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I will discuss our recent research in this direction: a concept that we call “jointly smooth functions”.
Her research focuses on the development and application of multi-omics strategies for
identifyingregulatory regions in cancer genomes and elucidating their role in disease development.
His work emphasizes on uncommon drug combinations and patient populations that are traditionally
underrepresented in genomic studies. Join Our Team Please contact us to learn more about career
opportunities and the philosophy of our lab. Her research interests include the use of machine
learning and other computational approaches to studying human genetic diseases and disorders. Ian
Lo, MSc Alumini (MSc student, Harvard, 2022-23) Subsequent Position: Data Scientist, Scripps
Health Ian Lo is a master’s student in the Health Data Science program at the Harvard T.H. Chan
School of Public Health. His long-term goal is to advance our biological understanding of pediatric
tumors and the efficacy of personalized therapies for children with cancer. By training autoencoder
models on multiomics data, he aims to illuminate the coordinated activity of mutations in
tumorigenesis and pave the way for genome-inspired personalized combination therapies. Her
research focuses on the development of statistical methods for identifying driver mutations in
noncoding parts of the cancer genome. He is also an Associate Member at the Broad Institute of
MIT and Harvard and an Investigator at the Dana-Farber Cancer Institute. Anran Tang, MSc
Alumini (MSc student, Harvard, 2019-20; co-mentored with Eliezer Van Allen) Subsequent position:
PhD student, MSKCC Anran Tang is a master’s student in the Biomedical Informatics program at
Harvard Medical School. His current work combines these tools with functional experimental data to
study the effect of somatic mutations on cancer gene expression. He pairs functional data from cell
lines with genomic profiles from cancer patients to dissect mechanisms that allow tumors to spread to
distant organs. He is also interested in translating genomic discoveries into new driver-directed
treatments (Cancer Discovery 2014; PNAS 2012). Sara Uhan, MSc PhD Student; co-mentored with
Dr. Wirth, Charite Berlin Sara Uhan is a PhD student and Fulbright Scholar. Platon Lukyanenko,
PhD Alumini (Postdoc, HMS) Subsequent Position: NIH T32 Fellow, CHIP Dr. Platon Lukyanenko
intersects cancer biology with machine learning methods to decode multifaceted roles of oncogenic
mutations. Identification of cancer driver genes based on nucleotide context. Nat Genet. 2020. He
also combines tumor biology with aspects of public health for harmonizing the assessment of
personalized cancer risk across demographics. His mission is to advance precision medicine by
identifying molecular vulnerabilities in tumor genomes, translating them into targeted therapies, and
improving diagnostics in the clinical setting. The multidisciplinary research program of his lab allows
computational trainees to immediately experience the translational potential of their work on the
future of precision cancer medicine. The researchers hope that this will become a model system for
using machine-learning to understand the cancer genome and that it will allow scientists to develop
experiments to confirm the role of these types of mutations in cancer development. He also designs
interactive web resources to communicate his science to a broad audience. With the start of each
trainee, he tailors a training plan to their specific strengths and needs, develops actionable teaching
goals, and identifies potential co-mentors and required resources. Even in case classical canonical
correlation analysis (CCA) is not applicable, nonlinear techniques can often successfully uncover the
relationship between the observations. She pairs experimental with computational strategies to define
SUMO-specific networks in cancer cells and translate them into new drug targets for precision
medicine. His multidisciplinary training in medicine, biology, and mathematics allows him to
approach complex problems from diverse perspectives. They will train the software to recognize
these mutations using a dataset of 2,500 cancer patients whose entire genomes have been sequenced
as part of the pan-cancer analysis of whole genomes (PCAWG). The construction of these functions
is fully data-driven, and relies on spectral methods from manifold learning and a Dirichlet energy-
based definition of smoothness. Genome-wide mapping of somatic mutation rates uncovers drivers
of cancer. Petr Holy, PhD Postdoc (co-mentored with Pavel Soucek, National Institute of Public
Health, Prague) Dr. Petr Holy converges patient health records with genomic analyses to uncover
novel clinico-genomic markers for predicting clinical outcomes, responses to therapy, and guiding the
selection of targeted therapies.
