FIMM Young Investigator of Month
The Young Investigator of the Month honor at FIMM is a monthly highlight of a FIMM PhD student or postdoctoral researcher for a recent significant accomplishment.
November 2019 – Rubina Tabassum, Postdoctoral researcher, Group Ripatti (FIMM)
Congratulations to Rubina Tabassum for her recent publication in Nature Communications.
Tabassum R, Rämö JT, Ripatti P, Koskela JT, Kurki M, Karjalainen J, Palta P, Hassan S, Nunez-Fontarnau J, Kiiskinen TTJ, Söderlund S, Matikainen N, Gerl MJ, Surma MA, Klose C, Stitziel NO, Laivuori H, Havulinna AS, Service SK, Salomaa V, Pirinen M; FinnGen Project, Jauhiainen M, Daly MJ, Freimer NB, Palotie A, Taskinen MR, Simons K, Ripatti S. Genetic architecture of human plasma lipidome and its link to cardiovascular disease. Nat Commun. 2019 Sep 24;10(1):4329. doi: 10.1038/s41467-019-11954-8.
Rubina Tabassum is a postdoctoral researcher in Samuli Ripatti’s research group. Rubina is trained as a geneticist and obtained her Ph.D. from the Institute of Genomics and Integrative Biology in India. Her Ph.D. thesis focused on the identification of genetic factors contributing to type 2 diabetes. After completing her Ph.D., she moved to Georgia Institute of Technology in the USA for postdoctoral training in Prof. Greg Gibson’s lab, where she used multi-omics approach to understand phenotypic variability among individuals and their utility in disease prevention and health promotion. At FIMM, her research work focuses on understanding the underpinnings of cardiovascular diseases using genomics and lipidomics data. The current work provides a comprehensive atlas of genetic regulation of lipid metabolism and link to cardiovascular diseases.
October 2019 – Sailalitha Bollepalli, Doctoral student, Group Ollikainen/ Kaprio (FIMM)
Congratulations to Sailalitha Bollepalli for her recent publication in Epigenomics.
Bollepalli S, Korhonen T, Kaprio J, Anders S*, Ollikainen M*. (2019) EpiSmokEr: a robust classifier to determine smoking status from DNA methylation data. Epigenomics DOI: 10.2217/epi-2019-0206. *equal contribution
Sailalitha Bollepalli is a doctoral candidate in the research groups of Miina Ollikainen and Jaakko Kaprio. She holds a Master's degree in Computational Biology from the University of East Anglia, UK. Her PhD thesis focuses on applying statistical and bioinformatic methods to unravel the contribution of epigenetic mechanisms, specifically DNA methylation to obesity and smoking. In the future, she is interested in applying and developing machine learning algorithms to enhance our understanding of disease mechanisms. Outside of science, she enjoys travelling, exploring nature and cooking.
September 2019 – Sarang Talwelkar, Doctoral student, Group Verschuren/ Wennerberg (FIMM)
Congratulations to Sarang Talwelkar for his recent publication in Molecular Cancer Therapeutics.
Receptor Tyrosine Kinase Signaling Networks Define Sensitivity to ERBB Inhibition and Stratify Kras Mutant Lung Cancers.Talwelkar SS, Nagaraj AS, Devlin JR, Hemmes A, Potdar S, Kiss EA, Saharinen P, Salmenkivi K, Mäyränpää MI, Wennerberg K, Verschuren EW. Mol Cancer Ther. 2019 Jul 18. DOI: 10.1158/1535-7163.MCT-18-0573
Sarang Talwelkar is a FIMM-EMBL PhD student, studying functional heterogeneity of lung cancer under the joint supervision of Emmy Verschuren and Krister Wennerberg. To achieve the therapeutic stratification of lung cancer subtypes, he is utilizing primary cancer cells derived from murine and clinical NSCLC tumors for pharmacogenomic testing. Ultimately, aim of his PhD work is to identify nontoxic precision treatments that could be translated to clinic. Also, he is very much interested in development of cancer models and technologies toward a functional approach for personalized medicine. In the current study, Sarang has worked in close collaboration with Ashwini Nagaraj (contributed equally) to demonstrates stratification of Kras-mutant lung cancer in functional subgroups using murine lung tumor-derived cultures.
August 2019 – Joel Rämö, Doctoral student, Group Palotie/ Ripatti (FIMM)
Congratulations to Joel Rämö for his recent publication in Journal of the American Heart Association.
Rämö JT, Ripatti P, Tabassum R, Söderlund S, Matikainen N, Gerl MJ, Klose C, Surma MA, Stitziel NO, Havulinna AS, Pirinen M, Salomaa V, Freimer NB, Jauhiainen M, Palotie A, Taskinen MRT, Simons K, Ripatti S. Coronary Artery Disease Risk and Lipidomic Profiles Are Similar in Hyperlipidemias With Family History and Population‐Ascertained Hyperlipidemias. 29 Jun 2019. JAHA. 2019;8:e012415. https://doi.org/10.1161/JAHA.119.012415
Joel is a PhD student in the research groups of Aarno Palotie, Samuli Ripatti and Kirsi Pietiläinen. He graduated last year from the medicine program at the University of Helsinki and is now finishing his thesis. His research focus has been on what separates familial from population-based hyperlipidemias. He is motivated by the uncertainty of treating familial disorders in the clinic without a clear monogenic diagnosis. Current results suggest, reassuringly, that many familial hyperlipidemias resemble population-based hyperlipidemias both genetically and with respect to cardiovascular risk. During his studies, Joel spent a research year at the Broad Institute and Massachusetts General Hospital in Boston, Massachusetts. In the future, he would like to tie together research and clinical medicine – his goal is to be in a place where the two cannot be easily picked apart. Outside of the hospital campus, Joel enjoys the outdoors, trail running, writing and travelling.
July 2019 – Alina Malyutina, Doctoral student, Group Tang/ Heckman (FIMM)
Congratulations to Alina Malyutina for her recent publication in PLoS computational biology.
Malyutina A, Majumder MM, Wang W, Pessia A, Heckman CA, Tang J. Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer. PLoS computational biology. 2019 May 20;15(5):e1006752. https://doi.org/10.1371/journal.pcbi.1006752
Alina Malyutina is a doctoral researcher whose main focus is on predicting personalized drug combinations for cancer patients. She is working on development of computational methods and clinically relevant informatics tools to gain understanding of drug combination responses at the molecular level which will help to identify more effective and safe treatment strategies that are urgently needed. She believes that the identified novel drug combinations may be considered for individual patients, especially for those characterized by high-risk profiles and intrinsic resistance to conventional therapies.
She received her MSc degree in Computational Engineering at the Lappeenranta University of Technology (2014), and joined FIMM as a FIMM-EMBL/HIIT PhD rotation student. Having worked in three different groups during her rotation, she joined two complementary teams - Jing Tang's and Caroline Heckman's groups at the beginning of 2017. During her free time, Alina enjoys various family activities, swimming and reading.
June 2019 – Bulat Zagidullin, Doctoral student, Group Tang (FIMM)
Congratulations to Bulat Zagidullin for his recent publication in Nucleic Acids Research.
Zagidullin B, Aldahdooh J, Zheng S, Wang W, Wang Y, Saad J, Malyutina A, Jafari M, Tanoli Z, Pessia A, Tang J. DrugComb: an integrative cancer drug combination data portal. Nucleic Acids Res. 2019 May 8. pii: gkz337. doi: 10.1093/nar/gkz337.
