2025
Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. (2025). kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq. Nature Protocols, 20(3):587-607. doi:10.1038/s41596-024-01057-0
Peyda P, Lin CH, Onwuzurike K, Black DL. (2025). The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multipart RNA regulatory modules. Genes & Development, 39(5-6):364-383. doi:10.1101/gad.352105.124
2024
Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh S, Chari T, Sullivan D, Blanco M, Guttman M. (2024). Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature.
Courellis HS, Minxha J, Cardenas AR, et al. (2024). Abstract representations emerge in human hippocampal neurons during inference. Nature, 632:841-849.
Wu MW, Kourdougli N, Portera-Cailliau C. (2024). Network state transitions during cortical development. Nature Reviews Neuroscience, 25(8):535-552. doi:10.1038/s41583-024-00824-y
Griggs WS, Norman SL, Deffieux T, Segura F, Osmanski BF, Chau G, Christopoulos V, Liu C, Tanter M, Shapiro MG, Andersen RA. (2024). Decoding motor plans using a closed-loop ultrasonic brain-machine interface. Nature Neuroscience, 27(1):196-207. doi:10.1038/s41593-023-01500-7
Xia S, Lu AC, Tobin V, Luo K, Moeller L, Shon DJ, Du R, Linton JM, Sui M, Horns F, Elowitz MB. (2024). Synthetic protein circuits for programmable control of mammalian cell death. Cell, 187(11):2785-2800.e16. doi:10.1016/j.cell.2024.03.031
2023
Maoz SLL, Stangl M, Topalovic U, Batista D, Hiller S, Aghajan ZM, Knowlton B, Stern J, Langevin JP, Fried I, Eliashiv D, Suthana N. (2023). Dynamic neural representations of memory and space during human ambulatory navigation. Nature Communications, 14(1):6643. doi:10.1038/s41467-023-42231-4
Cho NS, Sanvito F, Thakuria S, Wang C, Hagiwara A, Nagaraj R, Oshima S, Lopez Kolkovsky AL, Lu J, Raymond C, Liau LM, Everson RG, Patel KS, Kim W, Yang I, Bergsneider M, Nghiemphu PL, Lai A, Nathanson DA, Cloughesy TF, Ellingson BM. (2023). Multi-nuclear sodium, diffusion, and perfusion MRI in human gliomas. Journal of Neuro-Oncology, 163(2):417-427. doi:10.1007/s11060-023-04363-x
Frost IM, Mendoza AM, Chiou TT, Kim P, Aizenberg J, Kohn DB, De Oliveira SN, Weiss PS, Jonas SJ. (2023). Fluorinated Silane-Modified Filtroporation Devices Enable Gene Knockout in Human Hematopoietic Stem and Progenitor Cells. ACS Applied Materials & Interfaces, 15(35):41299-41309. doi:10.1021/acsami.3c07045
Qian K, Tol MJ, Wu J, Uchiyama LF, Xiao X, Cui L, Bedard AH, Weston TA, Rajendran PS, Vergnes L, Shimanaka Y, Yin Y, Jami-Alahmadi Y, Cohn W, Bajar BT, Lin CH, Jin B, DeNardo LA, Black DL, Whitelegge JP, Wohlschlegel JA, Reue K, Shivkumar K, Chen FJ, Young SG, Li P, Tontonoz P. (2023). CLSTN3β enforces adipocyte multilocularity to facilitate lipid utilization. Nature, 613(7942):160-168. doi:10.1038/s41586-022-05507-1
2022
Cooper YA, et al. (2022). Functional regulatory variants implicate distinct transcriptional networks in dementia. Science, 377:eabi8654.
Goronzy I, Quinodoz S, Jachowicz J, Ollikainen N, Bhat P, Guttman M. (2022). Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Cell Reports.
Quinodoz S, Bhat P, Chovanec P, Jachowicz JW, Ollikainen N, Detmar E, Soehalim E, Guttman M. (2022). SPRITE: A genome-wide method to map higher-order 3D spatial interactions in the nucleus using combinatorial split-and-pool barcoding. Nature Protocols.
