Team

Staff Profiles

Jim Berg, Ph.D.

Director, Scientific Operations

Jim Berg is the Director of Scientific Operations of a new research program in development at the Allen Institute, to be focused on neural dynamics. He joined the Allen Institute in 2012, leading the in vitro single cell characterization project where his team used patch clamp electrophysiology to characterize the morphoelectric properties of thousands of neurons from the mouse visual cortical and human neocortical sections, publicly released as part of the Allen Cell Types Database. To study each cell’s transcriptomic signature in addition to the morphoelectric properties, his team adopted the Patch-seq technique. Using a system of rapid feedback and increased automation, they increased the throughput and quality of the Patch-seq data to ultimately contribute >8,000 additional mouse and human neurons to the database. Previously he studied the role of the TMEM16A ion channel in pain processing as a postdoc at UCSF and engineered Perceval, a genetically encoded fluorescent sensor for energy metabolism, as a graduate student at Harvard University. Berg's first experiences with patch clamping were as an undergraduate at Rutgers University, where he studied potassium current in auditory neurons and earned a B.S. in neuroscience. Berg recently earned an MBA from the University of Washington with a focus on technology management.

Research

Research Interests

The primary question that drives my research is – How do ion channel proteins influence neuronal activity and ultimately behavior? The neuronal membrane is comprised of a vast collection of ion channels, and the activity of these proteins defines each neuron's innate electrical properties. It is these properties, combined with the neuron's morphology, that govern how a neuron integrates various timed inputs to yield an outgoing signal. The dysfunction of individual ion channels can disrupt neuronal behavior and may lead to serious diseases such as epilepsy and neuropathic pain. I am interested in cataloguing the intrinsic electrical properties of neurons and behavior and learning how the genetic expression of different ion channels shapes these properties. At the Allen Institute, we are currently building a team to record the intrinsic electrical properties of different cell types in the brain. We are developing cutting-edge techniques to increase the throughput of patch clamp electrophysiology from areas of the mouse brain in vitro. This program is highly integrative, as it uses Cre mouse lines generated and profiled for the Allen Mouse Brain Connectivity Atlas and will provide samples for morphological reconstruction and single cell transcription profiling by the anatomy and molecular networks teams, respectively. In addition, we work closely with theoreticians to provide data to test different models of circuit function. Our goal is to provide a solid base of physiology data as a core part of the cell types program. In the future, as we build upon this foundation, we will expand the program to include other directions such as exploring the role of individual ion channels using specific ion channel inhibitors, or using optogenetic stimulation of presynaptic neurons to study a cell type's integrative properties. In the end, we aim to provide a valuable resource to researchers around the world who study the brain in both healthy and diseased states.

Expertise

  • Patch clamp electrophysiology
  • Molecular biology
  • Behavior

Research Programs

  • Cell types

Selected Publications View Publications

Alternating sources of perisomatic inhibition during behavior

Neuron
January 27, 2021

Dudok B, Klein PM, Hwaun E, Lee BR, Yao Z, Fong O, Bowler JC, Terada S, Sparks FT, Szabo GG, Farrell JS, Berg J, Daigle TL, Tasic B, Dimidschstein J, Fishell G, Losonczy A, Zeng H, Soltesz I.

CamKIIα Positive Interneurons Identified via A microRNA Based Viral Gene Targeting Strategy

Journal of Neuroscience
November 5, 2020

Keaveney MK, Rahsepar B, Tseng HA, Fernandez FR, Mount RA, Ta T, White JA, Berg J, Han X

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells

Cell
November 12, 2020

Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H

Classification of electrophysiological and morphological neuron types in mouse visual cortex

Nature Neuroscience
June 17, 2019

Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin S, Feng D, Anastassiou C, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle T, Dalley R, Dee N, Desta T, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris J, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina C, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips J, Zeng H, Koch C

Systematic generation of biophysically detailed models for diverse cortical neuron types

Nature Communications
February 19, 2018

Gouwens NW, Berg J, Feng D, Sorensen SA, Zeng H, Hawrylycz MJ, Koch C, and Arkhipov A

Generalized leaky integrate-and-fire models classify multiple neuron types

Nature Communications
February 19, 2018

Teeter C, Iyer R, Menon V, Gouwens N, Feng D, Berg J, Szafer A, Cain N, Zeng H, Hawrylycz M, Koch C, Mihalas S

Visual physiology of the Layer 4 cortical circuit in silico

PLoS Computational Biology
November 12, 2018

Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-LLavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C

Voltage-gated potassium channel EAG2 controls mitotic entry and tumor growth in medulloblastoma via regulating cell volume dynamics

Genes & Development
August 2012

Huang X, Dubuc AM, Hashizume R, Berg J, He Y, Wang J, Chiang C, Cooper MK, Northcott PA, Taylor MD, Barnes MJ, Tihan T, Chen J, Hackett CS, Weiss WA, James CD, Rowitch DH, Shuman MA, Jan YN, Jan LY

Ca2+-activated Cl- channels at a glance

Journal of Cell Science
May 2012

Berg J, Yang H, Jan LY

A genetically encoded fluorescent reporter of ATP:ADP ratio

Nature Methods
February 2009

Berg, J, Hung YP, Yellen G

Ketogenic diet metabolites reduce firing in central neurons by opening KATP channels

Journal of Neuroscience
April 2007

Ma, W., Berg, J., Yellen, G

Truncated ClC-1 mRNA in myotonic dystrophy exerts a dominant-negative effect on the Cl current

Neurology
December 2004

Berg J, Jiang H, Thornton CA, Cannon SC