Bulat has been a PhD student in Jing Tang’s group since February 2018, where he has been working on modelling and predicting the effects of drug combinations in cancer treatment. He has got a BSc degree in Biochemical Engineering from the Jacobs University Bremen (2011), MSc in Pharmaceutical Biotechnology from the Martin Luther University Halle-Wittenberg (2017). Bulat has got industry experience working in various engineering positions in Italy and Germany. He is fascinated by the complexity, temporal variability and robustness of biological networks. Bulat strongly believes in making scientific research open, reproducible and accessible to general public. His ultimate goal is to find a way how to make people live a bit longer and healthier. When not staring in the computer screen for his work duties Bulat enjoys music in all its shapes and forms and cooking with friends. One day he hopes to complete an Ironman race, but that day might be far in the future.
May 2019 – Oscar Holmström, Doctoral student, Group Lundin (FIMM)
Congratulations to Oscar Holmström for his recent publication in PLOS One.
Holmstrom, O., Linder, N., Moilanen, H., Suutala, A., Nordling, S., Stahls, A., Lundin, M., Diwan, V. & Lundin, J. 2019. "Detection of breast cancer lymph node metastases in frozen sections with a point-of-care low-cost microscope scanner." PLoS ONE, vol. 14, no. 3, pp. e0208366.
Oscar is a PhD student in Johan Lundin's research group. He graduated last year from University of Helsinki, Faculty of Medicine and is currently working on finishing his thesis. Current area of research focuses on studying how low-cost digital microscopy and machine learning-based image analysis can be utilized to improve medical diagnostics, with an emphasis on applications in low-resource areas. For this, he has been involved in clinical field studies in Tanzania and Kenya to study how this type of technology can be implemented in real world settings for diagnostics of e.g. common parasitic diseases and analysis of cytological samples, such as pap smears. Apart from work, Oscar has developed a serious running addiction and enjoys long-distance running, preferably very early in the morning.
April 2019 – Emma Cazaly, Postdoctoral Researcher, Group Ollikainen (FIMM)
Congratulations to Emma Cazaly for her recent publication in Frontiers in Pharmacology.
Cazaly, E., Saad, J., Wang, W., Heckman, C., Ollikainen, M. & Tang, J. 2019, 'Making Sense of the Epigenome Using Data Integration Approaches', Frontiers in Pharmacology, vol. 10, 126. https://doi.org/10.3389/fphar.2019.00126
Emma Cazaly has been a post-doctoral researcher in Miina Ollikainen’s group for the past two years, where she has been examining epigenomics of complex diseases with Finnish Twin data. Prior to joining FIMM, Emma obtained her PhD in Prostate Cancer Genomics and Epigenomics at the Menzies Institute for Medical Research and the University of Tasmania in Australia. Outside of research Emma loves to be outdoors and to travel- so much so that from April she will leave FIMM to travel for the rest of the year.
February 2019 – Suvi Virtanen, Doctoral Student, Group Latvala (FIMM)
Congratulations to Suvi Virtanen for her recent publication in Addiction.
Virtanen S., Kaprio, J., Viken R.J., Rose R.J., Latvala A. Birth cohort effects on the quantity and heritability of alcohol consumption in adulthood: A Finnish longitudinal twin study. Addiction. doi: 10.1111/add.14533.
Suvi Virtanen is a doctoral candidate in Antti Latvala’s research group. She has Master’s degrees in Economic and Social History and Psychology from University of Helsinki. Before joining FIMM she gained research experience from a wide scope of topics such as sleep, mental health, and organized crime. Her current work centers around substance misuse, anxiety-related disorders, and anti-social behavior using advanced genetically informative research designs based on population-based samples with genotype and relatedness information. Substance use disorders and other common mental disorders are among the leading causes of disability and associated with reduced life expectancy and social marginalization. For these reasons, she finds psychiatric epidemiology to be critically important area of research. Outside of work, Suvi enjoys rock climbing, free skiing, and relaxing by reading good books.
December 2018 – Jaakko Leinonen, Doctoral Student, Group Widén (FIMM)
Congratulations to Jaakko Leinonen for his recent publication in Mol Cell Endocrinol.
Leinonen JT, Chen YC, Tukiainen T, Panula P, Widén E. (2019) Transient modification of lin28b expression - Permanent effects on zebrafish growth. doi: 10.1016/j.mce.2018.09.001.
Jaakko Leinonen is a doctoral candidate in Elisabeth Widén's group. He received his BSc in Human Genetics from Newcastle University, UK and completed his MSc in the same subject at the University of Helsinki. During his PhD studies here at FIMM, Jaakko has gained versatile experience in the field of genetics. His PhD thesis involves studying the genetics of puberty, where he has combined large-scale human cohort studies and model organism studies (e.g. CRISPR-Cas9 knockout models in zebrafish) to better understand the biology behind pubertal timing. Besides tackling complex, polygenic traits like puberty, Jaakko is also experienced in the field of cardiac arrhythmias, that are often caused by defects in a single gene. Through clinical collaborations he has been involved in exome sequencing studies that have led to the identification of novel genetic mutations causing these disorders. Besides his scientific projects, Jaakko has been actively involved in organising training in transferable "soft" skills for FIMM students. Outside FIMM, Jaakko enjoys keeping busy with his family including three children, and does his best to arrange time for his special interests that include endurance sports such as cross-country skiing, orienteering, and running.
September 2018 – Alyce Whipp, Doctoral Student, Group Kaprio/Vuoksimaa/ Korhonen (FIMM)
Congratulations to Alyce Whipp for her recent publication in Eur Child Adolesc Psychiatry.
Whipp, A. M., Korhonen, T., Raevuori, A., Heikkila, K., Pulkkinen, L., Rose, R. J., Kaprio, J., Vuoksimaa, E. (2018). Early adolescent aggression predicts antisocial personality disorder in young adults: a population-based study. Eur Child Adolesc Psychiatry. doi:10.1007/s00787-018-1198-9
Alyce Whipp is a doctoral candidate in Jaakko Kaprio’s group, supervised by Tellervo Korhonen and Eero Vuoksimaa. She received her BS in Biology and MPH in Epidemiology from the University of Michigan, USA and has since lived and worked in the USA, France, Canada, and Finland on projects related to health inequality, substance (ab)use, glaucoma genetics, organ transplantation, and maternal and child health issues. Her current work centers around adolescent aggression, investigating a broad range of associated co-occurring behaviors and young adult outcomes. The wide scope of her current and past work has been a happy accident, but one that has fostered a love for interdisciplinary engagement. Continuing along these lines in her non-research time, she also edits scientific manuscripts and teaches scientific soft skills (e.g., academic writing, conference presentation). When not working, she spends time visiting new places and sampling new food with her family, and tries to steal quiet moments for curling up with good books.
August 2018 – Komal Kumar Javarappa, Postdoctoral Researcher, Group Heckman (FIMM)
Congratulations to Komal Kumar for his recent publication in SLAS Discovery.
Komal K.Javarappa, Dimitrios Tsallos, Caroline A.Heckman. “A multiplexed Screening Assay to Evaluate Chemotherapy-Induced Myelosuppression Using Healthy Peripheral Blood and Bone Marrow” SLAS Discovery 2018 23:7, 687-696
Komal Kumar is a postdoctoral researcher in Caroline Hackman’s research group. He is trained as an environmental biologist and obtained his M.Sc and Ph.D degrees in the department of Environmental Science, University of Mysore, Karnataka, India. After completing his Ph.D in 2013, he moved to University of Linkoping, Sweden for his first postdoctoral training in Prof. Jan-Ingvar’s lab. His research focused on understanding the regulation and differentiation of hematopoietic stem cells and leukemia initiating cells. During this period, he gained extensive hands on experience on CyTOF technology and flow cytometry. Currently, Komal is working on understanding the mechanisms of disease pathogenesis and identifying novel treatments for hematological malignancies by applying High-throughput flow cytometry techniques.
