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Experienced Bioinformatics Consultant | R/Python Developer | Genomics • Transcriptomics • Data Science • Evolution

Profile Summary

Dr. Teofil Nakov is a biologist specializing in the evolution and phylogenetics of diatoms, a group of microalgae found in aquatic environments worldwide. His research focuses on understanding the evolutionary history and diversification of these ecologically significant organisms.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Evolutionary Biology
• ☆ Biostatistics
• ☆ Molecular Biology
• ☆ Genetics
• ☆ Omics
• ☆ Transcriptomics
• ☆ Comparative Genomics
• ☆ Genomics
• ☆ Molecular Evolution
• ☆ PCR
• ☆ Molecular Cloning
• ☆ Next Generation Sequencing (NGS)
• ☆ DNA Sequencing
• ☆ Gene Expression Analysis
• ☆ Genome Sequencing
• ☆ Exome Sequencing
• ☆ RNA Sequencing
• ☆ Molecular Ecology
• ☆ Marine Biology
• ☆ Microscopy
• ☆ Light Microscopy
• ☆ Electron Microscopy
• ☆ Data Analysis
• ☆ Data Collection
• ☆ Machine Learning
• ☆ Artificial Intelligence
• ☆ Statistics
• ☆ Comparative Analysis
• ☆ Regression Analysis
• ☆ Multivariate Analysis
• ☆ Nonlinear Regression
• ☆ Bayesian Statistics
• ☆ Statistical Computing
• ☆ Study Design
• ☆ Spatial Statistics
• ☆ Medical Statistics
• ☆ Health Data Analysis
• ☆ Trend Analysis
• ☆ Earth & Atmospheric Science
• ☆ Biogeography
• ☆ Lakes/Limnology
• ☆ Oceanography & Marine Science
• ☆ Ecology
• ☆ Marine Ecology
• ☆ Aquatic Ecology
• ☆ Biodiversity
• ☆ Microbial Ecology
• ☆ Taxonomy/Classification
• ☆ Biological Taxonomy/Classification
• ☆ Phylogenetics
• ☆ Population Genetics
• ☆ Data Storage
• ☆ Python
• ☆ SQL
• ☆ Excel
• ☆ LaTex
• ☆ R
• ☆ Scikit-learn
• ☆ Markup Languages
• ☆ Drug Discovery
• ☆ Software Development
• ☆ Software QA & Testing
• ☆ Mobile Application Development
• ☆ Desktop Application Development
• ☆ Web Application Development
• ☆ Cloud Application Development
• ☆ DevOps
• ☆ UI/UX Design
• ☆ Hypothesis
• ☆ Peer Review
• ☆ Research Methodology
• ☆ Survey Design & Methodology
• ☆ Technical & Scientific Writing
• ☆ Journal Selection
• ☆ Manuscript & Journal Article Writing
• ☆ Instructional Materials
• ☆ Release Notes
• ☆ Experimental Protocols
• ☆ SOP & Protocol Writing
• ☆ Textbook Content Writing
• ☆ Scientific Proofreading & Editing
• ☆ Proofreading & Editing
• ☆ Course Content Writing
• ☆ Grant Writing

Services

• Research
• Consulting
• Data & AI

Research Gray Literature Search, Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Consulting Digital Strategy Consulting, Healthcare Consulting, Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Image Processing, Algorithm Design-Non ML, Algorithm Design-ML, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights

Work Experience

Expert Data Scientist | Python/R Developer | Bioinformatician

Independant consultant

January 2020 - Present

Post-doctoral researcher

University of Arkansas at Fayetteville

September 2014 - December 2019

Graduate Research Assistant

University of Texas at Austin

September 2007 - May 2014

Teaching Assistant

Saints Cyril and Methodius University of Skopje

September 2004 - May 2007

Education

PhD (Integrative Biology)

The University of Texas at Austin

September 2007 - May 2014

BSci Biochemistry & Physiology (Institute of Biology)

