Naomi Habib Lab

ELSC Members

Goren-Khazzam Lecturer in Brain Sciences

Cognitive decline and resilience lab

We are interested in solving the secret of cognitive resilience. The cellular microenvironment in the brain is composed of multiple cell types, including neurons, astrocytes, microglia, vascular and other cells, and we are studying how interactions between different cell types in the brain are contributing to cognitive decline and to cognitive resilience, in particular in the context of aging-related pathologies. We also study how interactions between the brain and other systems in the aging body, such as immune and metabolic signaling, are mediating aging-related pathologies. The work is done using human brain tissue, animal models and cell cultures, combining cutting-edge technologies in the fields of genomics, imaging, molecular biology, and genome engineering, with advanced computational analysis and modeling. Specifically, we are pioneering the development and application of single nucleus RNA-sequencing technologies.

Danny Kitsberg

Lab Manager

Neta Rosner-Wach

PhD Student

Guy Lutsker

PhD Student

Daniel Bar Hanin

PhD Student

Masha Adam

Research Scientist

Anna Schmidtner

Post Doc

Inbar Shapira

PhD Student

Or Gold

PhD Student

Adi Ravid

PhD Student

Hodaya Vrubel

PhD Student

Dekel Wainer

PhD Student

Gilad Green

BSc student

Gilad Sahar Green, Masashi Fujita, Hyun-Sik Yang, Mariko Taga, Anael Cain, Cristin McCabe, Natacha Comandante-Lou, Charles C. White, Anna K. Schmidtner, Lu Zeng, Alina Sigalov, Yangling Wang, Aviv Regev, Hans-Ulrich Klein, Vilas Menon, David A. Bennett, Naomi Habib & Philip L. De Jager

Cellular communities reveal trajectories of brain ageing and Alzheimer’s disease

Nature (2024)

Chappleboim A, Joseph-Strauss D, Rahat A, Sharkia I, Adam M, Kitsberg D, Fialkoff G, Lotem M, Gershon O, Schmidtner AK, Oiknine-Djian E, Klochendler A, Sadeh R, Dor Y, Wolf D, Habib N, Friedman N.

Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing.

Sci Transl Med. (2021)

Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M.

Single cell biology-a Keystone Symposia report

Ann N Y Acad Sci. (2021)

. Habib, N., C. McCabe, S. Medina, M. Varshavsky, D. Kitsberg, R. Dvir-Szternfeld, G. Green, D. Dionne, L. Nguyen, J. L. Marshall, F. Chen, F. Zhang, T. Kaplan, A. Regev, and M. Schwartz

Diseaseassociated astrocytes in Alzheimer’s disease and aging

Nat Neurosci. (2020)

Olah M, Menon V, Habib N, Taga MF, Ma Y, Yung CJ, Cimpean M, Khairallah A, Coronas-Samano G, Sankowski R, Grün D, Kroshilina AA, Dionne D, Sarkis RA, Cosgrove GR, Helgager J, Golden JA, Pennell PB, Prinz M, Vonsattel JPG, Teich AF, Schneider JA, Bennett DA, Regev A, Elyaman W, Bradshaw EM, De Jager PL.

Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease

Nature Communications (2020)

Habib N, McCabe C, Medina S, et al.

Disease-associated astrocytes in Alzheimer’s disease and aging

Nat Neurosci. 23, 701–706 (2020)

Gaublomme, J.T., Li, B., McCabe, C. et al.

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Nat Commun (2019)

Olah, M., Menon, V., Habib, N., Taga, M., Yung, C.J., Sarkis, R.A., Schneider, J.A., Bennett, D.A., Regev, A., Elyaman, W., Bradshaw, E.M. and De Jager, P.L.