June 2018 – Kauko Heikkilä, Doctoral Student, Group Kaprio/Vuoksimaa (FIMM)
Congratulations to Kauko Heikkilä for his recent publication in PNAS.
Kauko Heikkilä, Catharina E. M. Van Beijsterveldt, Jari Haukka, Matti Iivanainen, Aulikki Saari-Kemppainen, Karri Silventoinen, Dorret I. Boomsma, Yoshie Yokoyama, and Eero Vuoksimaa (2018). Triplets, birthweight, and handedness. Proceedings of the National Academy of Sciences, 10.1073/pnas.1719567115
Kauko Heikkilä has been the data-manager of the Kaprio Group/Twin Registry since 1983. Formally retired, after 34 years, he, as-of-to-date, keeps supporting the efforts of the group, including through his doctoral studies. He started studying mathematics and physics in 1970 in the University of Helsinki, and reached his Phil. Lic. in 1982 in Nuclear Physics. Prenatal covariates of human handedness became his topic of interest when he, in March 2013, registered as a PhD student. As a result of earlier work, there arose a wish to confirm that twins had an increased proportion of left-handedness that prenatal covariates would explain. Longstanding co-work with Japanese and Dutch researchers opened a possibility to replicate the expected association with handedness using triplets from two countries. Clear associations emerged, and birthweight remained a more prominent covariate than gestational age, as also partially controlled within-triplets. Thus, he regards that growth factors (read genes) themselves should be looked into, as the association only shows up in the very low end (around 1500g, with triplets being approximately 1700g of weight) of the birthweight distribution, and because multiple births have their own special reasons for remaining small. His future plans are open, but are likely to be in connection with handedness research, as there is much to prove/disprove in the field. During his free time the Kauko likes to wander in nature and has had singing as a long-time hobby.
May 2018 - Mehreen Ali, Doctoral Student, Group Aitokallio (FIMM)
Congratulations to Mehreen Ali for her recent publication in Bioinformatics.
Ali M, Khan SA, Wennerberg K, Aittokallio T. Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. Bioinformatics 2018, 34(8), 1353-1362
Mehreen Ali is a PhD student in Tero Aittokallio’s group. She has a background in Bioinformatics. She obtained her dual Master’s degree as an Erasmus scholar in Computational and Systems Biology (euSYSBIO) from Aalto University, Finland and KTH Royal Institute of Technology, Sweden. Mehreen’s PhD research focuses on improving drug sensitivity predictions and identifying panels of response-predictive biomarkers in multi-omics data for translational applications. To achieve these aims, she applies probabilistic multi-source machine learning data integration approaches, and feature selection methods for in-depth pan-cancer analysis. A part of her thesis work will also focus on the translation of model predictions to personalized ovarian cancer (OvCa) treatments by identifying functional signatures in OvCa patient tumors, together with the clinical collaborators. Mehreen is also a strong advocate of gender diversity in Data Science and believes in mentoring more women to get in this field. She recently organized the first ever Global Women in Data Science (WiDS) regional session in Finland.
April 2018 - Andrew Erickson, Doctoral Student, Group Mirtti (FIMM)
Congratulations to Andrew Erickson not just for his recent publication in Human Pathology, but also for the acceptance of two more papers. Meaning that he can soon defend his thesis and join Johns Hopkins for a short term post-doctoral fellowship.
Erickson A, Sandeman K, Lahdensuo K, Nordling S, Kallajoki M, Seikkula H, Bützow A, Vasarainen H, Boström PJ, Taimen P, Rannikko A, Mirtti T (2018) New prostate cancer grade grouping system predicts survival after radical prostatectomy. Hum Pathol 0: doi:10.1016/j.humpath.2018.01.027.
Andrew is currently pursuing his PhD at FIMM in Dr. Tuomas Mirtti's research group. He completed his Bachelor's degree in Biology at Pacific University, Oregon, USA, before moving to Finland in 2011 to attend TRANSMED MSc studies at the University of Helsinki, Faculty of Medicine. During his MSc studies, he joined the former Helsinki Urological Biobank. Additionally, Andrew completed his Finnish civil service as a research assistant in the Department of Urology with Dr. Antti Rannikko. Andrew's core expertise is in designing and executing strategies to systematically query and organize hospital and registry data for research project datasets. His work has primarily utilized archival prostate cancer patient samples, modeling patient outcomes using novel biomarker and data-based prognostic markers. In addition to his doctoral work, Andrew works part time in the Helsinki Biobank as a project manager to identify and analyze patient data associated with biobank requests. Having submitted his dissertation for pre-examination, Andrew will be heading to an Academy of Finland funded fellowship in the group of Dr. Angelo De Marzo, Department of Pathology, John's Hopkins University, Baltimore, USA. In addition to his academic work, Andrew enjoys traveling, cooking, and learning new languages.
March 2018 - Heikki Kuusanmäki, Doctoral Student, Group Heckman (FIMM) and Satu Mustjoki (HRUH)
Congratulations to Heikki Kuusanmäki for his recent publication in Oncotarget!
Heikki Kuusanmäki., Olli Dufva, Elina Parri, Arjan J. van Adrichem, Hanna Rajala, Muntasir M. Majumder, Bhagwan Yadav, Alun Parsons, Wing C. Chan, Krister Wennerberg, Satu Mustjoki and Caroline Heckman. “Drug sensitivity profiling identifies potential therapies for lymphoproliferative disorders with overactive JAK/STAT3 signaling.” Oncotarget. 2017;8(57):97516–97527.
Heikki is balancing his PhD studies both in Caroline Heckman’s group at FIMM and Satu Mustjoki’s group at Hematology Research Unit Helsinki (HRUH). He has always been fascinated in translational research that could directly benefit the patient. After getting a BSc in Genetics, Heikki pursued a MSc in Translational Medicine at the University of Helsinki. In his early PhD projects Heikki was involved in studies identifying pathogenic STAT3 and STAT5B mutations in a subset of leukemias. His current project focuses on developing a novel drug-screening approach to screen acute myeloid leukemia (AML) patient cells at a single cell level. This method could be implemented to identify more effective targeted drugs and drug combinations, accelerating drug discovery and individualizing therapy for AML patients. Outside of work, Heikki enjoys swimming and skiing, playing board games and going to music festivals with friends.
February 2018 - Sami Blom, Doctoral Student, Group Kallioniemi (FIMM)
Congratulations to Sami Blom for his recent publication in Scientific Reports!
Blom S., Paavolainen L., Bychkov D., Turkki R., Mäki-Teeri P., Hemmes A., Välimäki K., Lundin J., Kallioniemi O., & Pellinen T. (2017) Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis. Scientific Reports. 7(1):15580.
Sami is currently pursuing his PhD at FIMM in Olli Kallioniemi´s research group. He completed his Master´s degree in biochemistry and biotechnology at the University of Turku, and moved to Helsinki for his PhD studies. Sami is experienced in developing and implementing immunoassays for in vitro diagnostics and for histology. As part of his thesis, a new analytical method was developed for histopathology providing a novel tool to study solid tumours. In his thesis, the developed method is utilised to study and identify prognostic biomarkers in prostate cancer. Alongside finalising his doctoral studies, Sami is working part-time in a R&D team at Fimmic Oy. He recovers from the busy working hours by sporting and spending time outdoors. He has visited 36 out of the 40 national parks in Finland, and aims to complete the list as soon as possible.
January 2018 - Ashwini Kumar, Doctoral Student, Group Heckman (FIMM)
Congratulations to Ashwini Kumar for his recent manuscript published in BMC Genomics!