Saints Cyril and Methodius University of Skopje

September 2000 - May 2005

Certifications

• Post Graduate Program in Artificial Intelligence and Machine Learning: Business Applications

  Post Graduate Program in Artificial Intelligence and Machine Learning: Business Applications

  https://www.mygreatlearning.com/eportfolio/teofil-nakov

  June 2025 - Present

• AWS Certified Cloud Practitioner

  AWS

  https://www.credly.com/badges/10220fb1-d5ab-455c-b6db-5e44709a5004

  October 2024 - Present

Publications

JOURNAL ARTICLE

Nakov, Teofil, Pinseel, Eveline, Ruck, Elizabeth C, Jonsson, Per R, Kourtchenko, Olga, Kremp, Anke, Pinder, Matthew IM, Roberts, Wade R, Sjöqvist, Conny, Töpel, Mats, et al.(2023). Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes. bioRxiv. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2023--09. Cold Spring Harbor Laboratory

Nakov, Teofil, Pinseel, Eveline, Van den Berge, Koen, Downey, Kala M, Judy, Kathryn J, Kourtchenko, Olga, Kremp, Anke, Ruck, Elizabeth C, Sjöqvist, Conny, Töpel, Mats, et al.(2022). Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline. The ISME Journal. 16. (7). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1776--1787. Oxford University Press

Nakov, Teofil, Alverson, Andrew J, Chafin, Tyler K, Jones, Kiley A, Manoylov, Kalina M, Johnson, Hillary, Julius, Matthew L, Ruck, Elizabeth C, Theriot, Edward C, Yeager, Kevin M, et al.(2021). Microbial biogeography through the lens of exotic species: the recent introduction and spread of the freshwater diatom Discostella asterocostata in the United States. Biological Invasions. 23. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2191--2204. Springer International Publishing

Nakov, Teofil, Hamlin, Jennafer AP, Williams-Newkirk, Amanda(2021). tinselR—an R Shiny Application for Annotating Phylogenetic Trees. Microbiology Resource Announcements. 10. (27). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 10--1128. American Society for Microbiology 1752 N St., NW, Washington, DC

Nakov, Teofil, Ozersky, Ted, Hampton, Stephanie E, Rodenhouse, Nicholas L, Woo, Kara H, Shchapov, Kirill, Wright, Katie, Pislegina, Helena V, Izmest'Eva, Lyubov R, Silow, Eugene A, et al.(2020). Hot and sick? Impacts of warming and a parasite on the dominant zooplankter of Lake Baikal. Limnology and Oceanography. 65. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2772--2786. John Wiley \& Sons, Inc. Hoboken, USA

Nakov, Teofil, Judy, Kathryn J, Downey, Kala M, Ruck, Elizabeth C, Alverson, Andrew J(2020). Transcriptional response of osmolyte synthetic pathways and membrane transporters in a euryhaline diatom during long-term acclimation to a salinity gradient. Journal of Phycology. 56. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1712--1728.

Nakov, Teofil, Onyshchenko, Anastasiia, Ruck, Elizabeth C, Alverson, Andrew J(2019). A single loss of photosynthesis in the diatom order Bacillariales (Bacillariophyta). American Journal of Botany. 106. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 560--572.

Nakov, Teofil, Beaulieu, Jeremy M, Alverson, Andrew J(2019). Diatoms diversify and turn over faster in freshwater than marine environments. Evolution. 73. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2497--2511. Blackwell Publishing Inc Malden, USA

Nakov, Teofil, Beaulieu, Jeremy M, Alverson, Andrew J(2018). Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta). New Phytologist. 219. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 462--473.

