauskas S, Kriukienė E. PLoS Biol. 2020 Apr 10;18(4):e3000684. doi: 10.1371/journal.pbio.3000684. PMID: 32275660.

  • DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity. Carlucci M, Kriščiūnas A, Li H, Gibas P, Koncevičius K, Petronis A, Oh G. Bioinformatics. 2019 Nov 8:btz834. doi: 10.1093/bioinformatics/btz834. PMID: 31702788.

  • Clinical significance of miRNA host gene promoter methylation in prostate cancer. Daniunaite K, Dubikaityte M, Gibas P, Bakavicius A, Rimantas Lazutka J, Ulys A, Jankevicius F, Jarmalaite S. Hum Mol Genet. 2017 Jul 1;26(13):2451-2461. doi: 10.1093/hmg/ddx138. PMID: 28398479

  • Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. Staševskij Z, Gibas P, Gordevičius J, Kriukienė E, Klimašauskas S. Mol Cell. 2017 Feb 2;65(3):554-564.e6. doi: 10.1016/j.molcel.2016.12.012. PMID: 28111014

Jonas Bačelis, PhD



When it comes to epidemiology and statistics, Jonas’ knowledge and skills are unrivaled.

Selected publications

  • Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors. Warrington NM, Beaumont RN, Horikoshi M, Day FR, Helgeland Ø, Laurin C, Bacelis J, et al. Nat Genet. 2019 May;51(5):804-814. doi: 10.1038/s41588-019-0403-1. PMID: 31043758.

  • Genome-wide association study identifies 74 loci associated with educational attainment. Okbay A, Beauchamp JP, Fontana MA, Lee JJ, Pers TH, Rietveld CA, Turley P, Chen GB, Emilsson V, Meddens SF, Oskarsson S, Pickrell JK, Thom K, Timshel P, de Vlaming R, Abdellaoui A, Ahluwalia TS, Bacelis J, et al. Nature. 2016 May 26;533(7604):539-42. doi: 10.1038/nature17671. PMID: 27225129.

  • Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis. Paternoster L, et al. Nat Genet. 2015 Dec;47(12):1449-1456. doi: 10.1038/ng.3424. PMID: 26482879.

  • Zhang G, Feenstra B, Bacelis J, et al. Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. N Engl J Med. 2017 Sep 21;377(12):1156-1167. doi:10.1056/NEJMoa1612665. PMID: 28877031.

  • Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. Liu X, et al. Nat Commun. 2019 Sep 2;10(1):3927. doi: 10.1038/s41467-019-11881-8. PMID: 31477735.

Contact

Vugene, LLC is incorporated in Delaware, USA. Contact us via an email and we can set up a video call.

 

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