Kumar, A., Kankainen, M., Parsons, A., Kallioniemi, O., Mattila, P., and Heckman, C.A. The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia. BMC Genomics, 2017, 18:629, doi: 10.1186/s12864-017-4039-1.
Ashwini is a PhD student in the Personalized Medicine research group led by Caroline Heckman. He obtained his Master by Research degree in bioinformatics and molecular biology from Nottingham Trent University, UK followed by research assistance experience at the Jon van Geest Cancer Research Center, Nottingham, UK. He was trained in biotechnology in India and subsequently worked as a research associate at Intas Biophamaceutical company. Ashwini is primarily working on analyzing next generation sequencing data to identify biomarkers for drug responses in various hematological malignancies. His main expertise lies in the analysis of clinically relevant RNA-seq gene expression and fusion genes in different tumor types. During his PhD he aspires to achieve broad knowledge and expand his expertise to the integration of multi-omics data with cellular phenotypes to identify actionable strategies towards precision cancer medicine care. He has an apt for scientific business ventures and was involved in the winning team “iCombine” in the Helsinki Challenge 2017. Along with research, he loves travelling and sports.
December 2017 - Anna Cichonska, FIMM-EMBL/HIIT Doctoral Student, Groups Aittokallio and Pirinen (FIMM) and Rousu (HIIT)
Congratulations to Anna Cichonska for her recent manuscript published in PLoS Computational Biology. This work, driven by Anna is a great example of team science and multi-university collaboration with both experimental and computational analyses.
Cichonska A, Ravikumar B, Parri E, Timonen S, Pahikkala T, Airola A, Wennerberg K, Rousu J, Aittokallio T: "Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors." PLoS Computational Biology 2017; 13(8): e1005678.
Anna is a doctoral student in the FIMM-EMBL/HIIT International PhD Program in Molecular Medicine and Bioinformatics, a collaborative training initiative between Helsinki Institute for Information Technology HIIT and Institute for Molecular Medicine Finland FIMM. Before coming to Finland, Anna completed both Bachelor’s and Master’s degrees in Bioinformatics at the Silesian University of Technology in Poland.
Anna is interested in the development and use of computational methods, especially machine learning, to facilitate different stages of drug development process, including drug-target binding affinity prediction and pharmacogenomic models linking genetic information to drug indications. Since the autumn of 2014, Anna co-organizes the Think Different seminar series at FIMM.
Outside of science, Anna enjoys travelling, hiking, fitness and baking.
November 2017 - Jarno Kivioja, Doctoral Student, Group Heckman (FIMM)
Congratulations to Jarno Kivioja for his recent publication in Leukemia & Lymphoma!
Jarno Kivioja, Jesus M. Lopez Marti, Ashwini Kumar, Mika Kontro, Henrik Edgren, Alun Parsons, Tuija Lundan, Maija Wolf, Kimmo Porkka & Caroline Heckman. Chimeric NUP98-NSD1 transcripts from the cryptic t(5;11)(q35.2;p15.4) in adult de novo acute myeloid leukemia. Leukemia & Lymphoma. Aug 2017. doi: 10.1080/10428194.2017.1357174
Jarno is a PhD student in the translational research and personalized medicine research group led by Caroline Heckman at FIMM. He received his Master’s degree in biotechnology from the University of Helsinki and Bachelor’s degree from the University of Northern Iowa, USA. His PhD thesis project focuses on improving the treatment and molecular detection of translocation (5;11) positive acute myeloid leukemia (AML), which defines a biologically distinct subset of AML patients with poor prognosis. Outside of the lab, Jarno enjoys pole vaulting, movies, and traveling.
October 2017 - Sini Kerminen, Doctoral Student, Groups Pirinen and Ripatti (FIMM)
Congratulations to Sini Kerminen for her recent publication in G3: Genes, Genomes, Genetics!
Sini Kerminen, Aki S. Havulinna, Garrett Hellenthal, Alicia R. Martin, Antti-Pekka Sarin, Markus Perola, Aarno Palotie, Veikko Salomaa, Mark J. Daly, Samuli Ripatti, and Matti Pirinen. Fine-Scale Genetic Structure in Finland. G3: Genes, Genomes, Genetics Oct 2017, doi: 10.1534/g3.117.300217
Sini is a doctoral student in groups Pirinen and Ripatti. She obtained her Master's degree at the University of Helsinki majoring in biotechnology. A firm background in biology and strong interest in computational methods drove her to continue work with population genetics. Her PhD project focuses on understanding genetic population structure in Finland and utilizing it in the studies of complex diseases. Sini is fascinated about how studies of population genetics can both give unique opportunities for genetic research and shed light on human history. To share her excitement with the general public, Sini, together with her supervisor and FIMM personal, set up a website where people can browse the above new results also in Finnish. In her free time, she enjoys walking in nature catching Pokémon.
September 2017 - Riikka Karjalainen, Doctoral Student, Group Heckman (FIMM)
Congratulations to Riikka Karjalainen for her recent publication in Blood!
Karjalainen R, Pemovska T, Popa M, Liu M, Javarappa KK, Majumder MM, Yadav B, Tamborero D, Tang J, Bychkov D, Kontro M, Parsons A, Suvela M, Mayoral Safont M, Porkka K, Aittokallio T, Kallioniemi O, McCormack E, Gjertsen BT, Wennerberg K, Knowles J, Heckman CA. JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML. Blood. 2017. 130:789-802. doi: 10.1182/blood-2016-02-699363.
Riikka Karjalainen is a PhD student in the Personalized Medicine research group led by Caroline Heckman. She holds a MSc degree in biochemistry from the University of Oulu, Finland. Before joining FIMM she gained experience from the fields of endocrinology and developmental biology by working at the Institute of Reproductive and Developmental Biology, Imperial College London, UK and U636 INSERM, Université de Nice Sophia Antipolis, France. Riikka’s PhD project is focused on acute myeloid leukemia (AML) and understanding the role of bone marrow microenvironment and its factors on drug resistance. More specifically she is studying mechanisms of drug resistance on AML and identifying novel treatment strategies for the disease. Outside of the lab, Riikka enjoys travelling and sports.
August 2017 - Alok Jaiswal, FIMM-EMBL Doctoral Student, Group Aittokallio (FIMM)
Congratulations to Alok Jaiswal for two recent first author publications!
Jaiswal A, Peddinti G, Akimov Y, Wennerberg K, Kuznetsov S, Tang J, Aittokallio T. Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells. Genome Med. 2017, 9: 51.
Gönen M*, Weir BA*, Cowley GS*, Vazquez F*, Guan Y*, Jaiswal A*, Karasuyama M*, Uzunangelov V*, Wang T* et al. A community-based challenge for building predictive models of gene essentialities over a large-scale functional screen of cancer cell lines. 2017 Cell Systems (in press).
Alok Jaiswal is a FIMM-EMBL PhD student in the Aittokallio group. He is trained as a biologist and earned his Masters degree in Jamia Hamdard, New Delhi. His PhD project focuses on finding better drug treatment strategies for breast cancer. He uses bioinformatics, data analysis techniques and machine learning methods to identify genes that are essential for survival of cancer cells. In the future, he is interested in data integration and applying systems-based computational models to predict the response of cancer cells to drug treatments. In the longer term, he is also interested in developing new experimental techniques that can provide a novel molecular portrait of cellular systems, similar to transcriptome, proteome, etc. Alok is also interested in science communication and outreach and a member of scicomm outfit, The Science Basement.
July 2017 - Balaguru Ravikumar, FIMM-EMBL Doctoral Student, Group Aittokallio (FIMM)
Congratulations to Balaguru Ravikumar for his recent paper entitled "C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms" published in May 2017 in Nucleic Acids Research!