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2021
Quinodoz S, Jachowicz J*, Bhat P*, Ollikainen N*, Banerjee A, Goronzy I, Blanco M, Chovanec P, Thai J, Chow A, Markaki Y, Plath K, Guttman M. (2021). RNA promotes the formation of spatial compartments in the nucleus. Cell.
Bhat P, Honson D, Guttman M. (2021). Nuclear compartmentalization as an emerging mechanism for gene expression. Nature Reviews Molecular and Cell Biology.
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Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. (2021). Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity, 54(5):916-930.e7. doi:10.1016/j.immuni.2021.04.011
2020
Esswein SR, Gristick HB, Jurado A, Peace A, Keeffe JR, Lee YE, Voll AV, Saeed M, Nussenzweig MC, Rice CM, Robbiani DF, MacDonald MR, Bjorkman PJ. (2020). Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody. Proceedings of the National Academy of Sciences USA, 117(18):9865-9875. doi:10.1073/pnas.1919269117
Aros CJ, Vijayaraj P, Pantoja CJ, Bisht B, Meneses LK, Sandlin JM, Tse JA, Chen MW, Purkayastha A, Shia DW, Sucre JMS, Rickabaugh TM, Vladar EK, Paul MK, Gomperts BN. (2020). Distinct Spatiotemporally Dynamic Wnt-Secreting Niches Regulate Proximal Airway Regeneration and Aging. Cell Stem Cell. doi:10.1016/j.stem.2020.06.019
Aros CJ, Paul MK, Pantoja CJ, Bisht B, Meneses LK, Vijayaraj P, Sandlin JM, France B, Tse JA, Chen MW, Shia DW, Rickabaugh TM, Damoiseaux R, Gomperts BN. (2020). High-Throughput Drug Screening Identifies a Potent Wnt Inhibitor that Promotes Airway Basal Stem Cell Homeostasis. Cell Reports, 30(7):2055-2064.e5. doi:10.1016/j.celrep.2020.01.059
2019
Hudson WH, Gensheimer J, Hashimoto M, Leonard WJ, Kissik HT, Ahmed R. (2019). Proliferating Transitory T Cells with an Effector-like Transcriptional Signature Emerge from PD-1+ Stem-like CD8+ T Cells during Chronic Infection. Immunity, Dec 03. doi:10.1016/j.immuni.2019.11.002
Morgan RA, Unti MJ, Aleshe B, Senadheera S, Hollis RP, Kohn D. (2019). Improved Titer and Gene Transfer by Lentiviral Vectors Using Novel, Small B-Globin Locus Control Region Elements. Molecular Therapy, Sep 27. doi:10.1016/j.ymthe.2019.09.020
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Balanis NG, Sheu KM, Esedebe FN, Huang J, Witte ON, Graeber TG. (2019). Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies. Cancer Cell, 36(1):17-34.e7. doi:10.1016/jccell.2019.06.005
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Yount NY, Weaver DC, Lee EY, Lee MW, Wang H, Cha LC, Wong GCL, Yeaman MR. (2019). A Unifying Structural Signature of Eukaryotic α-helical Host Defense Peptides. Proceedings of the National Academy of Sciences USA, in press.
Lee EY, Zhang C, Di Domizio J, Jin F, Connell W, Hung M, Malkoff N, Veksler V, Gilliet M, Ren P, Wong GCL. (2019). Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9. Nature Communications. doi:10.1038/s41467-019-08868-w
Lande R, Lee EY, Palazzo R, Pitraforte I, Mattenberger Y, Spadaro F, Stefanantoni K, Iannace N, Dufour AM, Falchi M, Bianco M, Alvarez M, Riccieri V, Truchetet ME, Wong GCL, Chizzolini C, Frasca L. (2019). CXCL4 assembles DNA into pro-inflammatory liquid crystalline complexes to amplify interferon-α production in systemic sclerosis. Nature Communications.
