nyu computational biology phd

NYU Center for Data Science

Harnessing Data’s Potential for the World

Computational Biology & Medicine Colloquium

Nyu center for data science nyugsom center for human genetics and genomics nyu courant institute for mathematical sciences, hosts: aravinda chakravarti, phd; julia kempe, phd; alex mogilner, phd; russel caflisch, phd; itai yanai, phd; andreas hielscher, phd.

The colloquium speakers will also offer a special informal session with trainees (students, postdocs), usually immediately after the seminar. We encourage all trainees to sign up for these sessions! Registration information will be posted in the center calendar.

Upcoming Sessions

Please note all sessions take place 12:15pm-1:15pm on the specified dates and can be accessed via the Computational Biology & Medicine Colloquium Zoom link: https://nyulangone.zoom.us/j/91601001443 .

SEPTEMBER 14

Christina Leslie, PhD Member, Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center |  Computational Biology & Medicine Colloquium Zoom link

Aryeh Warmflash, PhD Associate Professor and CPRIT Scholar, Department of Biosciences, Rice University |  Computational Biology & Medicine Colloquium Zoom link

NOVEMBER 9, 2021 

Sumit Chopra, PhD Associate Professor, Courant Institute and Department of Radiology, Grossman School of Medicine, NYU Director of Machine Leaming Research, Department of Radiology, NYU Langone Health |  Computational Biology & Medicine Colloquium Zoom link

JANUARY 11, 2022 

Peter Park, PhD Professor of Biomedical Informatics, Harvard Medical School |  Computational Biology & Medicine Colloquium Zoom link

FEBRUARY 8, 2022 

Yana Bromberg, PhD, MPhill Professor, Department of Biochemistry and Microbiology, Rutgers Adjunct Professor, Department of Genetics, Rutgers Vice President, Board of Directors of the International Society for Computational Biology |  Computational Biology & Medicine Colloquium Zoom link

MARCH 8, 2022 

Alexandria Volkening, PhD NSF-Simons Fellow, NSF-Simons Center for Quantitative Biology Engineering Sciences & Applied Mathematics, Northwestern University |  Computational Biology & Medicine Colloquium Zoom link

APRIL 12, 2022 

Simon Tavare, PhD Professor, Biological Sciences and Statistics, Director, Irving Institute for Cancer Dynamics, Columbia University |  Computational Biology & Medicine Colloquium Zoom link

MAY 10, 2022

Padmini Rangamani, PhD Professor, Department of Mechanical and Aerospace Engineering, University of California, San Diego  |  Computational Biology & Medicine Colloquium Zoom link

Contact Information: [email protected] | 212-263-8023

Past Events

November 17, 2020

David Haussler, PhD Investigator, Howard Hughes Medical Institute Scientific Director, UC Santa Cruz Genomics Institute University of California, Santa Cruz

David Haussler Recording

December 15, 2020

Edward Holmes, FAA FRS ARC Australian Laureate Fellow Marie Bashir Institute for Infectious Diseases and Biosecurity School of Life & Environmental Sciences, and Medical Sciences The University of Sydney

Edward Holmes Recording

January 5, 2021

Adrianna Heguy, PhD Assistant Dean, Advanced Research Technologies Professor, Department of Pathology NYU Langone Health

March 9, 2021

Viviana Risca, PhD, Assistant Professor Head, Laboratory of Genome Architecture and Dynamics The Rockefeller University

April 13, 2021

To be confirmed

May 4, 2021

Arthur Lander, MD, PhD Donald Bren Professor of Developmental and Cell Biology Director, Center for Complex Biological Systems University of California, Irvine

Zoom Link | Meeting ID: 940 9268 4648 | One tap mobile: 646-518-9805 | Contact information: Jessica Jaffe at 212-263-8023

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Bioinformatics and Systems Biology Track

This track has been designed for students who desire in-depth training in applications of bioinformatics and computational modeling.