Ravikumar, B., Alam, Z., Peddinti, G., Aittokallio, T. Nucleic Acids Res. (2017); 45 (W1): W495-W500. doi: 10.1093/nar/gkx384
Balaguru Ravikumar is a FIMM-EMBL Doctoral Student in the Computational Systems Medicine Group led by Tero Aittokallio. Prior to joining FIMM, Balaguru obtained his M. Tech degree in Computational and System Biology from Jawaharlal Nehru University, New Delhi and B. Tech in Biotechnology from Anna University, India. His doctoral dissertation focuses primarily on developing computational frameworks to aid pharmacological studies, and includes designing interactive visualization tools, implementing comprehensive databases and predictive models for compound-target interactions. Currently Balaguru is working towards developing a statistical model that could serve as a virtual compound screening platform targeting the kinase family of proteins. In the future, he would like to develop a systems-based computational model for identifying molecular biomarkers and predict drug-combination efficacies. Apart from research, he enjoys reading books, music and fishing.
June 2017 - Muntasir Mamun Majumder, FIMM-EMBL Doctoral Student, Group Heckman (FIMM)
Congratulations to Mamun Majumder for his recent paper entitled "Identification of precision treatment strategies for relapsed/ refractory multiple myeloma by functional drug sensitivity testing" published in May 2017 in Oncotarget!
Majumder, M.M., Silvennoinen, R., Anttila, P., Tamborero, D., Eldfors, S., Yadav, B., Karjalainen, R., Kuusanmäki, H., Lievonen, J., Parsons, A., Suvela, M., Jantunen, E., Porkka, K., Heckman, C.A. Oncotarget (2017) doi: 10.18632/oncotarget.17630.
Mamun is a FIMM/EMBL Doctoral Student in the Translational Research and Personalized Medicine research group headed by Caroline Heckman. He trained as a pharmacist and received his MSc degree in genetic toxicology from Stockholm University, Sweden. During his Masters studies he worked in the Thomas Helleday Laboratories to decipher mechanistic complexity of DNA damage repair signaling pathways induced by radiation. His PhD research project aims at understanding patient heterogeneity and improving precision treatment strategies in multiple myeloma (MM). MM is the second most common hematologic malignancy affecting 86,000 people annually worldwide. Although the recurrent molecular alterations and their prognostic importance are well characterized, the causal relationship of drug responses and their utility for matching therapeutics to individual patient is yet lacking. His work has applied high-throughput phenotypic screens (Drug Sensitivity and Resistance Testing (DSRT) and flow cytometry) and paired molecular profile data (mutations, gene and protein expression profiles) in a large cohort of myeloma patients and has steered exciting discoveries on i) patient stratification, ii) accelerated understanding of drug resistance mechanisms, iii) on/off-target effects of small molecules, and iv) molecular avenues to disease progression. His work has impact on the treatment outcome of multiple myeloma patients, boosting drug discovery efforts. Outside of his pipetting world, he enjoys photography, music, fishing, hiking in the Norwegian mountains and being rescued by helicopter.
May 2017 - Jenni Lahtela, Postdoctoral Researcher, FIMM Technology Centre Single Cell Analytics unit
Congratulations to Jenni Lahtela for a successful and very rapid implementation of the 10x Genomics Chromium single cell platform and services in the FIMM Technology Centre Single Cell Analytics unit!
The 10x Genomics Chromium platform produces gene expression data on a cell-by-cell basis from 100 to 10 000 cells and up to eight parallel samples. The rapidly growing field of single cell analytics seeks to answer questions about cellular heterogeneity in various diseases and developmental processes and can lead to the discovery of novel cell subtypes and stages. The Infrastructure for Single Cell Capture and Processing at FIMM received funding for three years from the Academy of Finland. The successful collaborative infrastructure application was coordinated by Pirkko Mattila the Head of the Single Cell Analytics unit at FIMM Technology Centre.
Jenni is a postdoctoral researcher in the FIMM Technology Centre where she coordinates the activities of the Single Cell Analytics unit. Jenni obtained her Master’s degree in biology from the University of Oulu. Her research experience extends from human genetics of early developmental disorders to functional in vitro and in vivo investigation of lung cancer molecular biology. Jenni did her PhD in the Lung Cancer Model Systems research group of Dr. Emmy Verschuren at FIMM. Jenni is fascinated about the new level of biological resolution that the single cell analytics provides. She enjoys working with a variety of research projects and hopes to continue in the field of single cell analytics in the future. Jenni also likes the joyful, highly motivated and professional working atmosphere at the FIMM Technology Centre. Outside of science, Jenni likes dancing, outdoor swimming and skiing.
April 2017 - Himanshu Chheda, FIMM-EMBL Doctoral Student, Groups Ripatti and Aitokallio (FIMM)
Congratulations to Himanshu Chheda for his recent paper entitled "Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom" published in February 2017 in the European Journal of Human Genetics!
Himanshu Chheda, Priit Palta, Matti Pirinen, Shane McCarthy, Klaudia Walter, Seppo Koskinen, Veikko Salomaa, Mark Daly, Richard Durbin, Aarno Palotie, Tero Aittokallio and Samuli Ripatti for the Sequencing Initiative Suomi (SISu) Project. European Journal of Human Genetics (2017) 25, 477–484; doi:10.1038/ejhg.2016.205
Himanshu is a FIMM-EMBL Doctoral Student in Prof. Samuli Ripatti’s and Prof. Tero Aittokallio’s groups. Before coming to Helsinki, Himanshu obtained his Master’s degree in Bioinformatics from the University of Pune, India. Himanshu is interested in studying the genetics of complex diseases. Today, we live in an exciting time with ever increasing data from various sources and access to electronic health records. Currently he is applying machine-learning approaches to integrate information from various sources to study time-to-event for coronary heart disease for better prognosis and identifying individuals at highest risk. In his free time, he enjoys outdoor sports and travelling.
March 2017 - Maija Puhka, Postdoctoral Researcher, Groups Kallioniemi and Groop (FIMM)
Congratulations to Maija Puhka for her recent paper entitled " KeepEX, a simple dilution protocol for improving extracellular vesicle yields from urine." published in February 2017 in the European Journal of Pharmaceutical Sciences!
Puhka, M., Nordberg, M.E., Valkonen, S., Rannikko, A., Kallioniemi, O., Siljander, P., Af Hällström, T.M. KeepEX, a simple dilution protocol for improving extracellular vesicle yields from urine. Eur. J. Pharm. Sci. 2017 Feb 15: 30-39.
Maija is a postdoctoral fellow in Olli Kallioniemi’s and Leif Groop’s research groups and manages the functions of the newly established Extracellular Vesicle (EV) core facility at FIMM. Maija obtained her Master’s degree in biochemistry in the University of Helsinki after which she focused PhD studies to clarify structural changes in the endoplasmic reticulum and Golgi apparatus during cell cycle with Eija Jokitalo at the the electron microscopy unit of the Institute of Biotechnology. At FIMM, Maija has set up methods for studying EVs, such as exosomes and microvesicles, as part of the Helsinki urological biobank, SalWe Get it done and Beat DKD projects. These projects have covered hot topics in the EV field from sample collection, storage, EV isolation and EV-specific antibody production to the quests of seeking biomarkers for prostate cancer and diabetic kidney disease. Since EVs play a fundamental role in cell-to-cell communication and offer new possibilities for therapies or monitoring health and disease, most investigators can find their own research topic linked to this new and exciting field. However, EV research is still young; methods and equipment suitable for the small particles and low-amounts are required and need to be improved or standardized. The EV core facility was established together with Pia Siljander’s EV research group in the Department of Biosciences at the University of Helsinki to support these needs and to provide researchers, hospitals and companies easier access to the EV field. In her spare time, Maija enjoys competing in badminton, playing Pokémon Go and spending time with her family and friends.
