Tom Kornberg, PhD

Professor
Cardiovascular Research Institute
+1 415 476-4963

We study mechanisms of cell-cell communication and signal transduction to understand the processes that regulate and sculpt organogenesis and morphogenesis. We apply a variety of approaches, including classical and molecular genetics and histological techniques ranging from fluorescence microscopy to fine structure EM analysis. The systems we study include oogenesis, embryogenesis, and the development of various organs including airway, lung and various other epithelial tissues.

Research Summary: 
Cell signaling and signal transduction

Websites

Publications: 

Metabolic control of progenitor cell propagation during Drosophila tracheal remodeling.

Nature communications

Li Y, Dong P, Yang Y, Guo T, Zhao Q, Miao D, Li H, Lu T, Xia F, Lyu J, Ma J, Kornberg TB, Zhang Q, Huang H

DaXi-high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy.

Nature methods

Yang B, Lange M, Millett-Sikking A, Zhao X, Bragantini J, VijayKumar S, Kamb M, Gómez-Sjöberg R, Solak AC, Wang W, Kobayashi H, McCarroll MN, Whitehead LW, Fiolka RP, Kornberg TB, York AG, Royer LA

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

Science (New York, N.Y.)

Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbic M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O'Brien LE, Dow JAT, FCA Consortium§, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP

Preface.

Current topics in developmental biology

Kornberg T

Elimination of nurse cell nuclei that shuttle into oocytes during oogenesis.

The Journal of cell biology

Ali-Murthy Z, Fetter RD, Wang W, Yang B, Royer LA, Kornberg TB

Cytonemes with complex geometries and composition extend into invaginations of target cells.

The Journal of cell biology

Wood BM, Baena V, Huang H, Jorgens DM, Terasaki M, Kornberg TB

Broadly conserved roles of TMEM131 family proteins in intracellular collagen assembly and secretory cargo trafficking.

Science advances

Zhang Z, Bai M, Barbosa GO, Chen A, Wei Y, Luo S, Wang X, Wang B, Tsukui T, Li H, Sheppard D, Kornberg TB, Ma DK

Cytoneme-mediated signaling essential for tumorigenesis.

PLoS genetics

Fereres S, Hatori R, Hatori M, Kornberg TB

Designing a green fluorogenic protease reporter by flipping a beta strand of GFP for imaging apoptosis in animals.

Journal of the American Chemical Society

Zhang Q, Schepis A, Huang H, Yang J, Ma W, Torra J, Zhang SQ, Yang L, Wu H, Nonell S, Dong Z, Kornberg TB, Coughlin SR, Shu X

Glutamate signaling at cytoneme synapses.

Science (New York, N.Y.)

Huang H, Liu S, Kornberg TB

Withdrawal: Dm1-MMP, a matrix metalloproteinase from Drosophila with a potential role in extracellular matrix remodeling during neural development.

The Journal of biological chemistry

Llano E, Pendás AM, Aza-Blanc P, Kornberg TB, López-Otín C

Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter.

Molecular cell

Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X

Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter.

Molecular cell

Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X

Scripting a place in time.

Developmental biology

Kornberg TB

Essential basal cytonemes take up Hedgehog in the Drosophila wing imaginal disc.

Development (Cambridge, England)

Chen W, Huang H, Hatori R, Kornberg TB

Hyperactive locomotion in a Drosophila model is a functional readout for the synaptic abnormalities underlying fragile X syndrome.

Science signaling

Kashima R, Redmond PL, Ghatpande P, Roy S, Kornberg TB, Hanke T, Knapp S, Lagna G, Hata A

Distributing signaling proteins in space and time: the province of cytonemes.

Current opinion in genetics & development

Kornberg TB

Augmented noncanonical BMP type II receptor signaling mediates the synaptic abnormality of fragile X syndrome.

Science signaling

Kashima R, Roy S, Ascano M, Martinez-Cerdeno V, Ariza-Torres J, Kim S, Louie J, Lu Y, Leyton P, Bloch KD, Kornberg TB, Hagerman PJ, Hagerman R, Lagna G, Hata A

A Path to Pattern.

Current topics in developmental biology

Kornberg TB

Developmental compartments in the larval trachea of Drosophila.

eLife

Rao PR, Lin L, Huang H, Guha A, Roy S, Kornberg TB

A naturally monomeric infrared fluorescent protein for protein labeling in vivo.

Nature methods

Yu D, Baird MA, Allen JR, Howe ES, Klassen MP, Reade A, Makhijani K, Song Y, Liu S, Murthy Z, Zhang SQ, Weiner OD, Kornberg TB, Jan YN, Davidson MW, Shu X

Paracrine signaling mediated at cell-cell contacts.

BioEssays : news and reviews in molecular, cellular and developmental biology

Roy S, Kornberg TB

Cytonemes and the dispersion of morphogens.

Wiley interdisciplinary reviews. Developmental biology

Kornberg TB

Hedgehog and its circuitous journey from producing to target cells.

Seminars in cell & developmental biology

Guerrero I, Kornberg TB

An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging.