P4‐256: A SINGLE‐CELL‐BASED ATLAS OF HUMAN MICROGLIAL STATES SHOWS DIVERGENT ASSOCIATIONS WITH AGING‐RELATED NEUROPATHOLOGIES AND DEMENTIA

Alzheimer's & Dementia 14: P1544-P1545 (2018)

Habib, N., Avraham-Davidi, I., Basu, A. et al.

Massively parallel single-nucleus RNA-seq with DroNc-seq

Nat Methods (2017)

NAOMI HABIB, YINQING LI, MATTHIAS HEIDENREICH, LUKASZ SWIECH, INBAL AVRAHAM-DAVIDI, JOHN J. TROMBETTA, CYNTHIA HESSION, FENG ZHANG, AVIV REGEV

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

Science (2016)

Gahl Levy, Naomi Habib, Maria Angela Guzzardi, Daniel Kitsberg, David Bomze, Elishai Ezra, Basak E Uygun, Korkut Uygun, Martin Trippler, Joerg F Schlaak, Oren Shibolet, Ella H Sklan, Merav Cohen, Joerg Timm, Nir Friedman, Yaakov Nahmias

Nuclear receptors control pro-viral and antiviral metabolic responses to hepatitis C virus infection

Nature Chemical Biology volume 12, pages 1037–1045 (2016)

Habib, N, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, Sur M, Zhang F.

In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9

Nat Biotechnol (2015)

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F.

Multiplex Genome Engineering Using CRISPR/Cas Systems

Science, Vol. 339, Issue 6121, pp. 819-823 (2013)

Media:
Divide and conquer. New single-cell approach broadens range of cell types that can be studied in the brain. 2016

Div-Seq – A single nucleus RNA-Seq method reveals dynamics of rare adult newborn neurons in the CNS. 2016

A Google Map of the Brain. 2017

DroNc-Seq – Single-nucleus RNA sequencing, droplet by droplet. 2017/2018

“Cellular landscapes of the mouse and human brains”. 2018.

“Single nucleus RNA-seq in the adult mammalian brain”. 2017.

Naomi Habib

Associate Professor

Email: naomi.habib@elsc.huji.ac.il

Phone: +972-2-5494818

Naomi Habib

@naomi_habib

Address: The Edmond and Lily Safra Center for Brain Sciences
The Suzanne and Charles Goodman Brain Sciences Building,
Level 2, Room 2207, Edmond J. Safra Campus,
The Hebrew University of Jerusalem, 9190401

Goren-Khazzam Lecturer in Brain Sciences

Cognitive decline and resilience lab

People

Abeer Karmi Hallak, Ph.D.

Lab Manager

Imri Lifshitz

Ph.D. Student

Shai Tishby

Ph.D. Student

Yoav Rubinstein

Ph.D. Student

Maayan Moshkovitz

PhD Student

Netta Livneh

PhD Student

Asia Prag

MSc Student

Or Nathan

Undergraduate Student

Hila Topaz

Undergraduate Student

Publications

Shai Tishby Tamari, Yoav Rubinstein, Netta Livneh, Maayan Moshkovitz, Abeer Karmi, Lilach Avitan

Neural temporal scaling accounts for robust hunting behavior across temperatures

Nature Communications (2026)

Imri Lifshitz, Asia Prag, Netta Livneh, Maayan Moshkovitz, Abeer Karmi, Lilach Avitan

Distinct distributed neural dynamics predict pallium-dependent social approach

Nature Communications (2026)

Y Rubinstein, M Moshkovitz, I Ottenheimer, S Shapira, S Tiomkin, L Avitan

A detailed quantification of larval zebrafish behavioral repertoire uncovers principles of hunting behavior

iScience (2025)

Suárez, Rodrigo, Tobias Bluett, Michael H. McCullough, Lilach Avitan, Dylan A. Black, Annalisa Paolino, Laura R. Fenlon, Geoffrey J. Goodhill, and Linda J. Richards.

