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Hire Dr. Teofil N.

Costa Rica

USD 85 /hr

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. p. 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). p. 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. p. 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). p. 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). p. 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). p. 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). p. 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). p. 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). p. 462--473.

Nakov, Teofil, Onyshchenko, Anastasiia, Ruck, Elizabeth C, Alverson, Andrew J(2018). A single loss of photosynthesis in diatoms. bioRxiv. p. 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). p. 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). p. 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). p. 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). p. 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. p. 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. p. 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). p. 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). p. 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. p. 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). p. 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). p. 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. p. 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. p. 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). p. 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). p. 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). p. 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). p. 15--26.

Nakov, Teofil, Jovanovska, Elena, Levkov, Zlatko(2013). Observations of the genus Diploneis from Lake Ohrid, Macedonia. Diatom Research. 28. (3). p. 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). p. 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. p. 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). p. 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). p. 147.

Nakov, Teofil, Levkov, Zlatko, Edlund, Mark B(2008). Identity and typification of Navicula hasta (Bacillariophyceae). Phycological Research. 56. (1). p. 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). p. 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. p. 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). p. 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). p. 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). p. 269--280. Taylor \& Francis

Nakov, Teofil, Levkov, Zlatko(2006). Department zyxwvutsrqponmlkj. Diatom Research. 21. (2). p. 269--280.

Nakov, Teofil, Levkov, Zlatko, Metzeltin, Ditmar(2006). New species and combination from the genus Sellaphora Mereschkowsky from Macedonia. Diatom Research. 21. (2). p. 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). p. 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. p. 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. p. 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. p. 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). p. 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. p. 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. p. 209--220.