Nature communications

Yu D, Gustafson WC, Han C, Lafaye C, Noirclerc-Savoye M, Ge WP, Thayer DA, Huang H, Kornberg TB, Royant A, Jan LY, Jan YN, Weiss WA, Shu X

Communicating by touch--neurons are not alone.

Trends in cell biology

Kornberg TB, Roy S

Cytonemes as specialized signaling filopodia.

Development (Cambridge, England)

Kornberg TB, Roy S

Cytonemes extend their reach.

The EMBO journal

Kornberg TB

An essential role for zygotic expression in the pre-cellular Drosophila embryo.

PLoS genetics

Ali-Murthy Z, Lott SE, Eisen MB, Kornberg TB

Direct delivery mechanisms of morphogen dispersion.

Science signaling

Roy S, Kornberg TB

Specificity of Drosophila cytonemes for distinct signaling pathways.

Science (New York, N.Y.)

Roy S, Hsiung F, Kornberg TB

Generalizing moving averages for tiling arrays using combined p-value statistics.

Statistical applications in genetics and molecular biology

Kechris KJ, Biehs B, Kornberg TB

Two patched protein subtypes and a conserved domain of group I proteins that regulates turnover.

The Journal of biological chemistry

Kawamura S, Hervold K, Ramirez-Weber FA, Kornberg TB

Organ renewal and cell divisions by differentiated cells in Drosophila.

Proceedings of the National Academy of Sciences of the United States of America

Guha A, Lin L, Kornberg TB

Linear RNA amplification for the production of microarray hybridization probes.

Methods in molecular biology (Clifton, N.J.)

Klebes A, Kornberg TB

Understanding morphogen gradients: a problem of dispersion and containment.

Current opinion in genetics & development

Kornberg TB, Guha A

Smoothened regulates activator and repressor functions of Hedgehog signaling via two distinct mechanisms.

The Journal of biological chemistry

Ogden SK, Casso DJ, Ascano M, Yore MM, Kornberg TB, Robbins DJ

Dependence of Drosophila wing imaginal disc cytonemes on Decapentaplegic.

Nature

Hsiung F, Ramirez-Weber FA, Iwaki DD, Kornberg TB

Regulation of cellular plasticity in Drosophila imaginal disc cells by the Polycomb group, trithorax group and lama genes.

Development (Cambridge, England)

Klebes A, Sustar A, Kechris K, Li H, Schubiger G, Kornberg TB

Drosophila signal peptide peptidase is an essential protease for larval development.

Genetics

Casso DJ, Tanda S, Biehs B, Martoglio B, Kornberg TB

Another arrow in the Drosophila quiver.

Proceedings of the National Academy of Sciences of the United States of America

Kornberg T

Dm1-MMP, a matrix metalloproteinase from Drosophila with a potential role in extracellular matrix remodeling during neural development.

The Journal of biological chemistry

Llano E, Pendás AM, Aza-Blanc P, Kornberg TB, López-Otín C

Functional studies of the BTB domain in the Drosophila GAGA and Mod(mdg4) proteins.

Nucleic acids research

Read D, Butte MJ, Dernburg AF, Frasch M, Kornberg TB

Expression of the vertebrate Gli proteins in Drosophila reveals a distribution of activator and repressor activities.

Development (Cambridge, England)

Aza-Blanc P, Lin HY, Ruiz i Altaba A, Kornberg TB

On the range of hedgehog signaling.

Current opinion in genetics & development

Chuang PT, Kornberg TB

Hedgehog signal transduction in the posterior compartment of the Drosophila wing imaginal disc.

Molecular cell

Ramírez-Weber FA, Casso DJ, Aza-Blanc P, Tabata T, Kornberg TB

The Drosophila genome sequence: implications for biology and medicine.

Science (New York, N.Y.)

Kornberg TB, Krasnow MA

GFP-tagged balancer chromosomes for Drosophila melanogaster.

Mechanisms of development

Casso D, Ramírez-Weber F, Kornberg TB

Ci: a complex transducer of the hedgehog signal.

Trends in genetics : TIG

Aza-Blanc P, Kornberg TB

GFP-tagged balancer chromosomes for Drosophila melanogaster.

Mechanisms of development

Casso D, Ramírez-Weber FA, Kornberg TB

Pictures in cell biology. Cytonemes.

Trends in cell biology

Kornberg T

Daughters against dpp modulates dpp organizing activity in Drosophila wing development.

Nature

Tsuneizumi K, Nakayama T, Kamoshida Y, Kornberg TB, Christian JL, Tabata T

Phosphorylation of the fused protein kinase in response to signaling from hedgehog.

Proceedings of the National Academy of Sciences of the United States of America

Thérond PP, Knight JD, Kornberg TB, Bishop JM

Creating a Drosophila wing de novo, the role of engrailed, and the compartment border hypothesis.

Development (Cambridge, England)

Tabata T, Schwartz C, Gustavson E, Ali Z, Kornberg TB

Selection and characterization of sequences with high affinity for the engrailed protein of Drosophila.

