Steen Laboratory - Lab Members

Dr. Judith Steen is an Associate Professor of Neurobiology at Harvard Medical School, a member of the Harvard Stem Cell Institute and the Director of the Neuroproteomics Laboratory in the F. M. Kirby Neuroscience Center at Boston Children’s Hospital. Her laboratory works to understand neuro-regeneration and neurodegenerative diseases using systems biology approaches. The laboratory develops novel qualitative and quantitative methodologies at the interface of proteomics and transcriptomics with special emphasis on computational proteomics approaches. These novel quantitative methods and bioinformatics tools developed by the Steen Laboratory are being applied to understand the biology of regeneration and neurodegeneration in both mouse models, stem cells and human tissues, to find molecular targets for therapeutics, and to identify biomarkers of the neurodegenerative process. Further functional studies using biochemical, molecular and cell biology approaches are used to verify and understand the role of the targets and biomarkers in the context of injury and disease. The goal of this research is to use molecular information provided by our quantitative proteomics measurements in order to ameliorate neurodegeneration and promote regeneration. judith.steen@childrens.harvard.edu


Dr. Hanno Steen, Ph.D., is an Associate Professor of Pathology at Harvard Medical School, whose laboratory is located at Boston Children's Hospital. Dr. Steen's group research has three focal areas:

i) The discovery of urinary biomarkers for diagnostic purposes  in a wide range of acute and chronic diseases including appendicitis, Kawasaki disease, TB,  traumatic brain injury, and Crohn’s Diseases. To this end the Steen Lab has developed a urine proteomics platform which allows for the fast and efficient processing and proteomic analysis of urine specimens.

ii) Use of proteomics to study post-translational mechanisms of protein regulation, with particular emphasis on protein degradation in mitosis and development. The Steen group developed the concept of co-regulation proteomics algorithms that correlates protein abundance traces specific enzyme activities and functions. This work resulted in the identification of kinens, as a new class of cell cycle dependent substrates of the Anaphase Promoting Complex.

iii) Method development to improve a) processing of proteomic samples, b) accuracy and precision of protein quantification and iii) computational methods for the qualitative and quantitative analysis of proteomic data. For instance, the FLEXIQuant approach developed by the Steen lab, which allows for the exquisitely detailed characterization of selected proteins and their post-translational modification, has been instrumental for studying multikinase mechanisms (Nat Methods. 2012;9:504), and the post-translational regulation of Tiki1 in Xenopus development (Cell. 2012;149:1565) and kinesin C1 during mitosis (EMBO J. 2014;33:385). hanno.steen@childrens.harvard.edu


Ceren Uncu, is from Antalya, Turkey. She graduated from Istanbul University. After teaching high school biology for a year she decided to move to the US and became a member of Steen Lab in 2011. She is currently the lab supervisor and the animal surgeon of Steen Lab. Aside from managing the lab, Ceren is working on developing new mouse models to get a better understanding on neurodegenerative diseases like Spinal Muscular Atrophy, Alzheimer's disease and Parkinson's disease and she is preparing samples for Mass Spectrometry. Outside the lab Ceren practices and teaches Yoga and enjoys cooking with friends and family. ceren.uncu@childrens.harvard.edu

 


Long Cheng is an instructor of Neurology at Harvard Medical School working as a senior scientist and lab manager of Steen Lab. He received Ph.D. and had been trained at Beijing University of Chinese Medicine and Tsinghua University in China.  His research had been focused on the neurobiology of neural stem cells in cerebral lesions and diseases as well as the molecular mechanisms of several of cellular signaling pathways underlying human neurological diseases and cancers. At end of 2006, he joined Boston’s Children’s Hospital and Harvard Medical School working as a postdoctoral research fellow to study neurobiology and mechanisms of motor neuron developmental diseases, neurodegeneration and regeneration. He became a team member of Steen Lab since 2017 and has been working on functional studies to try to translate the proteomics findings in the lab into neurobiology and molecular mechanisms underlying human neurodegenerative diseases. Long enjoys cooking, listening to music and radio, playing soccer with friends and traveling with family. He enjoys very much making delicious food for his family and friends. long.Cheng@childrens.harvard.edu