Highly Recommended Courses

• Statistics in Biology  - BIOL-GA 2030, 4 points, which is a pre-requisite for several other bioinformatic courses. Advanced course on techniques of statistical analysis and experimental design that are useful in research and in the interpretation of biology literature. Students will be trained to use the programming package R.
• Applied Genomics: Introduction to Bioinformatics and Network Modeling  - BIOL-GA 1130, 4 points. Introduces fundamental methods of analyzing large data sets from genomics experiments. Through a combination of lectures, hands-on computational training, and in-depth discussions of current scientific papers, students learn the conceptual foundations of basic analytical methods, the computational skills to implement these methods, and the reasoning skills to read critically the primary literature in genomics.
• Programming for Biologists  - BIOL-GA.1007, 4 points. Provides introductory theory and hands-on training in bioinformatics. Students are introduced to the Linux operating system and basic computer programming skills (Perl and Bioconductor). Topics covered: biological databases, pairwise and multiple sequence alignment, BLAST and related algorithms, sequence motifs, Hidden Markov Models, gene expression analysis, and resources for functional associations (gene ontology, pathways and networks).
• Biological Databases and Datamining  - BIOL-GA 1009, 4 points. The course is divided into three sections: 1) Introduction to MySQL and R. 2) Introduction to different data types, and 3) Machine learning methods for data mining. Students will learn to create their own database using MySQL and SQLite containing different types of biological data. Students will also learn to mine the heterogeneous biological data using machine-learning methods such as Support Vector Machines and Multiple Regressions. We will apply these methods on experimental data in order to classify and prediction gene function and regulation.
• Genomics of Human Populations - BIOL-GA 1132, 4 points. This course covers topics in the field of human population genetics including human ancestry and admixture, human demography, linkage disequilibrium, genome-wide association studies (GWAS), genetic architecture of human traits and diseases, natural selection in the human genome, and application of population genomics to the study of cancer and disease. The course includes lecture and recitation components with the latter geared to teaching students basic skills in population genomic data analysis.
• Statistics and Machine Learning for Genomics  - BIOL-GA 2031, 4 points .  Next‐generation sequencing has led to the rise of large and noisy biological datasets, which require increasingly advanced analytical methods to glean biological insights. This course aims to enable students to analyze diverse types of genomic data, ranging from studies focused on human genetics (i.e. Genome‐wide association studies), to functional genomics (i.e. ChIP‐seq or RNA_seq, extending even to the single cell level) To accomplish this, we will review the theory and implementation behind key concepts and methods in statistical learning, and apply these to genomic datasets.
• Research  - BIOL-GA 3303-3304, 1-6 points. Students in this track also typically take research credits, since hands-on experience in bioinformatics/genomics is especially important. Each student must complete a research paper under the supervision of a Biology faculty member, however, students may seek approval from the Director of the Master’s Program, for a main sponsor who is outside the Biology Department.

ADDITIONAL COURSES

• Bio Core 1: Molecular Systems  - BIOL-GA 1001, 4 points.
• Bio Core 2: Cellular Systems  - BIOL-GA 1001, 4 points.
• Metabolic Disorders  - BIOL-GA 1032
• Protein Biochemistry -  BIOL-GA 1045
• Emerging Pathogens  - BIOL-GA 1080, 4 points.
• Hot Topics in Microbiology and Infectious Diseases  - BIOL-GA 1023, 4 points.
• Systems Biology  - BIOL-GA 1128, 4 points.
• Cell Biology  - BIOL-GA 1051, 4 points.
• Current Topics in Biology -  BIOL-GA 2005-2008, 2 points each.
• Biophysical Modeling of Cells & Populations  - BIOL-GA 1131, 4 points.
• Evolutionary Genetics & Genomics  - BIOL-GA 1129, 4 points.
• Research  - BIOL-GA 3303-3304, 1-6 points.

For additional course offerings through the Departments of Biology, Biomaterials, and Basic Medical Sciences (NYU medical school), please see the GSAS Bulletin , or at the registrar’s web site for the schedule of course offerings.

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Biology PhD Program

Supervising faculty.