Nakov, Teofil, Onyshchenko, Anastasiia, Ruck, Elizabeth C, Alverson, Andrew J(2018). A single loss of photosynthesis in diatoms. bioRxiv. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 298810. Cold Spring Harbor Laboratory

Nakov, Teofil, Mejdandžić, Maja, Bosak, Sunčica, Ruck, Elizabeth, Orlić, Sandi, Gligora Udovič, Marija, Peharec Štefanić, Petra, Špoljarić, Igor, Mršić, Gordan, Ljubešić, Zrinka(2018). Morphological diversity and phylogeny of the diatom genus Entomoneis (Bacillariophyta) in marine plankton: six new species from the Adriatic Sea. Journal of phycology. 54. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 275--298.

Nakov, Teofil, Beaulieu, Jeremy M, Alverson, Andrew J(2018). Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time. The ISME journal. 12. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2807--2810. Oxford University Press

Nakov, Teofil, Parks, Matthew B, Ruck, Elizabeth C, Wickett, Norman J, Alverson, Andrew J(2018). Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). American journal of botany. 105. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 330--347.

Nakov, Teofil, Guillory, Wilson X, Onyshchenko, Anastasiia, Ruck, Elizabeth C, Parks, Matthew, Wickett, Norman J, Alverson, Andrew J(2018). Recurrent loss, horizontal transfer, and the obscure origins of mitochondrial introns in diatoms (Bacillariophyta). Genome biology and evolution. 10. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1504--1515. Oxford University Press

Nakov, Teofil, Ruck, Elizabeth C, Linard, Samantha R, Theriot, Edward C, Alverson, Andrew J(2017). Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta). Current Genetics. 63. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 499--507. Springer Berlin Heidelberg

Nakov, Teofil, Chust, Guillem, Vogt, Meike, Benedetti, Fabio, Villéger, Sébastien, Aubert, Anais, Vallina, Sergio M, Righetti, Damiano, Not, Fabrice, Biard, Tristan, et al.(2017). Mare incognitum: A glimpse into future plankton diversity and ecology research. Frontiers in Marine Science. 4. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 68. Frontiers Media SA

Nakov, Teofil, Boyko, James, Alverson, Andrew, Beaulieu, Jeremy(2017). Models with unequal transition rates favor marine origins of Cyanobacteria and photosynthetic eukaryotes. PNAS. 114. (50). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 13055--13056.

Nakov, Teofil, Ruck, Elizabeth C., Alverson, Andrew J., Theriot, Edward C.(2016). Nomenclatural transfers associated with the phylogenetic reclassification of the Surirellales and Rhopalodiales. Notulae Algarum. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--4.

Nakov, Teofil, Ruck, Elizabeth C, Alverson, Andrew J, Theriot, Edward C(2016). Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales. Molecular phylogenetics and evolution. 103. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 155--171. Academic Press

Nakov, Teofil, Ashworth, Matt, Theriot, Edward C(2015). Comparative analysis of the interaction between habitat and growth form in diatoms. The ISME Journal. 9. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 246--255. Oxford University Press

Nakov, Teofil, Guillory, Wilson, Julius, Matthew, Theriot, Edward, Alverson, Andrew(2015). Towards a phylogenetic classification of species belonging to the diatom genus Cyclotella (Bacillariophyceae): Transfer of species formerly placed in Puncticulata, Handmannia, Pliocaenicus and Cyclotella to the genus Lindavia. Phytotaxa. 217. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 249--264.

Nakov, Teofil, Theriot, Edward C, Ashworth, Matt P, Ruck, Elizabeth, Jansen, Robert K(2015). Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular phylogenetics and evolution. 89. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 28--36. Academic Press

Nakov, Teofil, Jovanovska, Elena, Buczkó, Krisztina, Levkov, Zlatko(2014). Diploneis transylvanica (Bacillariophyceae), a new diatom species from the Neogene fossil deposit in Romania. Nova Hedwigia. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 413--427. Schweizerbart'sche Verlagsbuchhandlung

Nakov, Teofil, Ruck, Elizabeth C, Jansen, Robert K, Theriot, Edward C, Alverson, Andrew J(2014). Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms. Genome Biology and Evolution. 6. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 644--654. Oxford University Press

Nakov, Teofil, Ruck, Elizabeth C, Galachyants, Yuri, Spaulding, Sarah A, Theriot, Edward C(2014). Molecular phylogeny of the Cymbellales (Bacillariophyceae, Heterokontophyta) with a comparison of models for accommodating rate variation across sites. Phycologia. 53. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 359--373. Taylor \& Francis

Nakov, Teofil, Theriot, Edward C, Alverson, Andrew J(2014). Using phylogeny to model cell size evolution in marine and freshwater diatoms. Limnology and oceanography. 59. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 79--86.