 

Meenakshi Jha was born and raised in India. She post graduated in Biotechnology from Bangalore University, India. After her post graduation, she worked for the firm Ernst & Young. She moved to the United States in Jan 2018. Her interest in Science made her switch her career to Science and she eventually got an opportunity to join Steen lab as a Research Assistant in May 2018. Currently, she is exploring the different facets of quantitative proteomics. She loves music, singing is her favorite pastime. She also loves traveling and exploring new places around the world. meenakshi.jha@childrens.harvard.edu

 

 

 

Christoph Schlaffner was born and raised in Germany. He graduated from the University of Applied Sciences Upper Austria with a Bachelor of Science in Engineering (Bioinformatics) and a Master of Science in Engineering (Bioinformatics). He went on to receive his PhD from the University of Cambridge, UK where he worked with Dr. Jyoti Choudhary at the Wellcome Trust Sanger Institute and Dr. Andreas Bender at the Center for Molecular Informatics, University of Cambridge, on developing tools and analyzing data for proteogenomics and personal proteomics. Christoph is interested in developing bioinformatics tools to understand the function of non-canonical RNA and translation products and untangling disease related from personal variation. Outside the lab, Christoph enjoys cooking and baking, traveling, and choral music. christoph.schlaffner@childrens.harvard.edu

 

Pieter Beerepoot graduated from McMaster University Department of Biology & Pharmacology in Canada. He continued his training in pharmacology at the University of Toronto, Canada  in the department of Pharmacology, where he worked on small molecule approaches to rescue membrane protein folding in the context of neurological disorders. Pieter is primarily focused on development of therapeutics in the neuroscience area, and is pursuing training in mass spectrometry proteomics as a target discovery tool. Currently Pieter is characterizing proteomic changes associated with the neurodegenerative disorder chronic traumatic encephalopathy (CTE).  CTE is a devastating condition caused by traumatic brain injury that has been diagnosed post-mortem in contact sport athletes and militairy personnel. There is currently no method to diagnose living invididuals with CTE, and Pieter is therefore focused on identifying potential biomarkers. Pieter is also engaged in identification of posttranslational modifications that can serve as targets for antibody development in the neurodegeneration field. As if mass spectrometry was not exciting enough, Pieter fills his free time with rockclimbing, mountainbiking, martial arts, and endurance sports. pieter.beerepoot@childrens.harvard.edu

 

Ying Xiong graduated from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. During her Ph.D, she focused on identifying suppressors of abnormal phenotypes associated with tau aggregation in Alzheimer’s disease and other tauopathies through genetic screen. She joined the Steen’s Lab as a postdoc seeking to understand the pathological mechanism and identify potential biomarkers for another group of neurodegenerative diseases - synucleiopathies using proteomics. Ying likes music and enjoys spending time with friends and family. ying.xiong@childrens.harvard.edu

 

Saima Ahmed graduated in 2016 with a Master's in Biotechnology from Harvard Extension School. She completed her Master Thesis " Biomarker Discovery for Bronchopulmonary Dysplasia using Mass Spectrometry Based Urine Proteomics" under supervision of Dr. Hanno Steen. Her affinity for the Steen Lab was so strong she decided to pursue her PhD in the lab. Her project involves improving proteomic workflows for biomarker discovery as well as investigating the phosphoproteome of body fluids such as human cerebrospinal fluid and urine. She will also analyze the proteome of infant brains in hopes to understand the pathophysiological impact resulting from brain injury. Saima's love for the color pink shades all aspects of her life, including her lab bench. saima.ahmed@childrens.harvard.edu

 

Benoit Fatou obtained his Ph.D. in physics and biology focused on the development a new mass spectrometry-based instrument for real-time guided surgery of cancer at the University of Lille in France. After receiving his Ph.D., he did his first postdoctoral training during one year on the same projects in the lab where he did his thesis. Dr. Fatou is now a postdoctoral researcher under the PI Dr. H. Steen at Boston Children’s Hospital/Harvard Medical School. His research focuses on developing and applying targeted and quantitative proteomics methods for biomarker discovery neurodegenerative diseases. Outside the work, Benoit likes to spend some time cooking, fishing during summer and skiing during winter. benoit.fatou@childrens.harvard.edu