February 2017 - Ashwini Nagaraj, PhD Student, Group Verschuren (FIMM)
Congratulations to Ashwini Nagaraj for her recent paper entitled "Cell of Origin Links Histotype Spectrum to Immune Microenvironment Diversity in Non-small-Cell Lung Cancer Driven by Mutant Kras and Loss of Lkb1" published in January 2017 in Cell Reports!
Nagaraj AS, Lahtela J, Hemmes A, Pellinen T1, Blom S, Devlin JR, Salmenkivi K, Kallioniemi O, Mäyränpää MI4, Närhi K, Verschuren EW. Cell of Origin Links Histotype Spectrum to Immune Microenvironment Diversity in Non-small-Cell Lung Cancer Driven by Mutant Kras and Loss of Lkb1. Cell Rep. 2017 Jan 17;18(3):673-684. doi: 10.1016/j.celrep.2016.12.059.
Ashwini is a PhD student in Emmy Verschuren’s group. She obtained her Master’s degree in biochemistry from Bangalore University, India. Before joining FIMM, Ashwini worked as a Junior Research Fellow at the Indian Institute of Science Bangalore and then as a Research Associate at Syngene International Ltd (A Biocon Company). Ashwini’s PhD research is focused on understanding phenotypic, molecular and immune microenvironmental heterogeneity in non-small cell lung cancer (NSCLC) using in vivo and in vitro model systems. A part of her thesis work is also focused on investigating in vivo heterogeneity-related therapeutic responses in ex vivo and in vitro cultures of murine NSCLC. Ashwini is exited to work in collaborative projects involving scientists from various disciplines and looks forward to learning new things. Outside of work, Ashwini likes playing badminton and spending time with family and friends.
January 2017 - Disha Malani, PhD Student, Group Kallioniemi (FIMM)
Congratulations to Disha Malani for her recent paper entitled “Enhanced sensitivity to glucocorticoids in cytarabine resistant AML,” published in November 2016 in Leukemia.
D Malani, A Murumägi, B Yadav, M Kontro, S Eldfors, A Kumar, R Karjalainen, M M Majumder, P Ojamies, T Pemovska, K Wennerberg, C Heckman, K Porkka, M Wolf, T Aittokallio, O Kallioniemi. Enhanced sensitivity to glucocorticoids in cytarabine resistant AML. Leukemia 2016. doi:10.1038/leu.2016.314
Disha is a doctoral student in Olli Kallioniemi’s research group. She has been working on drug resistance, a major challenge in the treatment of Acute Myeloid Leukemia (AML). Disha joined FIMM as a part of the Individualized Systems Medicine grand challenge research program, a collaborative effort among scientists and clinicians with the goal to improve treatment in AML. Disha was awarded her Masters by Research degree from The Nottingham Trent University in the United Kingdom, where she worked on identifying prognostic gene expression biomarkers, using bioinformatics approaches, for improved survival of breast cancer patients. She was trained in Biotechnology in India and subsequently worked as a research associate at Intas Biopharmaceuticals for one year. Currently, Disha is working primarily with a large cohort of AML patient samples with ex vivo drug sensitivity and resistance testing (DSRT) and molecular profiling, to (i) understand the functional biology of the disease, (ii) identify possible molecular features defining specific drug response patterns, and (iii) study patient cases with DSRT-based clinical translation towards patient care. In addition to research at FIMM, she is fond of travelling, exploring nature and cooking.
December 2016 - Poojitha Ojamies, PhD Student, Group Kallioniemi (FIMM)
Congratulations to Poojitha Ojamies for her recent paper entitled “Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia” published online in November 2016 in Leukemia.
P N Ojamies, M Kontro, H Edgren, P Ellonen, S Lagström, H Almusa, T Miettinen, S Eldfors, D Tamborero, K Wennerberg, C Heckman, K Porkka, M Wolf and O Kallioniemi. Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia. Leukemia 2016. doi: 10.1038/leu.2016.286
Poojitha is currently pursuing her PhD at FIMM with Olli Kallioniemi and Maija Wolf. As part of her thesis, she is studying clonal evolution and heterogeneity in acute myeloid leukaemia patients. More specifically, she aims to understand how the cancer subclones evolve and respond to therapy as well as develop new assays to monitor the same. Poojitha is trained as bioinformatician but dabbles in wet lab work, as well. She primarily works with next generation sequencing and amplicon sequencing data. Poojitha is very excited to be part of AML personalised medicine project and finds it very rewarding to work towards patient care and cancer treatment. Outside of work, she is part of organising startup events and works with health-based companies and public organisations. She also loves reading books and watching television series.
November 2016 - Yu Fu, Master's student, Group Kainov (FIMM)
Congratulations to Yu Fu for several recent publications during 2016:
Fu Y, Gaelings L, Söderholm S, Belanov S, Nandania J, Nyman TA, Matikainen S, Anders S, Velagapudi V, Kainov DE. JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses. Antiviral Research. 2016; 133:23-31.
Fu Y, Gaelings L, Jalovaara P, Kakkola L, Kinnunen MT, Kallio-Kokko H, Valkonen M, Kantele A, Kainov D. Protein profiling of nasopharyngeal aspirates of hospitalized and outpatients revealed cytokines associated with severe influenza A(H1N1)pdm09 virus infections: A pilot study. Cytokine. 2016; 86:10-14.
Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE. Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction. Viruses. Accepted.
Yu is a Master’s degree student in the Translational Medicine (TRANSMED) Program in the Faculty of Medicine at the University of Helsinki. The title of her project is “Application of multi-omics analysis to novel anti-influenza agent discovery.” She completed her Bachelor’s degree in Biotechnology in Wuhan, China. During the last year of her bachelor’s training, she went to Tampere to study bioinformatics as an exchange student. Yu joined Denis Kainov’s research group in January 2016 and worked as a bioinformatician, analysing ‘omics data to identify pathways and biological processes most affected during influenza virus infection and how different anti-viral agents affect such responses. She is interested in the application of genomics data or any clinically-generated data to promote the understanding of diseases and to help find the most effective way to treat patients. Yu plans to pursue a Ph.D. in the near future, because she feels there is still a lot to learn and science is too fun to quit. Outside of science, Yu enjoys jogging, yoga, swimming, and sketching.
October 2016 - Suleiman Ali Khan, Postdoctoral Researcher, Group Aittokallio (FIMM)
Congratulations to Suleiman Ali Khan for being awarded a three-year Academy of Finland Postdoctoral Researcher grant starting in September 2016.
Suleiman graduated with a PhD in statistical machine learning from Aalto University in 2015, with a focus on computational biology and bioinformatics applications. He developed novel Bayesian methods to integrate multiple datasets, and studied relationships between drug responses and their structural properties. He subsequently joined FIMM as a postdoctoral researcher and has been working on the identification of genomic factors of drug response using integrative and predictive machine learning methods. The project involves combining information from multiple genomic, molecular and drug response datasets. He has authored 14 scientific publications and participated in writing a book chapter. His current research interests include computational biology, medicine and statistical machine learning. In his free time, Suleiman enjoys nature and playing with data analysis for social-media.
September 2016 - Samuli Eldfors, PhD Student, Group Heckman (FIMM)
Congratulations to Samuli Eldfors for his recent paper entitled “Idelalisib sensitivity and mechanisms of disease progression in relapsed TCF3-PBX1 acute lymphoblastic leukemia,” published in July 2016 in Leukemia.