Nakov, Teofil, Jovanovska, Elena, Buczko, Krisztina, Ognjanova-Rumenova, Nadja G, Levkov, Zlatko(2013). Identity and typification of Diploneis ostracodarum, Diploneis budayana and Diploneis praeclara (Bacillariophyta). Phytotaxa. 137. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 15--26.

Nakov, Teofil, Jovanovska, Elena, Levkov, Zlatko(2013). Observations of the genus Diploneis from Lake Ohrid, Macedonia. Diatom Research. 28. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 237--262. Taylor \& Francis

Nakov, Teofil, Ashworth, Matt P, Theriot, Edward C(2013). Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae). Journal of Phycology. 49. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1207--1222.

Nakov, Teofil, Theriot, Edward C, Ruck, Elizabeth, Ashworth, Matt, Jansen, Robert K(2011). Status of the pursuit of the diatom phylogeny: are traditional views and new molecular paradigms really that different?. The diatom world. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 119--142. Springer Netherlands

Nakov, Teofil, Theriot, Edward C, Ashworth, Matt, Ruck, Elizabeth, Jansen, Robert(2010). A preliminary multigene phylogeny of the diatoms (Bacillariophyta): challenges for future research. Plant Ecology and Evolution. 143. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 278--296. Meise Botanic Garden and Royal Botanical Society of Belgium

Nakov, Teofil, Pavlov, Aleksandar, Levkov, Zlatko, Furey, Paula, Lowe, Rex, Ector, Luc(2009). Luticola grupcei (Bacillariophyceae)-a new freshwater diatom from Mountain Baba (Macedonia) and Great Smoky Mountains National Park (USA): comparison with the type material of L. goeppertiana (Bleisch) DG Mann. Nova Hedwigia. 89. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 147.

Nakov, Teofil, Levkov, Zlatko, Edlund, Mark B(2008). Identity and typification of Navicula hasta (Bacillariophyceae). Phycological Research. 56. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 46--57. Blackwell Publishing Asia Melbourne, Australia

Nakov, Teofil, Levkov, Zlatko(2008). Rhoicosphenia tenuis, a new diatom species from Lake Ohrid. Diatom Research. 23. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 377--388. Taylor \& Francis Group

Levkov, Z, Krstic, S, Metzeltin, D, Nakov, T(2007). Diatoms of Lakes Prespa and Ohrid. About 500 taxa from ancient lake system. Iconographia Diatomologica 16. Iconographia Diatomologica 16. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 611. Koeltz Scientific Books

Nakov, TEOFIL, Levkov, Zlatko, Blanco, Saúl, Krstic, SVETISLAV, Ector, L(2007). Ecology of benthic diatoms from Lake macro Prespa (Macedonia). Algological Studies. 124. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 71--83. Schweizerbart'sche Verlagsbuchhandlung

Nakov, Teofil, Krstic, Svetislav, Svircev, Zorica, Levkov, Zlatko(2007). Selecting appropriate bioindicators regarding Water Framework Directive guidelines for freshwaters-a Macedonian experience. International journal on algae. 9. (1). Begel House Inc.

Nakov, Teofil, Svirčev, Zorica, Krstić, Svetislav, Simeunović, Jelica, Dulić, Tamara(2006). Comparative analysis of water quality methods for the monitoring of eutrophication regarding implementation of WFD in Serbia. Geographica Pannonica. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 32--42.