• Program Structure

Current Students

• Application

NYU Shanghai, in partnership with the NYU Graduate School of Arts and Science and the NYU Department of Biology, invites applications from exceptional students for PhD study and research in Biology.   Participating students are enrolled in the NYU GSAS Biology PhD program, complete their coursework at the NYU Department of Biology in New York, and then transition to full-time residence at NYU Shanghai where they undertake their doctoral research under the supervision of NYU Shanghai faculty.

Highlights of the Program

• NYU degree upon graduation
• Graduate coursework at the NYU Department of Biology in New York
• Research opportunities with and close mentorship by NYU Shanghai faculty
• Access to the vast intellectual resources of NYU GSAS and NYU Department of Biology
• Cutting-edge research environment at NYU Shanghai, including a thriving community of PhD students, post-doctoral fellows, and research associates, activities such as a regular program of seminars and visiting academics, and links with other universities within and outside China
• Financial aid through the NYU Shanghai Doctoral Fellowship , including tuition, fees, and an annual stipend
• Additional benefits exclusive to the NYU Shanghai program, including international health insurance, housing assistance in New York, and travel funds

Genomics, Bioinformatics, Evolutionary Analysis of Large-Scale Genomics Data, Molecular Evolution, Computational Biology

Jungseog Kang

Chromosome Segregation, Mitosis, Antimitotic Cancer Drug Screen

Recent Publications by NYU Shanghai Faculty

• KBase: The United States Department of Energy Systems Biology Knowledgebase.Nature biotechnology 36 (7), 566, 2018
• Pangolin genomes and the evolution of mammalian scales and immunity Genome research 26(10):1312-1322, 2016
• Unknown unknowns: essential genes in quest for function. A Danchin, G Fang, Microbial biotechnology 9 (5), 530-540 2016
• Comparative analysis of the transcriptome across distant species Nature 512 (7515), 445 166 2014
• Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution G Fang, KD Passalacqua, J Hocking, PM Llopis, M Gerstein, NH Bergman, BMC genomics 14 (1), 450, 2014

Jungseog Kang

• Improving drug discovery with high-content phenotypic screens by systematic selection of reporter cell lines. Kang J et. al. Nature Biotechnology (2016) 34:70-77.
• Mitotic centromeric targeting of HP1 and its binding to Sgo1 are dispensable for sister-chromatid cohesion in human cells. Kang J et. al. Mol. Biol. Cell (2011) 22:1181-1190.
• Kinase signaling in the spindle checkpoint. Kang J et. al. J. Biol. Chem. (2009) 284:15359-63.

Selected Faculty and Student Features

" Communicating Science: NYU Shanghai’s First Postdoctoral and Doctoral Research Assembly " (Xiaoai Lyu)

" A New Way to Screen Cancer Drugs " (Jungseog Kang)

" Professor Gang Fang Wins NYU GIPH Research Affinity Group Network Challenge " (Gang Fang)

Structure of Program

Participating students complete the PhD degree requirements set by the NYU Department of Biology and in accordance with the academic policies of NYU GSAS. Each student develops an individualized course and research plan in consultation with the Director of Graduate Study at the NYU Department of Biology and the student’s NYU Shanghai faculty advisor. A typical sequence follows:

Begin program with funded research rotation, up to 3 months preceding first Fall semester, to familiarize with NYU Shanghai and faculty as well as lay a foundation for future doctoral study.

Complete PhD coursework at Department of Biology alongside other NYU PhD students. 

Return to Shanghai for second funded research rotation to solidify relationships with NYU Shanghai faculty and make further progress in research.

Under supervision of NYU Shanghai faculty advisor, pursue dissertation research and continue coursework. Depending on each student’s individualized course of study, return visits to New York may also occur. Complete all required examinations and progress evaluations, both oral and written, leading up to submission and defense of doctoral thesis.

To learn more about the NYU Biology PhD program degree requirements, please visit this page .