S Eldfors, H Kuusanmäki, M Kontro, M M Majumder, A Parsons, H Edgren, T Pemovska, O Kallioniemi, K Wennerberg, N Gökbuget, T Burmeister, K Porkka and C A Heckman; Leukemia, accepted article preview 27 July 2016
Samuli is a bioinformatician at the FIMM Technology Center, and he is concurrently working on his Ph.D. in genetics as a member of the group lead by Caroline Heckman. He holds an MSc in biochemistry from the University of Helsinki. Before joining FIMM, he worked at the Institute of Biotechnology, University of Helsinki and the EMBL-European Bioinformatics Institute in Cambridge, UK. His work entails identification of somatic mutations in cancer samples using next-generation-sequence data and computational methods. His research is focused on the role of somatic mutations in the pathogenesis and drug sensitivity of leukemias. He is excited to see that the research at FIMM is helping clinicians to improve the treatment of cancer patients in real time. Outside of work he spends time exercising and exploring the museums of Helsinki with his family; his favorite is the Natural History Museum.
August 2016 - Pietari Ripatti, PhD Student, Group Ripatti (FIMM)
Congratulations to Pietari Ripatti for his recent paper entitled “The Contribution of GWAS Loci in Familial Dyslipidemias,” published in May 2016 in PLOS Genetics.
Pietari is both a fifth–year medical student and a doctoral student in the Doctoral Programme in Population Health at the University of Helsinki in the Ripatti research group at FIMM. Last year, he took a year off from his medical studies to pursue research in Aarno Palotie’s group at the Analytics and Translational Genomics Unit of Massachusetts General Hospital in Boston, MA, USA. Currently working with the genetics of common and complex familial dyslipidemias and heart disease utilizing both family and population–based cohorts, Pietari is developing his ideas for future medical specialization. He is excited about enabling the regular generalist to apply genomic knowledge in clinical decision-making using smart, integrated electronic medical record tools.
Outside of science and medicine, Pietari recently took up skateboarding and otherwise enjoys skiing and sous-vide cooking.
July 2016 - Prson Gautam, PhD Student, Group Wennerberg (FIMM)
Congratulations to Prson Gautam for his recent paper entitled “Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells”, published in May 2016 in Molecular Cancer.
Prson is a doctoral student enrolled in the Doctoral Programme in Biomedicine (DPBM) at the University of Helsinki, working in Krister Wennerberg’s group at FIMM. Prson hails from Nepal, a small country rich in mountains, rivers and biodiversity. He completed his Bachelor’s degree in Biotechnology in Nepal, and then entered the Nordic countries for higher education. After completing his M.Sc. in Applied Biotechnology from Uppsala University, Sweden, he moved to Finland for PhD research and studies. With an early vision of working in the field of medicine/biomedicine, from the start of his bachelor studies, Prson’s doctoral thesis is focused on identifying potential drug combinations strategies that are effective against ductal adenocarcinomas, particularly breast and pancreatic cancer. With a strong interest in translational research that is applicable in routine clinics, he uses a drug sensitivity-based functional approach to study the diseases. Outside of science, he enjoys sports, outdoor activities, and hanging out with friends and family.
June 2016 - Khalid Saaed, PhD Student, Group Kallioniemi (FIMM)
Congratulations to Khalid Saeed for his recent paper entitled “Comprehensive drug testing of patient-derived conditionally reprogrammed cells from castration-resistant prostate cancers,” a successful collaborative effort of scientists, urologists, and pathologists, published in April 2016 in European Urology.
Khalid started his Ph.D. in 2010 in Olli Kallioniemi’s research group on a three year funded period through the Marie Curie Initial Training Network “Prostate Research Organizations-Network of Early Stage Training” programme PRO-NEST. He is currently enrolled in Doctoral Programme in Biomedicine (DPBM) at the University of Helsinki. Khalid received both Bachelor’s and Master’s (Biotechnology) degrees from University of Karachi, Pakistan in 2007. Before starting his PhD, he spent two years to gather research experience as project student at Uppsala University and Karolinska Institute. Khalid’s PhD thesis project consists of two systematic screening-based projects to 1) identify genes that contribute to decreased proliferation during androgen-deprivation, and 2) identify drug-response profiles in conditionally reprogrammed prostate and renal cancer patient-derived cells (CRCs). The latter project is aimed to utilize the application of drug testing together with patient-specific primary models to understand and identify novel treatment possibilities for advanced fatal diseases. Currently, he is finalizing his final mansucript for the thesis and aiming to defend his dissertation by the end of the year.
Outside of science, Khalid is a passionate cricketer, a registered player for the league games organized by the Finnish Cricket Association.
May 2016 - Dmitrii Bychkov, FIMM-EMBL/HIIT PhD Student, Group Lundin (FIMM)
Congratulations to Dmitrii Bychkov for winning the Poster Award at the SPIE Medical Imaging Conference in March 2016 in San Diego, CA, USA with the abstract: "Deep learning for tissue microarray image-based outcome prediction in patients with colorectal cancer!"
Dmitrii is a FIMM-EMBL doctoral student in Johan Lundin’s Clinical Informatics and Image-based Diagnostics research group. Dmitrii received his Masters degree in Bioinformatics from Aalto University, Finland and then joined FIMM-EMBL International PhD Program in 2014. Dmitrii’s research focus is on image analysis and machine learning for digital pathology. He is particularly interested in the application of deep learning techniques to identify new tissue or cellular patterns that are clinically relevant, could improve reliability in diagnostic decision-making, and eventually lead to more accurate targeted treatments for cancer patients. In his free time Dmitrii enjoys outdoor sports.
April 2016 - Anna Cichonska, FIMM-EMBL/HIIT PhD Student, Groups Aittokallio (FIMM), Pirinen (FIMM), and Rousu (HIIT)
Congratulations to Anna Cichonska, whose paper was recently published in Bioinformatics:
metaCCA: Summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis
Anna Cichonska, Juho Rousu, Pekka Marttinen, Antti J Kangas, Pasi Soininen, Terho Lehtimäki, Olli T Raitakari, Marjo-Riitta Järvelin, Veikko Salomaa, Mika Ala-Korpela, Samuli Ripatti, and Matti Pirinen
Bioinformatics (March 2016), doi: 10.1093/bioinformatics/btw052
Anna is a doctoral student in the FIMM-EMBL/HIIT International PhD Program in Molecular Medicine and Bioinformatics and the Helsinki Doctoral Education Network in Information and Communications Technology (HICT), a collaborative doctoral education network hosted jointly by Aalto University and the University of Helsinki. Before coming to Finland, Anna received both Bachelor’s and Master’s degrees in Biotechnology with specialization in Bioinformatics from the Silesian University of Technology, Poland.
Given Anna’s interests in computational biomedicine as well as her enthusiasm to constantly learn more and the strong inclination toward problem solving, she found this PhD position to be a perfect fit for her. Perspectives gained during the rotation in the groups of Juho Rousu (HIIT), Tero Aittokallio and Samuli Ripatti (FIMM) gave her an opportunity to focus her research on developing new computational approaches for identifying associations between genomes and health-related traits, as well as predictive modeling of drug targets. In the future, she would like to integrate machine learning algorithms with combinatorial network analysis to facilitate understanding drugs’ modes of action and finding targeted treatment options for complex disease phenotypes.
Anna finds FIMM and HIIT truly multidisciplinary research environments with brilliant people with different expertise, which allows her to look at both science, in general, and her projects, in particular, from various angles. Since the autumn of 2014, Anna co-organizes the Think Different seminar series at FIMM.
Outside of science, Anna enjoys travelling and any activities involving outdoors and sports.