Nakov, Teofil, Edlund, Mark B, Brant, Lynn A, Levkov, Zlatko(2006). An emended description of Decussata (Patrick) Lange-Bertalot & Metzeltin that includes protoplast organization and detailed valve and cingulum ultrastructure. Diatom Research. 21. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 269--280. Taylor \& Francis

Nakov, Teofil, Levkov, Zlatko(2006). Department zyxwvutsrqponmlkj. Diatom Research. 21. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 269--280.

Nakov, Teofil, Levkov, Zlatko, Metzeltin, Ditmar(2006). New species and combination from the genus Sellaphora Mereschkowsky from Macedonia. Diatom Research. 21. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 297--312. Taylor \& Francis

Levkov, Z, Krstic, S, Nakov, T, Melovski, Lj(2005). Diatom assemblages on Shara and Nidze Mountains, Macedonia. Nova Hedwigia. 81. (3-4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 501--537.

Cox, Eileen J, Alverson, Andrew, Beszteri, Bank, Bixby, Rebecca J, Eriksen, Ruth, Harwood, David, Juettner, Ingrid, Julius, Matthew, Karthick, Balasubramanian, Kroth, Peter, et al.(1995). About this journal.

Nakov, Teofil, Beaulieu, Jeremy M, Alverson, Andrew JArticle title: Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta).

Solidoro, Cosimo, Weslawski, Jan Marcin, Riascos, Jose M, D’Alcala, Maurizio Ribera, Chust, Guillem, Chust, G, Vogt, M, Benedetti, F, Nakov, T, Villéger, S, et al.Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research.

Nakov, Teofil, Ashworth, Edward C Theriot1 Matthew P, Brady, Mariska, Yu, Elizabeth C Ruck3& AnnaTHE DIATOM PHYLOGENY AS INFERRED FROM NSSU AND 6 CHLOROPLAST GENES.

CONFERENCE PAPER

Pinseel, E, Nakov, T, Van den Berge, K, Downey, KM, Judy, KJ, Kourtchenko, O, Krempf, A, Ruck, EC, Sjoqvist, C, Topel, M, et al.(2023). Unravelling a natural evolutionary experiment: The colonization of low-salinity habitats in the Baltic Sea by the marine diatom Skeletonema marinoi. INTEGRATIVE AND COMPARATIVE BIOLOGY. 62. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString S247--S248.

Nakov, Teofil, Pinseel, Eveline, Van den Berge, Koen, Downey, Kala, Judy, Kathryn, Ruck, Elizabeth, Alverson, Andrew J(2021). Transcriptional Response of the Marine Diatom Skeletonema Marinoi During Acclimation along a Salinity Gradient. Phycologia. 60. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 112--112.

Nakov, Teofil, Mucko, Maja, Bosak, Sunčica, Ruck, Elizabeth, Gligora Udovič, Marija, Ljubešić, Zrinka(2018). ˝ Planktonic lifestyle lovers˝: a story of eight new marine Entomoneis species. 25th International Diatom Symposium. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 119--119.

Nakov, T, Ruck, EC, Galatchyants, Y, Likhoshway, E, Spaulding, SA, Theriot, EC(2013). PHYLOGENETIC SIGNAL, NOISE AND THE PHYLOGENY OF CYMBELLALES (BACILLARIOPHYCEAE). PHYCOLOGIA. 52. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 77--77.

Edlund, MB, Levkov, Z, Soninkhishig, N, Krstic, S, Nakov, T(2006). Diatom species flocks in large ancient lakes: the Navicula reinhardtii complex from Lakes Hövsgöl (Mongolia) and Prespa (Macedonia). Proceeding of 18 International Diatom Symposium. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 61--74.

Krstic, S, Levkov, Z, Nakov, T(2004). Diatom diversity in Republic of Macedonia-our present knowledge. Proceedings of the Eighteenth International Diatom Symposium. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 209--220.