Cortical activity emerges in region-specific patterns during early brain development

Proc. Natl. Acad. Sci. (2023)

Zhu, Shuyu I., Michael H. McCullough, Zac Pujic, Jordan Sibberas, Biao Sun, Thomas Darveniza, Bianca Bucknall, Lilach Avitan, and Geoffrey J. Goodhill

fmr1 Mutation Alters the Early Development of Sensory Coding and Hunting and Social Behaviors in Larval Zebrafish

Journal of Neuroscience (2023)

Triplett MA, Pujic Z, Sun B, Avitan L, Goodhill GJ.

Model-based decoupling of evoked and spontaneous neural activity in calcium imaging data

PLoS Comput Biol. (2020)

Avitan L, Pujic Z, Mölter J, Zhu S, Sun B, Goodhill GJ

Spontaneous and evoked activity patterns diverge over development

Elife, 19;10:e61942 (2021)

Lilach Avitan, Carsen Stringer

Not so spontaneous: Multi-dimensional representations of behaviors and context in sensory areas

Neuron (2022)

Marcus A. Triplett , Lilach Avitan , and Geoffrey J. Goodhill

Emergence of spontaneous assembly activity in developing neural networks without afferent input.

Computational Biology (2020)

Avitan, L., Pujic, Z., Molter, J., Sun, B., Myhre,A.E., Goodhill, G.J.

Behavioral Signatures of a Developing Neural Code

Current Biology (2020)

Avitan L. and Goodhill G.J.

Code Under Construction: Neural Coding Over Development

Trends in Neurosciences (2018)

Mölter, J., Avitan, L. & Goodhill, G.

Detecting neural assemblies in calcium imaging data

BMC Biol (2018)

Triplett, M., Avitan, L. and Goodhill, G.J.

Emergence of spontaneous assembly activity in developing neural networks without afferent input

PLoS Computational Biology, 14(9):e1006421 (2018)

Marachlian, E., Avitan, L., Goodhill, G.J., and Sumbre, G.

Principles of Functional Circuit Connectivity: Insights From Spontaneous Activity in the Zebrafish Optic Tectum

Frontiers in Neural Circuits, 12, 46 (2018)

Avitan L., Pujic Z., Mölter J., Sun B., Van De Poll1 M., Teng H.,Amor R., Scott E.K., and Goodhill G.J.

Spontaneous Activity in the Zebrafish Tectum Reorganizes over Development and Is Influenced by Visual Experience

Current Biology, Volume 27, Issue 16, Pages 2407-2419.e4 (2017)

Avitan, L., Pujic Z., Hughes J.N., Scott E.K. and Goodhill J.G.

Limitations of Neural Map Topography for Decoding Spatial Information

Journal of Neuroscience, 36(19):5385–5396 (2016)

Suarez, R., Fenlon, L., Marek, R., Avitan, L., Sah, P., Goodhill, G.J. and Richards, L.J.

Balanced Interhemispheric Cortical Activity Is Required for Correct Targeting of the Corpus Callosum

Neuron, Volume 82, Issue 6, Pages 1289-1298 (2014)

Avitan L., Teicher M., and Abeles M.

EEG Generator—A Model of Potentials in a Volume Conductor

Journal of Neurophysiology, 102: 3046-3059 (2009)

Avitan L., Teicher M., and Abeles M.

Resolving the dynamics of EEG generators by multichannel recordings

Biological Cybernetics, 98(1):49-59 (2008)

Open Positions

We are looking for bright and highly motivated doctoral and postdoctoral students.

Additional Information

Media:
ABC Science show Australia

Cosmos magazine

Australasian Science

Lilach Avitan

Assistant Professor

Email: lilach.avitan@mail.huji.ac.il

Phone: +972-2-5494829

Lilach Avitan

@LilachAvitan

Address: The Edmond and Lily Safra Center for Brain Sciences
The Suzanne and Charles Goodman Brain Sciences Building,
Level 2, Room 1203, Edmond J. Safra Campus,
The Hebrew University of Jerusalem, 9190401