Akin O, Bajar BT, Keles MF, Frye MA, Zipursky SL. (2019). Cell-Type-Specific Patterned Stimulus-Independent Neuronal Activity in the Drosophila Visual System during Synapse Formation. Neuron, Jan 30. doi:10.2016/j.neuron.2019.01.008
Masiuk KE, Laborada J, Roncarolo MG, Hollis RP, Kohn DB. (2019). Lentiviral Gene Therapy in HSCs Restores Lineage-Specific Foxp3 Expression and Suppresses Autoimmunity in a Mouse Model of IPEX Syndrome. Cell Stem Cell, Jan 10. doi:10.1016/j.stem.2018.12.003
2018
Mehta A, Kim YJ, Robert L, Tsoi J, Comin-Anduix B, Berent-Maoz B, Cochran AJ, Economou J, Tumeh PC, Puig-Saus C, Ribas A. (2018). Immunotherapy resistance by inflammation-induced dedifferentiation. Cancer Discovery. doi:10.1158/2159-8290.CD-17-1178
Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng CL, Koulena N, Cronin C, Karp C, Liaw EJ, Amin M, Cai L. (2018). Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. Cell, 174(2):363-376.e16. doi:10.1016/j.cell.2018.05.035
2017
Shah S, Lubeck E, Zhou W, Cai L. (2017). seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus. Neuron, 94(4):752-758.e1. doi:10.1016/j.neuron.2017.05.008
Patel AA, Oztug Durer ZA, van Loon AP, Bremer KV, Quinlan ME. (2017). Drosophila and human FHOD family formins nucleate actin filaments. Journal of Biological Chemistry, Nov 10. doi:10.1074/jbc.M117.800888
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De Anda J*, Lee EY*, Lee CK*, Bennett RR, Ji X, Soltani S, Harrison MC, Baker AE, Luo Y, Chou T, O’Toole GA, Armani AM, Golestanian R, Wong GCL. (2017). High-speed “4D” computational microscopy of bacterial surface motility. ACS Nano, 11(9):9340-9351. doi:10.1021/acsnano.7b04738 (*Co-first authorship)
Lee EY, Takahashi T, Curk T, Dobnikar J, Gallo RL, Wong GCL. (2017). Crystallinity of double-stranded RNA-antimicrobial peptide complexes modulates Toll-Like receptor 3-mediated inflammation. ACS Nano. doi:10.1021/acsnano.7b05234
Chai H, Diaz-Castro B, Shigetomi E, Whitelegge JP, Coppola G, Khakh BS. (2017). Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence. Neuron, 95(3):531-549.e9.
Landaw J, Garfinkel A, Weiss JN, Qu Z. (2017). Memory-Induced Chaos in Cardiac Excitation. Physical Review Letters, 118:138101. doi:10.1103/PhysRevLett.118.138101
2016
Shah S, Lubeck E, Zhou W, Cai L. (2016). In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus. Neuron, 92(2):342-357. doi:10.1016/j.neuron.2016.10.001
Srinivasan R, Lu TY, Chai H, Xu J, Huang BS, Golshani P, Coppola G, Khakh BS. (2016). New Transgenic Mouse Lines for Selectively Targeting Astrocytes and Studying Calcium Signals in Astrocyte Processes In Situ and In Vivo. Neuron, 92(6):1181-1195. doi:10.1016/j.neuron.2016.11.030
Parikshak NN, Swarup V, Belgard TG, Irimia M, Ramaswami G, Gandal MJ, Hartl C, Leppa V, de la Torre Ubieta L, Huang J, Lowe JK, Blencowe BJ, Horvath S, Geschwind DH. (2016). Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature, 540:423-427. doi:10.1038/nature20612
Lee EY, Fulan B, Wong GCL, Ferguson A. (2016). Mapping membrane activity in undiscovered peptide sequence space using machine learning. Proceedings of the National Academy of Sciences USA.