March 2016 - Katja Närhi, Postdoctoral Researcher, Group Verschuren
Congratulations to Katja Närhi for a successful, multi-center project coordinated by and communicated with four consortium members and resulting in a first author publication in Scientific Reports:
Capturing complex tumour biology in vitro: histological and molecular characterisation of precision cut slices. Davies, E.J.*, Dong, M.*, Gutekunst, M.*, Närhi, K.*, van Zoggel, H.*, et al. Published in Scientific Reports, December 2015.
Katja is a biochemist (M. Sc.) and graduated with a PhD in developmental biology in 2012 from the University of Helsinki. She studied the genetic basis of ectodermal organ development using physiological models and tissue culture techniques. As a postdoctoral researcher in Emmy Verschuren’s group, Katja has mainly focused on developing a complex tissue slice culture method for lung tumors as a part of the EU consortium PREDECT. The project has involved detailed biological characterization of the cultivated tissue and optimization of the tumor slice culture method for cancer target validation. Next, Katja would be interested in better understanding the molecular basis underlying tumorigenesis and early disease progression using functional in vivo and in vitro studies. At FIMM, Katja enjoys having great colleagues and good team spirit. She has been part of the FIMM PhD Student & Postdoc Council (2013-14) and currently, she is responsible for the institute’s biosafety issues. Katja balances her busy work life by horse riding, sports, and enjoying nature with her family.
February 2016 – John Patrick Mpindi, PhD student, Group Kallioniemi
Congratulations to John Patrick Mpindi for receiving an award of 3 500 € from the Cancer Foundation (Cancer Society of Finland) for his doctoral thesis work: Bioinformatic tools for analysis, mining and modeling large-scale gene-expression and drug testing cancer datasets.
John Patrick is a Doctoral Programme In Biomedicine PhD candidate in Prof. Olli Kallioniemi’s research group at FIMM and the University of Helsinki, Finland. He received a Bachelor’s degree in Statistics from Makerere University, Kampala, Uganda. His research started in Uganda with a Makerere University and University of California, San Francisco Research Collaboration. His interests in computational biology led him to pursue Master’s Studies in bioinformatics, and he earned his Master’s degree at the University of Turku, Finland. While finishing his Master’s degree in 2007, he joined the research group led by Prof. Olli Kallioniemi at VTT Technical Research Centre of Finland, Medical Biotechnology, in Turku. John Patrick is experienced in medical research statistical modeling and big data analytics with the aim of helping to identify novel treatments and diagnostic markers. He co-developed the big data analytics portal for FIMM's personalized medicine research program in 2012 along with several researchers at FIMM to enable non-data scientists to use complex algorithms without the need to understand programming languages. His tools and methods have been part of over 40 high impact scientific papers. He is grateful that Cancer Society of Finland recognizes the work of young scientists. He believes the future could be better than the past and every one of us has to find a way to try to make a positive impact. He spends his free time with family and friends.
January 2016 – Bhagwan Yadav, PhD student, Group Aittokallio
Congratulations to Bhagwan Yadav on his recent back-to-back publications in computational biology as part of FIMM's personalized medicine research program.
Yadav B, Gopalacharyulu P, Pemovska T, Khan SA, Szwajda A, Tang J, Wennerberg K, Aittokallio T. From drug response profiling to target addiction scoring in cancer cell models. Dis Model Mech 2015;8:1255–64. doi:10.1242/dmm.021105.
Yadav B, Wennerberg K, Aittokallio T, Tang J. Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model. Comput Struct Biotechnol J 2015;13:504–13. doi:10.1016/j.csbj.2015.09.001.
Bhagwan is a Doctoral Programme In Biomedicine (DPBM) student in Tero Aittokallio’s research group at FIMM and the University of Helsinki, Finland. He received his MSc (Tech) degree in Computational and Systems Biology from the Royal Institute of Technology, Sweden, focusing on mathematical modeling of biological systems. He joined Tero Aittokallio's group for PhD studies in computational systems medicine with the aim of developing mathematical models and tools for personalized cancer treatment. He has developed drug sensitivity, target addiction and drug combination scoring to better understand drug screening data and utilize it for personalized treatment of cancer. He is also involved in integration of genomic, proteomic and drug screening data. He enjoys developing new models and tools for personalized treatment of patients in the future. In his free time, he enjoys swimming and playing badminton.
December 2015 – Anna Aakula, PhD student, Group Kallioniemi
Congratulations to Anna Aakula on the recent publication of her paper, "Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue" in European Urology in October 2015.
Anna graduated from the Bioscience MSc program at Åbo Akademi University in 2008, after which, she joined the research group led by Prof. Olli Kallioniemi at VTT Technical Research Centre of Finland, Medical Biotechnology, in Turku. There, she worked in the ProspeR EU-FP7 effort (2008-2012) with the aim to evaluate microRNAs as diagnostic and prognostic tools as well as therapeutic targets in prostate cancer. In the beginning of 2011, she joined FIMM as a PhD student, when she was selected to the Doctoral Programme in Biomedicine (DPBM, 2011-2014), University of Helsinki, Faculty of Medicine. In her PhD project, she has been studying the impact of microRNAs on prostate and breast cancer proliferation, as well as on two of the key players in these cancers, the androgen and estrogen receptors. In order to comprehensively map the microRNA regulation of relevant genes, she utilized functional high-throughput screens with viability- and reverse phase protein array (RPPA)-based endpoint measurements. In this particular study, the functional results have also been integrated with microRNA expression data from tumors. Currently, she is finalizing her thesis with the aim to defend her work in the beginning of 2016. Anna finds the close collaboration between researchers at FIMM and clinicians extremely important and highly motivating. After her PhD studies, she aims to continue to work in such networks improving treatment regimens and individualized care for cancer patients.
November 2015 – Arjan van Adrichem, PhD student, Group Wennerberg
Congratulations to Arjan van Adrichem on the recent acceptance of his paper, "MgcRacGAP inhibition stimulates JAK-dependent STAT3 activity" for publication in FEBS Letters.
Arjan is a Doctoral Programme In Biomedicine student in the group of Krister Wennerberg at FIMM and University of Helsinki, Finland. He received his BSc in biomedical engineering and MSc degree in medical engineering from the University of Technology in Eindhoven, the Netherlands focusing on clinical chemistry. He joined Krister Wennerberg’s group for PhD studies in cancer chemical biology with the aim of elucidating the oncogenic function and therapeutic potential of key regulatory proteins of the Rho family of small GTPases. As a member of the FIMM PhD and Postdoc Council, he co-founded FIMM’s Peer Mentoring in Soft Skills. During these sessions, doctoral students and postdoctoral fellows at the institute are encouraged to exchange knowledge and expertise.
October 2015 – Luca Trotta, PhD student, Group Saarela
Luca Trotta was recently awarded the "Reviewer's Choice Abstract" honor for the top presented posters and was selected for the "Poster Walk" at the American Society for Human Genetics Annual Meeting, October 2015.
Luca is a geneticist with special interest in providing molecular diagnoses to inherited disorders. He obtained his B.Sc. in Biology and Licentiate in Medical Genetics degrees from the University of Milan and built up his medical genetics expertise by serving seven years in clinical diagnostic laboratories. Motivated to broaden his competence in the field of novel genomics methods, in 2012 he moved to Finland to join FIMM, acknowledged as a fertile environment for cutting-edge genetics research. He is currently a PhD candidate in Janna Saarela’s research group, enhancing the understanding of biological pathways and pathogenic mechanisms behind human immune diseases. In his thesis project, he attempts to elucidate the molecular basis of rare immune deficiencies in Finland availing of state-of-art next-generation sequencing methods and sequence-level data from large population cohorts.