Publications

Widening the Scientific Excellence for Studies on Women’s and Fetal Health and Wellbeing - WIDENLIFE, Universitas Tartuensis DSpace

 

1. Saare, Merli; Modhukur, Vijayachitra; Suhorutshenko, Marina; Rajashekar, Balaji; Rekker, Kadri; Sõritsa, Deniss; Karro, Helle; Soplepmann, Pille; Sõritsa, Andrei; Lindgren, Cecilia M; Rahmioglu, Nilufer; Drong, Alexander; Becker, Christian M; Zondervan, Krina T; Salumets, Andres; Peters, Maire. The influence of menstrual cycle and endometriosis on endometrial methylome. Clin Epigenetics. 2016 Jan 12;8:2. doi: 10.1186/s13148-015-0168-z (JP)

2. Pervjakova, Natalia; Kasela, Silva; Morris, Andrew P; Kals, Mart; Metspalu, Andres; Lindgren, Cecilia M; Salumets, Andres; Mägi, Reedik. Imprinted genes and imprinting control regions show predominants intermediate methylation in adult somatic tissues. Epigenomics, 8(6), 789-799, 23.03.2016. doi: 10.2217/epi.16.8 (JP)

3. Triin Laisk-Podar, Cecilia M. Lindgren, Maire Peters, Juha S. Tapanainen, Cornelis B. Lambalk, Andres Salumets, Reedik Mägi. Ovarian Physiology and GWAS: Biobanks, Biology and Beyond. Trends in endocrinology and metabolism: TEM. 27 (7),  516−528, doi:10.1016/j.tem.2016.04.011, 21.05.2016. (JP)

4. Tšuiko, O.; Nõukas, M.; Žilina, O.; Hensen, K.; Tapanainen, J.; Mägi, R.; Kals, M.; Kivistik, PA.; Haller-Kikkatalo, K.; Salumets, A.; Kurg, A. (2016). Copy number variation analysis detects novel candidate genes involved in follicular growth and oocyte maturation in a cohort of premature ovarian failure cases. Human Reproduction, 31 (8). 2016 Jun 14. doi: 10.1093/humrep/dew142

5. Tiirats, Airi; Viltrop, Triin; Nõukas, Margit; Reimann, Ene; Salumets, Andres; Kõks, Sulev. C14orf132 gene is possibly related to extremely low birth weight. BMC genetics. 2016, 17 (1), 132-132, doi: 10.1186/s12863-016-0439-5

6. Boggavarapu, Nageswara Rao; Lalitkumar, Sujata; Joshua, Vijay; Kasvandik, Sergo; Salumets, Andres; Lalitkumar, Parameswaran Grace; Gemzell-Danielsson, Kristina. Compartmentalized gene expression profiling of receptive endometrium reveals progesterone regulated ENPP3 is differentially expressed and secreted in glycosylated form. Scientific reports. 2016, 6,  33811−33811, doi: 10.1038/srep33811

7. Krjutškov, Kaarel; Koel, Mariann; Roost, Anne Mari; Katayama, Shintaro; Einarsdottir, Elisabet; Jouhilahti, Eeva-Mari; Söderhäll, Cilla; Jaakma, Ülle; Plaas, Mario; Vesterlund, Liselotte; Lohi, Hannes; Salumets, Andres; Kere, Juha (2016). Globin mRNA reduction for whole-blood transcriptome sequencing. Scientific Reports, 6,  31584−31584, doi: 10.1038/srep31584

8. Aghajanova, Lusine; Altmäe, Signe; Kasvandik, Sergo; Salumets, Andres; Stavreus-Evers, Anneli; Giudice, Linda C. (2016). Stanniocalcin-1 expression in normal human endometrium and dysregulation in endometriosis. Fertility and Sterility, 106 (3),  681−691, doi: 10.1016/j.fertnstert.2016.05.023

9. Gerly Sillaste; Lauris Kaplinski; Riho Meier; Ülle Jaakma; Elo Eriste; Andres Salumets (2016). A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa. Reproduction, 153 (3): 241-251
Published online 2016 Dec 21. doi: 10.1530/REP-16-0441