 

Mukesh Kumar joined the Steen lab as Postdoc in Oct 2017. He did his PhD work in the lab of Dr. Andrej Shevchenko at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany. Currently, in the lab he is employing his favorite quantitative mass spectrometry to understand the role of proteins (abundance, aggregation, post-translational modification etc.) in neurodegeneration. In free time, he likes bike riding, cooking, playing cricket, and sleeping. mukesh.kumar@childrens.harvard.edu

 


 

Kathrin Wenger studied in Germany and graduated with a M.Sc. in analytical und bioanalytical chemistry from Aalen University, Germany. Due to her interests in mass spectrometry, biochemistry and statistical data analysis of multivariate datasets, she decided to join the Steen lab as a PhD student in 2019. Her project involves the comparison of different mouse models of Alzheimer’s disease to human samples to identify the best matching model for further investigation. In her free time Kathrin likes hiking, rock climbing, knitting and cooking. kathrin.wenger@childrens.harvard.edu

Eva-Maria Schneeberger joined the Steen lab as a postdoc in October 2018 after receiving her PhD in Chemistry at the Institute of Organic Chemistry, University of Innsbruck (Austria). As a graduate student in the research group of Dr. Kathrin Breuker, she developed methodologies for the characterization of oncovalent intra- and intermolecular interactions in RNA, proteins, and peptides by native top-down mass spectrometry, which sparked her interest in incorporating her broad expertise into a biological context. In the Steen lab, Eva-Maria applies her background in top-down mass spectrometry to the elucidation of posttranslational modifications (PTMs) in intact proteins associated with neurodegenerative disease. Complementary to this work, she is expanding her knowledge and learning about the workflows in bottom-up proteomics. By combining both methodologies, her goal is to understand the PTM pattern underlying neurodegenerative disease and thus can serve as targets for treatment. Outside the lab, Eva-Maria likes exploring new places outdoors whether close or far and also enjoys hiking tours. Eva-Maria.Schneeberger@childrens.harvard.edu

 

 

Anaïs Meziani joined the Steen lab in 2017 as a student to complete her master program. She graduated with a B.S. in Biochemistry from Lille University (France).  She continued with a M.S. program in Genomics and Proteomics in Lille. October 2018 Anaïs has started start her PhD thesis in the lab. Anaïs enjoys team sport as hand-ball and loves to eat mangos from Mexico! anais.meziani@childrens.harvard.edu

 

Michaela Svrdlikova was born in Czech Republic. She holds a master’s degree in Cognitive and Clinical Neuroscience from University of Maastricht, Netherlands. Her Master’s degree was specialized in topics on drug discovery for CNS diseases. She conducted her master’s internship in Steen Laboratory, during which she has learnt a lot about proteomics and mass spectrometry. She really enjoyed the work and atmosphere in the lab during her internship therefore she was very happy when she got an offer to stay for her PhD at Steen laboratory. She is studying tau protein in Alzheimer’s disease and Chronic Traumatic Encephalopathy (CTE). Particularly, she is focusing on aspects of tau degradation. In her free time, she likes to do skiing, hiking, running or cycling. michaela.svrdlikova@childrens.harvard.edu

Sinead Greally graduated with a BSc in Biomedical Science from the National University of Ireland, Galway and due to her interest in pharmacology and neuroscience, she continued her studies with a Research Masters in Drug Development and NeuroHealth from Maastricht University, in the Netherlands. During her second year of this Master’s, Ms. Greally carried out a 9-month internship at the Steen Laboratory, working with Ying Xiong, PhD, using mass spectrometry and proteomics to characterize and quantify alpha-synuclein in the neurodegenerative disease Multiple System Atrophy (MSA). After Ms. Greally obtained her MSc from Maastricht University, she returned to the Steen Laboratory to begin a PhD, continuing her work on the proteomic characterization of alpha-synuclein, now in both MSA and Parkinson’s disease.While completing her PhD, Sinead enjoys soaking up the American culture here in Boston, and likes travelling, movies and going out with friends. sinead.greally@childrens.harvard.edu

