Tony Zador

Principal Investigator

I have been on the faculty at Cold Spring Harbor Laboratory since 1999, serving as Chair from 2008-2018. As a graduate student at Yale, I trained in theoretical neuroscience and neural networks. During this time collaborated with Christof Koch, who was then at Caltech. Along the way I also obtained an MD degree, from Yale. I then did postdoctoral work on synaptic physiology with Chuck Stevens at the Salk Institute.

When I came to CSHL I decided to study sensory processing and decision-making in rodents. At that time no one had yet developed a rodent behavior comparable to the classic two-alternative choice paradigms used to study decision making in nonhuman primates. Therefore, in collaboration with my close (former) colleague Zach Mainen, we set out to develop such a paradigm. This paradigm is now used by many labs to study sensory processing and decision making in rodents, and has emerged as a well-established alternative to traditional primate studies.

Around 2010 I embarked upon a new line of research: Barcoding neurons, to enable us to use high-throughput sequencing technology to readout the brain’s wiring diagram. We are now using these tools to understand circuits in the auditory cortex and elsewhere.

As a postdoc I also organized a series of workshops on Neural Information and Coding. I then broadened the scope of these and founded the annual Computational and Systems Neuroscience (COSYNE) meeting, which now draws over 900 participants, and is arguably the leading meeting on theoretical and systems neuroscience. I am also a founder of NAIsys (, a meeting at the intersection of AI and neuroscience.

Alexander Vaughan

Scientific Project Manager

Huiqing Zhan

Research Investigator

National University of Singapore, PhD. Molecular and Cellular Biology

In addition to running the MAPseq Core Facility I work on mapping synaptic connectivity in situ by PLA (proximity Ligation Assay). I have been trying to combine the PLA technique with BARseq to identify the synaptic connectivity between neurons.

Gilbert Henry

Research Investigator

Akihiro Funamizu

Post Doc

University of Tokyo, PhD. Information science and Technology
1st Postdoc, Okinawa Institute of Science and Technology, Okinawa, Japan

My project focuses on integrating value-based and perceptual decision making. I also work on identifying the relationship between neural functions and connections.

Xiaoyin Chen

Post Doc

My project focuses on understanding neuronal circuits using BARseq. To understand the structures and functions of cortical circuits, I am developing techniques to associate different neuronal characteristics, such as anatomy, gene expression, connectivity, and activity, at cellular resolution with high throughput. To achieve this goal, we are developing BARseq, an in situ sequencing technique that allows high-throughput axonal projection mapping at cellular resolution. BARseq further associates projection patterns with other neuronal properties, such as gene expression, Cre labeling, and neuronal activity. Currently we are using BARseq to identify how long-range cortical projections are arranged by cortical neuronal types defined by transcription and how these projections are perturbed in models of neurological diseases. These works are the first steps towards a multi-modal description of cortical circuits using BARseq.

Longwen Huang

Post Doc

Baylor College of Medicine, PhD

My project focuses on developing and utilizing novel sequencing-based connectome mapping methods to determine brain-wide connectivity.

Li Yuan

Post Doc

University of Nebraska, Ph.D.

I am working on developing axonal BARseq techniques. By improving the sensitivity of BARseq I hope to sequence axonal terminals in cortical and subcortical structures.

Sanchari Ghosh

Graduate Student, Post

My project involves understanding the role of auditory stratum in learning auditory-motor association. I study the cortico-striatal synapses in the auditory system of animals trained to learn and then reverse specific auditory-motor associations, with the goal of identifying the cell-type specificity and understanding the role of these synapses in the learning process, using electrophysiological and molecular approaches.

Christopher Krasniak

Graduate Student WSBS

Colby College, B.A. Biology and Psychology

I am splitting my time between two projects for my PhD in the Zador lab. One is contributing to the International Brain Laboratory  a large-scale collaboration with the goal to standardize systems neuroscience while investigating the mechanisms for complex behaviors brain wide.  My individual project focuses on how the brain is able to solve the same tasks using different neural circuits following damage to the brain.

Shaina Lu

Graduate Student WSBS

Swarthmore College, B.S. Biology

My project involves pairing gene expression and spatial location to lean whole brain patterns of transcription.  I am using spatially resolved whole-transcriptome data from the mouse brain to determine if canonical, anatomically-derived brain areas can be learned using only transcription.

Colin Stoneking

Graduate Student WSBS

University of Cambridge, BA Natural Science

The main focus of my project is combining functional imaging with connectomics. I am developing methods for integrating functional imaging data (2-phton) with high-throughput connectivity data (BARseq).

Anqi Zhang

Graduate Student WSBS

McGill University, B.S.

My project focuses on understanding cortical representations in visual decision making. To accomplish this we are probing the logic of stimulus and other task-reated representations in the visual cortex and crticostriatal projection during a visual discrimination task.

Dennis Maharjan

Graduate Student WSBS

I am working on understanding the role of cortical circuits in driving auditory decision-making behavior. I am interested in characterizing the activity of cortical neurons, specifically cortical internourons, based on their projections as well as gene expression and studying how this activity plays a role in regulating decision-making during an auditory task.

Wiktor Wadolowski

Laboratory Manager

Yu-Chi Sun

Research Technician

Yan Li

Research Technician

Valeria Aguillon Rodriguez

Research Technician

Eugene Fong

Research Technician

Nicole Gemmill

Research Technician

Shupei Zhang

Research Technician

Faculty Alumni

Follow the links to learn more about faculty positions and projects of the Zador Lab Alumni.

Petr Znamenskiy (grad student) — Crick Institute, England (2020)

Justus Kebschull (grad student) — Johns Hopkins (2020)

Mike Deweese (postdoc) — U.C. Berkeley

Qiaojie Xiong (postdoc) — Stony Brook

Yang Yang (grad student) — Shanghai Tech

Simon Rumpel (postdoc) — University of Mainz, Germany

Gonzalo Otazu (postdoc) — NY Institute of Technology

Tomas Hromadka (grad student) — Slovak Academy of Sciences

Marta Moita (postdoc) — Champalimaud, Portugal

Susana Lima (postdoc) — Champalimaud, Portugal

Hysell Oviedo (postdoc) — CUNY

Hiro Asari (grad student) — EMBO, Rome

Santiao Jaramillo (postdoc) — U of Oregon, Eugene

Mike Wehr (postdoc) — U of Oregon, Eugene