Application Process and Dates

Applications are to be submitted through the NYU GSAS Application portal , within which students should select the Biology PhD as their program of interest, and then indicate their preference for NYU Shanghai by marking the appropriate checkbox when prompted. Applicants will be evaluated by a joint admissions committee of New York and Shanghai faculty. Application requirements are set by the NYU Department of Biology and are the same as those for all NYU PhD applicants, no matter their campus preference; however, candidates are recommended to elaborate in their application and personal statements about their specific interests in the NYU Shanghai program and faculty.

For admission in Fall 2024, the application deadline is December 1, 2023.

Interested students are welcome to contact Vivien Du , PhD Program Manager, at [email protected] with any inquiries or to request more information.

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Reprogramming Transcription Factors with a Universal Zinc Finger Model

Marcus Noyes, PhD

Assistant Professor, Dept. of Biochemistry and Molecular Pharmacology

Institute for Systems Genetics, NYU Grossman School of Medicine

The ability to understand and manipulate the interactions between proteins and their targets represents a frontier of both theoretical and practical significance. Dr. Noyes and his research group l has been at the forefront of this exploration, developing innovative methodologies to map out these interactions with unprecedented depth and breadth. This talk will delve into the group's pioneering work on reprogramming transcription factors—a breakthrough that marks a significant leap forward in our capacity to influence cellular functions and gene expression patterns. By harnessing the power of systems and synthetic biology, the team has not only shed light on the binding potential of common protein domains but has also opened the door to understanding the full functional capacity of proteins beyond their evolved roles. Through comprehensive synthetic screens, the research has unveiled new proteins with novel functions, paving the way for groundbreaking applications in therapeutic intervention, including artificial regulation, protein inhibition, and precise genome editing. This colloquium promises to offer valuable insights into the intersection of cell biology, synthetic biology, and computational approaches, highlighting the potential of these advances to revolutionize our approach to understanding and manipulating the complex machinery of life.

Dr. Marcus Noyes joined the NYU Institute for Systems Genetic and the Department of Biochemistry and Molecular Pharmacology in July of 2015. He received his PhD from the University of Massachusetts Medical School where he developed tools for the high-throughput characterization of protein-DNA interactions. He was next recruited as an independent Lewis-Sigler Fellow at Princeton University where he ran a small lab for 5 years before accepting his current position at NYU.

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Lomonosov Moscow State University

Preparatory course (pre-university programme).

• Duration of study: March 2024 – July 2025.
• Holidays: July – August 2024.
• Start date: 1 March – 30 March 2024.
• Exams: June 2025.
• Tuition: $8900.
• The level of Russian: Beginner.
• Duration of study: September/October 2024 – July 2025.
• Start date: September – October.
• Tuition: $7000.
• The level of Russian: All levels.

• 1 BUSINESS SCHOOL
• 2 FACULTY OF BIOENGINEERING AND BIOINFORMATICS
• 3 FACULTY OF BIOLOGY
• 4 FACULTY OF BIOTECHNOLOGY
• 5 FACULTY OF CHEMISTRY
• 6 FACULTY OF COMPUTATIONAL MATHEMATICS AND CYBERNETICS
• 7 FACULTY OF EDUCATIONAL STUDIES
• 8 FACULTY OF ECONOMICS
• 9 FACULTY OF FOREIGN LANGUAGES
• 10 FACULTY OF FINE AND PERFORMING ARTS
• 11 FACULTY OF FUNDAMENTAL MEDICINE
• 12 FACULTY OF FUNDAMENTAL PHYSICAL-CHEMICAL ENGENEERING
• 13 FACULTY OF GEOLOGY
• 14 FACULTY OF GEOGRAPHY
• 15 FACULTY OF HISTORY
• 16 FACULTY OF JOURNALISM
• 17 FACULTY OF LAW
• 18 FACULTY OF MATERIALS SCIENCE
• 19 FACULTY OF MECHANICS AND MATHEMATICS
• 20 FACULTY OF PHYSICS
• 21 FACULTY OF PHILOLOGY
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• 34 INSTITUTE OF ASIAN AND AFRICAN STUDIES
• 35 MOSCOW SCHOOL OF ECONOMICS
• 36 SOIL SCIENCE FACULTY
• Admission procedure