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.
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.