Mechanisms of development

Saenz-Robles MT, Maschat F, Tabata T, Scott MP, Kornberg TB

Analysis of the genes involved in organizing the tail segments of the Drosophila melanogaster embryo.

Mechanisms of development

Kuhn DT, Turenchalk G, Mack JA, Packert G, Kornberg TB

Analysis of cubitus interruptus regulation in Drosophila embryos and imaginal disks.

Development (Cambridge, England)

Schwartz C, Locke J, Nishida C, Kornberg TB

polyhomeotic appears to be a target of engrailed regulation in Drosophila.

Development (Cambridge, England)

Serrano N, Brock HW, Demeret C, Dura JM, Randsholt NB, Kornberg TB, Maschat F

Phosphorylation of the Drosophila engrailed protein at a site outside its homeodomain enhances DNA binding.

The Journal of biological chemistry

Bourbon HM, Martin-Blanco E, Rosen D, Kornberg TB

Allele-specific quantification of Drosophila engrailed and invected transcripts.

Proceedings of the National Academy of Sciences of the United States of America

Goldsborough AS, Kornberg TB

Blistered: a gene required for vein/intervein formation in wings of Drosophila.

Development (Cambridge, England)

Fristrom D, Gotwals P, Eaton S, Kornberg TB, Sturtevant M, Bier E, Fristrom JW

Understanding the homeodomain.

The Journal of biological chemistry

Kornberg TB

Isolation of cDNAs encoding the Drosophila GAGA transcription factor.

Molecular and cellular biology

Soeller WC, Oh CE, Kornberg TB

Segmentation of the Drosophila embryo.

Current opinion in genetics & development

Kornberg TB, Tabata T

Development of the D. melanogaster caudal segments involves suppression of the ventral regions of A8, A9 and A10.

Development (Cambridge, England)

Kuhn DT, Sawyer M, Packert G, Turenchalk G, Mack JA, Sprey TE, Gustavson E, Kornberg TB

A gene related to the proto-oncogene fps/fes is expressed at diverse times during the life cycle of Drosophila melanogaster.

Molecular and cellular biology

Katzen AL, Montarras D, Jackson J, Paulson RF, Kornberg T, Bishop JM

MYB and MYC in the cell cycle.

Cold Spring Harbor symposia on quantitative biology

Bishop JM, Eilers M, Katzen AL, Kornberg T, Ramsay G, Schirm S

Expression of engrailed during segmentation in grasshopper and crayfish.

Development (Cambridge, England)

Patel NH, Kornberg TB, Goodman CS

Expression of engrailed proteins in arthropods, annelids, and chordates.

Cell

Patel NH, Martin-Blanco E, Coleman KG, Poole SJ, Ellis MC, Kornberg TB, Goodman CS

Patterns of engrailed protein in early Drosophila embryos.

Development (Cambridge, England)

Karr TL, Weir MP, Ali Z, Kornberg T

Spatial regulation of engrailed expression in the Drosophila embryo.

Genes & development

Weir MP, Edgar BA, Kornberg T, Schubiger G

In vitro transcription of the Drosophila engrailed gene.

Genes & development

Soeller WC, Poole SJ, Kornberg T

Modifying expression of the engrailed gene of Drosophila melanogaster.

Development (Cambridge, England)

Poole SJ, Kornberg TB

The transcription unit of the Drosophila engrailed locus: an unusually small portion of a 70,000 bp gene.

The EMBO journal

Drees B, Ali Z, Soeller WC, Coleman KG, Poole SJ, Kornberg T

Molecular cloning of engrailed: a gene involved in the development of pattern in Drosophila melanogaster.

Cell

Kuner JM, Nakanishi M, Ali Z, Drees B, Gustavson E, Theis J, Kauvar L, Kornberg T, O'Farrell PH

Isolation of the proto-oncogene c-myb from D. melanogaster.

Cell

Katzen AL, Kornberg TB, Bishop JM

Proto-oncogenes of Drosophila melanogaster.

Cold Spring Harbor symposia on quantitative biology

Bishop JM, Drees B, Katzen AL, Kornberg TB, Simon MA

Structure and expression of two classes of mammalian homeo-box-containing genes.

Cold Spring Harbor symposia on quantitative biology

Joyner A, Hauser C, Kornberg T, Tjian R, Martin G

The engrailed locus of Drosophila melanogaster: genetic, developmental, and molecular studies.

Cold Spring Harbor symposia on quantitative biology

Ali Z, Drees B, Coleman KG, Gustavson E, Karr TL, Kauvar LM, Poole SJ, Soeller W, Weir MP, Kornberg T

The phenotype of engrailed mutations in the antenna of Drosophila.

Developmental biology

Morata G, Kornberg T, Lawrence PA

Small nuclear RNA transcription and ribonucleoprotein assembly in early Xenopus development.

The Journal of cell biology

Forbes DJ, Kornberg TB, Kirschner MW

Engrailed: a gene controlling compartment and segment formation in Drosophila.

Proceedings of the National Academy of Sciences of the United States of America

Kornberg T