10. Olga Mazina; Anni Allikalt; Juha S. Tapanainen; Andres Salumets; Ago Rinken (2017). Determination of biological activity of gonadotropins hCG and FSH by Förster resonance energy transfer based biosensors. Scientific Reports, 7, 42219,  doi:  10.1038/srep42219

11. Kadri Haller-Kikkatalo; Kristi Alnek; Andres Metspalu, Evelin Mihailov; Kaja Metsküla; Kalle Kisand; Heti Pisarev, Andres Salumets, Raivo Uibo (2017). Demographic associations for autoantibodies in disease-free individuals of a European population. Scientific Reports, 7, 44846,  doi:  10.1038/srep44846
 

12. Rekker Kadri, Saare Merli, Eriste Elo, Tasa Tõnis, Kukuškina Viktorija, Roost Anne Mari, Anderson Kristi, Samuel Kadri, Karro Helle, Salumets Andres, Peters Maire. (2017) High-throughput mRNA sequencing of stromal cells from endometriomas and endometrium. Reproduction. 154(1):93-100. doi https://doi.org/10.1530/REP-17-0092

13. Saare Merli, Rekker Kadri, Laisk-Podar Triin, Rahmioglu Nilufer, Zondervan Krina, Salumets Andres, Götte Martin, Peters Maire. (2017) Challenges in endometriosis miRNA studies - From tissue heterogeneity to disease specific miRNAs. Biochim Biophys Acta. 1863(9):2282-2292. doi: 10.1016/j.bbadis.2017.06.018 (JP)

14. Kukushkina V, Modhukur V, Suhorutšenko M, Peters M, Mägi R, Rahmioglu N, Velthut-Meikas A, Altmäe S, Esteban FJ, Vilo J, Zondervan K, Salumets A, Laisk-Podar T. (2017) DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase. Sci Rep. 20;7(1):3916.

Published online 2017 Jun 20. doi: 10.1038/s41598-017-03682-0 (JP)

15. OlgaTšuiko, Maaike Catteeuw, Masoud Zamani Esteki, Aspasia Destouni, Osvaldo Bogado Pascottini, Urban Besenfelder, Vitezslav Havlicek,Katrien Smits, Ants Kurg, Andres Salumets, Thomas D’Hooghe, Thierry Voet, Ann Van Soom,  Joris Robert Vermeesch (2017). Genome stability of bovine in vivo-conceived cleavage-stage embryos is higher compared to in vitro-produced embryos. Human Reproduction, Vol.32, No.11 pp.2348–2357. doi:10.1093/humrep/dex286 (JP)

16. Dimitriadou E, Melotte C, Debrock S, Esteki MZ, Dierickx K, Voet T, Devriendt K, de Ravel T, Legius E, Peeraer K, Meuleman C, Vermeesch JR (2017). Principles guiding embryo selection following genome-wide haplotyping of preimplantation embryos. Human Reproduction, 2017 Mar 1;32(3):687-697. doi: 10.1093/humrep/dex011

17. Rahmioglu N, Drong AW, Lockstone H, Tapmeier T, Hellner K, Saare M, Laisk-Podar T, Dew C, Tough E, Nicholson G, Peters M, Morris AP, Lindgren CM, Becker CM, Zondervan KT. Variability of genome-wide DNA methylation and mRNA expression profiles in reproductive and endocrine disease related tissues. Epigenetics. 2017 Nov 3:0. doi: 10.1080/15592294.2017.1367475  (JP)

18. OlgaTšuiko, Tatjana Jatsenko, Lalit Kumar Parameswaran Grace, Ants Kurg, Joris Robert Vermeesch, Fredrik Lanner, Signe Altmäe, Andres Salumets. A speculative outlook on embryonic aneuploidy: Can molecular pathways be involved? Developmental Biology. Available online 31 January 2018. https://doi.org/10.1016/j.ydbio.2018.01.014 (JP)

19. Olga Tšuiko, Daria I.Zhigalina, Tatjana Jatsenko, Nikolay A.Skryabin, Olga R.Kanbekova, Victoria G.Artyukhova, Anatoly V.Svetlakov, Katre Teearu, Aleksander Trošin, Andres Salumets, Ants Kurg, Igor N.Lebedev. Karyotype of the blastocoel fluid demonstrates low concordance with both trophectoderm and inner cell mass. Fertility and Sterility, 2018 Jun;109(6):1127-1134.e1.  https://doi.org/10.1016/j.fertnstert.2018.02.008.