He holds an MD and PhDs in mathematics and molecular medicine. His ultimate goal is to create
comprehensive multi-omics strategies for decoding complex regulatory mechanisms in oncogenesis
that could offer innovative avenues for drug targets in precision cancer medicine. The researchers
hope that this will become a model system for using machine-learning to understand the cancer
genome and that it will allow scientists to develop experiments to confirm the role of these types of
mutations in cancer development. Ian Lo, MSc Alumini (MSc student, Harvard, 2022-23)
Subsequent Position: Data Scientist, Scripps Health Ian Lo is a master’s student in the Health Data
Science program at the Harvard T.H. Chan School of Public Health. She studies SUMOylation as a
pivotal post-translational modification in tumor cells and its effect on the localization, stability, and
activity of proteins. In the future, a more in-depth understanding of mutations in non-coding DNA
may help scientists develop new anti-cancer therapies as well as give doctors new tools to identify
tumor subtypes and determine the best therapies for their patients. He also designs interactive web
resources to communicate his science to a broad audience. Robert Khashan Medical Graduate
Student, University of Gothenburg, Sweden Robert Khashan is a medical student specializing in
pediatric tumor biology. He is dedicated to training the next generation of interdisciplinary scientists
by providing mentorship to researchers at various stages in their careers and integrating them into an
inclusive and collaborative laboratory environment. Her research focuses on the development of
statistical methods for identifying driver mutations in noncoding parts of the cancer genome. Even
in case classical canonical correlation analysis (CCA) is not applicable, nonlinear techniques can often
successfully uncover the relationship between the observations. He combines genomic, proteomic,
and expression data with innovations in data science for an in-depth analysis of oncogenic pathways
that drive lymphomas and neuroblastomas. Integrating molecular profiles into clinical frameworks
through the Molecular Oncology Almanac to prospectively guide precision oncology. Nat. Cancer.
2021. His multidisciplinary training in medicine, biology, and mathematics allows him to approach
complex problems from diverse perspectives. Anran Tang, MSc Alumini (MSc student, Harvard,
2019-20; co-mentored with Eliezer Van Allen) Subsequent position: PhD student, MSKCC Anran
Tang is a master’s student in the Biomedical Informatics program at Harvard Medical School. Most
cancers have numerous mutations in their non-coding DNA, but, with few exceptions, the impact of
these mutations on cancer is not known. He is also an Associate Member at the Broad Institute of
MIT and Harvard and an Investigator at the Dana-Farber Cancer Institute. They will train the
software to recognize these mutations using a dataset of 2,500 cancer patients whose entire genomes
have been sequenced as part of the pan-cancer analysis of whole genomes (PCAWG). Yuelai (Eli)
Wang, BSc MSc student, Harvard Eli Wang is a master’s student in the Computational Biology and
Quantitative Genetics program of the Harvard School of Public Health. He combines cancer
genomics mechanisms with clinical observational phenotypes to define early lesions that prime cells
for tumor development. He pairs functional data from cell lines with genomic profiles from cancer
patients to dissect mechanisms that allow tumors to spread to distant organs. By training autoencoder
models on multiomics data, he aims to illuminate the coordinated activity of mutations in
tumorigenesis and pave the way for genome-inspired personalized combination therapies. Petr Holy,
PhD Postdoc (co-mentored with Pavel Soucek, National Institute of Public Health, Prague) Dr. Petr
Holy converges patient health records with genomic analyses to uncover novel clinico-genomic
markers for predicting clinical outcomes, responses to therapy, and guiding the selection of targeted
therapies. Researchers in the Ma and Van Allen labs are developing a machine-learning algorithm
that can identify mutations in non-coding DNA that allow tumor cells to proliferate and outcompete
healthy cells because of their effect on the genome’s 3D structure. Yi-Ting Tsai, MSc Alumini (MSc
student, Harvard, 2022-23) Subsequent Position: PhD Student, Stanford University Yi-Ting Tsai is a
master’s student in the Health Data Science program at the Harvard T.H. Chan School of Public
Health. Aniket Dey Alumini (Research Intern 2022-23) Subsequent Position: Undergraduate Student,
Dartmouth College Aniket Dey studies interactions of tumor cells and the microenvironment.
Yuxiang Zhou, BSc MSc student, Boston University Yuxiang Zhou has extensive experience in the
design of differential expression analyses and their application to diverse diseases. She pairs
experimental with computational strategies to define SUMO-specific networks in cancer cells and
translate them into new drug targets for precision medicine. His work emphasizes on uncommon
drug combinations and patient populations that are traditionally underrepresented in genomic studies.