Realegeno S, Kelly-Scumpia KM, Dang AT, Lu J, Teles R, Liu PT, Schenk M, Lee EY, Schmidt NW, Wong GCL, Sarno EN, Rea TH, Ochoa MT, Pellegrini M, Modlin RL. (2016). S100A12 is part of the antimicrobial network against Mycobacterium leprae in human macrophages. PLoS Pathogens, 12(6):e1005705. doi:10.1371/journal.ppat.1005705
Sankhagowit S, Lee EY, Wong GCL, Malmstadt N. (2016). Oxidation of membrane curvature-regulating phosphatidylethanolamine lipid results in formation of bilayer and cubic structures. Langmuir, 32(10):2450-2457. doi:10.1021/acs.langmuir.5b04332
Lee EY, Lee CK, Schmidt NW, Jin F, Lande R, Curk T, Frenkel D, Dobnikar J, Gilliet M, Wong GCL. (2016). A review of immune amplification via ligand clustering by self-assembled liquid-crystalline DNA complexes. Advances in Colloid and Interface Science, 232:17-24. doi:10.1016/j.cis.2016.02.003
Zaretsky JM, Garcia-Diaz A, Shin DS, Escuin-Ordinas H, Hugo W, Hu-Lieskovan S, Torrejon DY, Abril-Rodriguez G, Sandoval S, Barthly L, Saco J, Homet Moreno B, Mezzadra R, Chmielowski B, Ruchalski K, Shintaku IP, Sanchez PJ, Puig-Saus C, Cherry G, Seja E, Kong X, Pang J, Berent-Maoz B, Comin-Anduix B, Graeber TG, Tumeh PC, Schumacher TNM, Lo RS, Ribas A. (2016). Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma. New England Journal of Medicine, 375:819-829. doi:10.1056/NEJMoa1604958
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Tong AJ, Liu X, Thomas BJ, Lissner MM, Baker MR, Senagolage MD, Allred AL, Barish GD, Smale ST. (2016). A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation. Cell, 165(1):165-79. doi:10.1016/j.cell.2016.01.020
2015
Mehta A, Mann M, Zhao JL, Marinov GK, Majumdar D, Garcia-Flores Y, Du X, Erikci E, Chowdhury K, Baltimore D. (2015). The microRNA-212/132 cluster regulates B cell development and apoptosis by targeting Sox4. Journal of Experimental Medicine, 212(10):1679-92.
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Thai M, Thaker SK, Feng J, Du Y, Hu H, Wu TT, Graeber TG, Braas D, Christofk HR. (2015). MYC-induced reprogramming of glutamine catabolism supports optimal virus replication. Nature Communications, 6:8873. doi:10.1038/ncomms9873
Linares AJ, Lin CH, Damianov A, Adams KL, Novitch BG, Black DL. (2015). The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation. eLife, 4:e09268. doi:10.7554/eLife.09268
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2013
O’Donnell KC, Vargas ME, Sagasti A. (2013). WldS and PGC-1 regulate mitochondrial transport and oxidation state after axonal injury. Journal of Neuroscience, 33(37):14778-90.
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2012
Ch’ng TH, Uzgil B, Lin P, Avliyakulov NK, O’Dell TJ, Martin KC. (2012). Activity-dependent transport of the transcriptional coactivator CRTC1 from synapse to nucleus. Cell, 150(1):207-21.
Arboleda VA, Lee H, Parnaik R, Fleming A, Banerjee A, Ferraz-de-Souza B, Délot EC, Rodriguez-Fernandez IA, Braslavsky D, Bergadá I, Dell’Angelica EC, Nelson SF, Martinez-Agosto JA, Achermann JC, Vilain E. (2012). Mutations in the PCNA-binding domain of CDKN1C cause IMAGe syndrome. Nature Genetics, 44(7):788-92.
Rudie JD, Hernandez LM, Brown JA, Beck-Pancer D, Colich NL, Gorrindo P, Thompson PM, Geschwind DH, Bookheimer SY, Levitt P, Dapretto M. (2012). Autism-associated promoter variant in MET impacts functional and structural brain networks. Neuron, 75(5):904-15.
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Liu SY, Sanchez DJ, Aliyari R, Lu S, Cheng G. (2012). Systematic identification of type I and type II interferon-induced antiviral factors. Proceedings of the National Academy of Sciences USA, 109(11):4239-44.
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