20. Sauk M, Žilina O, Kurg A, Ustav EL, Peters M, Paluoja P, Roost AM, Teder H, Palta P, Brison N, Vermeesch JR, Krjutškov K, Salumets A, Kaplinski L. NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies. Sci Rep. 2018 Apr 4;8(1):5616. https://doi.org/10.1038/s41598-018-23589-8. (JP)

21. Saare M, Krigul KL, Laisk-Podar T, Ponandai-Srinivasan S, Rahmioglu N, Lalit Kumar PG, Zondervan K, Salumets A, Peters M. DNA methylation alterations-potential cause of endometriosis pathogenesis or a reflection of tissue heterogeneity? Biology of Reproduction, Volume 99, Issue 2, 1 August 2018, Pages 273–282. Published 21 March 2018. doi: 10.1093/biolre/ioy067. (JP)

22. PhD defence:
Thesis of Natalia Pervjakova (UTARTU) "Genomic imprinting in complex traits" (22.06.2018 in UTARTU)
Curriculum: Molecular and Cell Biology
Speciality: Molecular Biomedicine
Supervisors: Senior Research Fellow Reedik Mägi, Institute of Genomics and Professor Andres Metspalu, Institute of Genomics and Molecular and Cell Biology, University of Tartu
Opponent: Professor Stephan Beck, University College London, London, UK

23. Public outreach:
"Genetic profiling could improve IVF success". 29.03.2018.
Horizon, The EU Research&Innovation Magazine
An interview of Frieda Klotz with Prof. Joris Vermeesch

24. Le MT, Nguyen TTA, Nguyen TTT, Nguyen VT, Le DD, Nguyen VQH, Cao NT, Aints A, Salumets A. Thinning and drilling laser-assisted hatching in thawed embryo transfer: A randomized controlled trial. Clinical and Experimental Reproductive Medicine. Published online 3 Sept 2018; 45(3):129-134.  https://doi.org/10.5653/cerm.2018.45.3.129

25. Ponandai-Srinivasan S, Andersson KL, Nister M, Saare M, Hassan HA, Varghese SJ, Peters M, Salumets A, Gemzell-Danielsson K, Lalitkumar PGL. Aberrant expression of genes associated with stemness and cancer in endometria and endometrioma in a subset of women with endometriosis. Human Reproduction, Volume 33, Issue 10, 1 October 2018, Pages 1924–1938. doi: 10.1093/humrep/dey241. Free PMC article.

26. Marjonen H, Auvinen P, Kahila H, Tšuiko O, Kõks S, Tiirats A, Viltrop T, Tuuri T, Söderström-Anttila V, Suikkari AM, Salumets A, Tiitinen A, Kaminen-Ahola N. rs10732516 polymorphism at the IGF2/H19 locus associates with genotype-specific effects on placental DNA methylation and birth weight of newborns conceived by assisted reproductive technology. Clinical Epigenetics. Published 2018 June 18; 10:80. doi: 10.1186/s13148-018-0511-2. eCollection 2018.

27. Marina Suhorutshenko, Viktorija Kukushkina, Agne Velthut-Meikas, Signe Altmäe, Maire Peters, Reedik Mägi, Kaarel Krjutškov, Mariann Koel, Francisco M Codoñer, Juan Fco Martinez-Blanch, Felipe Vilella, Carlos Simón, Andres Salumets, Triin Laisk. Endometrial receptivity revisited: endometrial transcriptome adjusted for tissue cellular heterogeneity. Human Reproduction, dey301, https://doi.org/10.1093/humrep/dey301; Published 08.10.2018.

28. Kadri Rekker, Signe Altmäe, Marina Suhorutshenko, Maire Peters, Juan F. Martinez-Blanch, Francisco M. Codoñer, Felipe Vilella, Carlos Simón, Andres Salumets,  Agne Velthut-Meikas. A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women, Genes 2018, 9(12), 574; https://doi.org/10.3390/genes9120574; Published: 23.11.2018.