 

 

Lucrezia Favi was born and raised in Fossombrone. Her love for science stems from unravelling its complexity, especially in the field of neurodegeneration. Combined with the passion for travelling, Lucrezia’s interests have first led her to London, where she refined her proficiency of English. Next, she moved to The Netherlands where she completed her Bachelor of Science in Psychology with Honours at Leiden University. Driven by her enthusiasm for neuroscience she then started a Research Master in Cognitive and Clinical Neuroscience with the specialization in Fundamental Neuroscience at Maastricht University. As part of this Master’s education she is currently at the Steen Lab to complete her master thesis’ internship. Here she is focusing on the alterations of the proteome and Tau post-translational modifications in tauopathies, and investigating the functional role of these findings in the human pathogenesis with a cell model. After completing her Master, Lucrezia plans to start her PhD in the lab. Besides her dedication to unravel the mystery underlying neurodegenerative diseases Lucrezia travels the world as much as she can. She also keeps herself active practicing a wide range of sports from dance to trapeze, at the same time never forgetting her Italian roots alive by origins alive with her love for cooking. lucrezia.favi@childrens.harvard.edu

 

Patrick W. van Zalm was born and raised in the Netherlands. He started his academic training at the University of Amsterdam where he did a bachelor’s program in Psychobiology. Still being interested in neuroscience he continued his academic training at Maastricht University where he did the master’s program cognitive and clinical neuroscience with the specialization drug development and neurohealth. During his master’s programme Patrick joined the Steen lab due to his interest in neurodegenerative diseases. For his master’s program project Patrick has focused on finding new biomarkers in body fluids in Alzheimer’s Disease. Patrick will continue his work at the Steen lab as a Ph.D. student where he will continue his work on biomarker discovery & validation in body fluids of different neurodegenerative diseases. Besides working in the lab Patrick tries to stay fit by hitting the gym or going for a run. He also enjoys going to concerts, festivals and exploring the exciting brewery culture that Boston has to offer. Patrick.vanZalm@childrens.harvard.edu

 

 

 

Kyle Higgins obtained his B.Sc. in Physics from Lehigh University in the United States. During this time, he researched high energy hadron collision experiments in collaboration with the Brookhaven National Lab. This work involved design and construction of an optic fiber scintillation detector for the identification of collision products as well as computational analysis of experimental detector data. Kyle began as a research assistant in the field of bioinformatics at the Steen Laboratory in 2019 and he is applying statistical and algorithmic techniques to integrate data regarding single nucleotide polymorphisms (SNPs) with genomic and transcriptomic reference sequences to better understand their resulting proteomes. He is additionally managing data storage and transfer for the lab. kyle.higgins@childrens.harvard.edu

Zainab Wurie joined the Steen lab in February 2017 as an undergraduate researcher, where she worked on optimization of human cerebrospinal fluid peptidomics methods and mass spectral analysis for her senior thesis. She graduated with a B.A. in Neurobiology from Harvard University in 2018. She loved the lab so much that she decided to join full-time. As a research assistant, she is working under Benoit Fatou, PhD and performing blood plasma and serum sample processing for proteomic/mass spectral analysis, as well as proteomics/peptidomics method optimization. Outside of lab, she loves taking long walks, watching funny YouTube videos, and spending time with friends and family. zainab.wurie@childrens.harvard.edu

 

 

Konstantin Kahnert developed a strong interest in natural sciences early on and focused on Chemistry and Biology in High School (Abitur) already. During his bachelor’s degree in Biotechnology at the Berlin Institute of Technology he discovered his passion for proteomics. After realizing that the bioinformatic analysis of MS data is one of the biggest challenges in proteomic research, he focused on bioinformatics, data analysis and machine learning during his master’s degree. Paired with his general interest in neurodegenerative disorders this made him a perfect fit for the Steen lab, where he is now working on his master thesis project. While Konstantin isn’t sitting in front of a computer writing code and analyzing data, he enjoys being outside and doing all sorts of sports, especially cycling, hiking and weight lifting. konstantin.kahnert@childrens.harvard.edu