The construction of these functions is fully data-driven, and relies on spectral methods from
manifold learning and a Dirichlet energy-based definition of smoothness.
She studies SUMOylation as a pivotal post-translational modification in tumor cells and its effect on
the localization, stability, and activity of proteins. He holds an MD and PhDs in mathematics and
molecular medicine. Mirue Kang BSc student, Brandeis Subsequent Position: Undergraduate
Student, Brandeis University Mirue Kang is an undergraduate student at Brandeis University. I will
illustrate the theoretical results on simple examples, discuss our efficient implementation, and show
improvements over existing nonparametric and kernel CCA techniques for real physiological signals
in sleep stage identification, the construction of effective parameters in dynamical systems, and
positional alignment from different video camera feeds of a race track. Cancer mutational signatures
representation by large-scale context embedding. Her research interests include the use of machine
learning and other computational approaches to studying human genetic diseases and disorders.
Among its many roles, non-coding DNA affects the 3D structure of the genome, which in turn
partially determines which genes in the coding region are turned on. I will discuss our recent research
in this direction: a concept that we call “jointly smooth functions”. Researchers in the Ma and Van
Allen labs are developing a machine-learning algorithm that can identify mutations in non-coding
DNA that allow tumor cells to proliferate and outcompete healthy cells because of their effect on the
genome’s 3D structure. He focuses on single-cell epigenomics and studies regulatory regions in
cancer genomes. His work emphasizes on uncommon drug combinations and patient populations that
are traditionally underrepresented in genomic studies. Antti Haekkinen, PhD Senior Postdoc, HMS
Dr. Antti Haekkinen has in-depth expertise in computational methods for phenotype profiling and an
established track record of analyzing multi-omics data of ovarian cancer. Platon Lukyanenko, PhD
Alumini (Postdoc, HMS) Subsequent Position: NIH T32 Fellow, CHIP Dr. Platon Lukyanenko
intersects cancer biology with machine learning methods to decode multifaceted roles of oncogenic
mutations. His mission is to bring scientists from different disciplines together and train the next
generation of exceptional scientists in his lab. His long-term goal is to advance our biological
understanding of pediatric tumors and the efficacy of personalized therapies for children with
cancer. His long term vision is to advance personalized medicine by the rational design of
combination therapies that leverage mechanisms in noncoding cancer genomics, DNA repair, and the
translational potential of clinical data. Even in case classical canonical correlation analysis (CCA) is
not applicable, nonlinear techniques can often successfully uncover the relationship between the
observations. By training autoencoder models on multiomics data, he aims to illuminate the
coordinated activity of mutations in tumorigenesis and pave the way for genome-inspired
personalized combination therapies. With the start of each trainee, he tailors a training plan to their
specific strengths and needs, develops actionable teaching goals, and identifies potential co-mentors
and required resources. He further aims to characterize complex oncogenic signaling changes that
cause malignant transformation. He also combines tumor biology with aspects of public health for
harmonizing the assessment of personalized cancer risk across demographics. They will train the
software to recognize these mutations using a dataset of 2,500 cancer patients whose entire genomes
have been sequenced as part of the pan-cancer analysis of whole genomes (PCAWG). In the future, a
more in-depth understanding of mutations in non-coding DNA may help scientists develop new anti-
cancer therapies as well as give doctors new tools to identify tumor subtypes and determine the best
therapies for their patients. Anran Tang, MSc Alumini (MSc student, Harvard, 2019-20; co-mentored
with Eliezer Van Allen) Subsequent position: PhD student, MSKCC Anran Tang is a master’s
student in the Biomedical Informatics program at Harvard Medical School. Identification of cancer
driver genes based on nucleotide context. Nat Genet. 2020. He combines genomic, proteomic, and
expression data with innovations in data science for an in-depth analysis of oncogenic pathways that
drive lymphomas and neuroblastomas. The construction of these functions is fully data-driven, and
relies on spectral methods from manifold learning and a Dirichlet energy-based definition of
smoothness. Yuelai (Eli) Wang, BSc MSc student, Harvard Eli Wang is a master’s student in the
Computational Biology and Quantitative Genetics program of the Harvard School of Public Health.
Sara Uhan, MSc PhD Student; co-mentored with Dr. Wirth, Charite Berlin Sara Uhan is a PhD
student and Fulbright Scholar. Genome-wide mapping of somatic mutation rates uncovers drivers of
cancer.