29. PhD defence
Thesis of Olga Tšuiko (UTARTU) "Unravelling chromosomal instability in mammalian preimplantation embryos using single-cell genomics" (26.11.2018 in UTARTU)
Curriculum: Medical Science
Supervisors: Professor Andres Salumets, Department of Obstetrics and Gynaecology / Institute of Biomedicine and Translational Medicine, University of Tartu; Professor Joris Robert Vermeesch, Laboratory for Cytogenetics and Genome Research / Center for Human Genetics, KU Leuven, Belgium; Professor Ants Kurg, Department of Biotechnology / Institute of Molecular and Cell Biology, University of Tartu
Opponent: Professor Joyce Harper, Department of Reproductive Health / Institute for Women’s Health / University College London, United Kingdom

30. Kadri Rekker, Tõnis Tasa, Merli Saare, Külli Samuel, Ülle Kadastik, Helle Karro, Martin Götte, Andres Salumets, Maire Peters. Differentially-Expressed miRNAs in Ectopic Stromal Cells Contribute to Endometriosis Development: The Plausible Role of miR-139-5p and miR-375
Int. J. Mol. Sci. 2018, 19(12), 3789; doi:10.3390/ijms19123789; Published: 28.11.2018.

31. Felix Day, Tugce Karaderi, Michelle R Jones, Cindy Meun, Chunyan He, Alex Drong, Peter Kraft, Nan Lin, Hongyan Huang, Linda Broer, Reedik Magi, Richa Saxena, Triin Laisk-Podar, Margrit Urbanek, Geoffrey M Hayes, Gudmar Thorleifsson, Juan Fernandez-Tajes, Anubha Mahajan, Benjamin H Mullin, Bronwyn G.A. Stuckey, Timothy D. Spector, Scott G Wilson, Mark O Goodarzi, Lea Davis, Barbara Obermeyer-Pietsch, Andre G Uitterlinden, Verneri Anttila, Benjamin M Neale, Marjo-Riitta Jarvelin, Bart Fauser, Irina Kowalska, Jenny A Visser, Marianne Anderson, Ken Ong, Elisabet Stener-Victorin, David Ehrmann, Richard S Legro, Andres Salumets, Mark I McCarthy, Laure Morin-Papunen, Unnur Thorsteinsdottir, Kari Stefansson, 23andMe Research Team, Unnur Styrkarsdottir, John Perry, Andrea Dunaif, Joop S.E. Laven, Steve Franks, Cecilia M Lindgren, Corrine K Welt. 
Large-Scale Genome-Wide Meta Analysis of Polycystic Ovary Syndrome Suggests Shared Genetic Architecture for Different Diagnosis Criteria.
PLOS Genetics.
doi: 10.1371/journal.pgen.1007813 (JP)

32. Hindrek Teder, Mariann Koel, Priit Paluoja, Tatjana Jatsenko, Kadri Rekker, Triin Laisk-Podar, Viktorija Kukuškina, Agne Velthut-Meikas, Olga Fjodorova, Maire Peters, Juha Kere, Andres Salumets, Priit Palta, Kaarel Krjutškov. TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting.
Published onlice, Dec 2018, doi: 10.1038/s41525-018-0072-5

33. Aspasia Destouni, Eftychia Dimitriadou, Heleen Masset, Sophie Debrock, Cindy Melotte, Kris Van Den Bogaert, Masoud Zamani Esteki, Jia Ding, Thiery Voet, Ellen Denayer, Thomy de Ravel, Eric Legius, Christel Meuleman, Karen Peeraer, and Joris R Vermeesch. Genome-wide haplotyping embryos developing from 0PN and 1PN zygotes increases transferrable embryos in PGT-M.
Human Reproduction, Vol.33, No.12 pp. 2302–2311, 2018; Published 31.10.2018; doi:10.1093/humrep/dey325

34. Bovijn J, Jackson L, Censin J, Chen CY, Laisk T, Laber S, Ferreira T, Pulit SL, Glastonbury CA, Smoller JW, Harrison JW, Ruth KS, Beaumont RN, Jones SE, Tyrrell J, Wood AR, Weedon MN, Mägi R, Neale B, Lindgren CM, Murray A, Holmes MV.
GWAS Identifies Risk Locus for Erectile Dysfunction and Implicates Hypothalamic Neurobiology and Diabetes in Etiology.
Am J Hum Genet. 2019 Jan 3;104(1):157-163. doi: 10.1016/j.ajhg.2018.11.004. Epub 2018 Dec 21.
PMID: 30583798 (JP)

35. Laisk T, Kukuškina V, Palmer D, Laber S, Chen CY, Ferreira T, Rahmioglu N, Zondervan K, Becker C, Smoller JW, Lippincott M, Salumets A, Granne I, Seminara S, Neale B, Mägi R, Lindgren CM.
Large-scale meta-analysis highlights the hypothalamic-pituitary-gonadal axis in the genetic regulation of menstrual cycle length.
Hum Mol Genet. 2018 Dec 15;27(24):4323-4332. doi: 10.1093/hmg/ddy317.
PMID: 30202859 (JP)

36. L.C. Gemmell K.E. Webster S. Kirtley K. Vincent K.T. Zondervan C.M. Becker
The management of menopause in women with a history of endometriosis: a systematic review
Human Reproduction Update, Volume 23, Issue 4, 1 July 2017, Pages 481–500, https://doi.org/10.1093/humupd/dmx011
Published: 11 May 2017 Article history
https://academic.oup.com/humupd/article/23/4/481/3814217
Hum Reprod Update. 2017 Jul; 23(4): 481–500.
Published online 2017 May 11
doi: 10.1093/humupd/dmx011

37. Tiina Drell, Jelena Štšepetova, Jaak Simm, Kristiina Rull, Aira Aleksejeva, Anne Antson, Vallo Tillmann, Madis Metsis, Epp Sepp, Andres Salumets, Reet Mändar
The Influence of Different Maternal Microbial Communities on the Development of Infant Gut and Oral Microbiota
Sci Rep. 2017; 7: 9940.
Published online 2017 Aug 30. doi: 10.1038/s41598-017-09278-y
PMCID: PMC5577157
PMID: 28855595

38. Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, GIANT Consortium, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson, Tuomas O. Kilpeläinen, Robert A. Scott, Reedik Mägi, Guillaume Paré, Paul W. Franks
Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions
PLoS Genet. 2017 Jun; 13(6): e1006812.
Published online 2017 Jun 14. doi: 10.1371/journal.pgen.1006812
PMCID: PMC5489225
PMID: 28614350 (JP)

39. Olavi Reinsalu, Ott Scheler, Ruth Mikelsaar, Aavo-Valdur Mikelsaar, Triin Hallap, Ülle Jaakma, Peeter Padrik, Ants Kavak, Andres Salumets, Ants Kurg.  reinsalu_et_al-2019-bmc_veterinary_research.pdf. BMC Veterinary Research (2019) 15:104, https://doi.org/10.1186/s12917-019-1839-3

40. Merli Saare, Triin Laisk, Hindrek Teder, Priit Paluoja, Priit Palta, Mariann Koel, Fred Kirss, Helle Karro, Deniss Sõritsa, Andres Salumets, Kaarel Krjutškov, Maire Peters.
A molecular tool for menstrual cycle phase dating of endometrial samples in endometriosis transcriptome studies. (2019) Biology of Reproduction, ioz072, https://doi.org/10.1093/biolre/ioz072

41. Masoud Zamani Esteki, Triin Viltrop, Olga Tšuiko, Airi Tiirats, Mariann Koel, Margit Nõukas, Olga Žilina, Katre Teearu, Heidi Marjonen, Hanna Kahila, Jeroen Meekels, Viveca Söderström-Anttila, Anne-Maria Suikkari, Aila Tiitinen, Reedik Mägi, Sulev Kõks, Nina Kaminen-Ahola, Ants Kurg, Thierry Voet, Joris Robert Vermeesch & Andres Salumets. In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages. (2019) Nature Medicine. Published 04.11.2019.

42. Olga Žilina, Kadri Rekker, Lauris Kaplinski, Martin Sauk, Priit Paluoja, Hindrek Teder, Eva‐Liina Ustav, Neeme Tõnisson, Tiia Reimand,  Konstantin Ridnõi, Priit Palta, Joris Robert Vermeesch, Kaarel Krjutškov, Ants Kurg, Andres Salumets. Creating basis for introducing non‐invasive prenatal testing in the Estonian public health setting. Prenatal Diagnosis. (2019) First published: 06 November 2019 https://doi.org/10.1002/pd.5578