Jennifer Fung, PhD
Professor
Ob/Gyn, Reproductive Sciences
School of Medicine

Education & Training

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• Ph.D. Graduate Division (Biophysics) University of California, San Francisco 1996

Interests

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• recombination and DNA repair
• cellular and subcellular morphological changes
• Environmental Health
• Fluorescence microscopy
• reproductive health
• Meiotic chromosome segregation

Websites

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• Fung Lab Website (funglab.ucsf.edu)

Grants and Projects

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• Quantitative Analysis of Meiotic Chromosome Motion and Pairing, NIH, 2020-2024
• Modeling and Analysis of Meiotic Homolog Pairing, NIH, 2016-2020
• Kinetics of Chromosome Synapsis During Meiosis, NIH, 2011-2016
• Upgrading the OMX microscope for extended live imaging and fast live 3-D structur, NIH, 2012-2013

Publications (48)

Top publication keywords:
Nuclear EnvelopeChromosomesRecombination, GeneticSaccharomyces cerevisiae ProteinsChromosome SegregationSynaptonemal ComplexSaccharomyces cerevisiaeKinetochoresFlap EndonucleasesChromosome PairingSaccharomycetalesTelomereMeiosisRecQ HelicasesCrossing Over, Genetic

• A high-throughput method for quantifying Drosophila fecundity.
  bioRxiv : the preprint server for biology 2024 Gomez A, Gonzalez S, Oke A, Luo J, Duong JB, Esquerra RM, Zimmerman T, Capponi S, Fung JC, Nystul TG
• Screening and characterization of 133 physiologically-relevant environmental chemicals for reproductive toxicity.
  bioRxiv : the preprint server for biology 2024 Ulaganathan G, Jiang H, Canio N, Oke A, Armstrong SS, Abrahamsson D, Varshavsky JR, Lam J, Cooper C, Robinson JF, Fung JC, Woodruff TJ, Allard P
• An Unsupervised Learning Approach to Resolve Phenotype to Genotype Mapping in Budding Yeasts Vacuoles.
  Image Analysis and Processing – ICIAP 2023 2023 Vito Paolo Pastore, Paolo Didier Alfano, Ashwini Oke, Sara Capponi, Daniel Eltanan, Xavier Woodruff-Madeira, Anita Nguyen, Jennifer Carol Fung, Simone Bianco
• Efficient unsupervised learning of biological images with compressed deep features.
  Image and Vision Computing 2023 Vito Paolo Pastore, Massimiliano Ciranni, Simone Bianco, Jennifer Carol Fung, Vittorio Murino, Francesca Odone
• Homologous chromosome recognition via nonspecific interactions.
  bioRxiv : the preprint server for biology 2023 Marshall WF, Fung JC

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• Kinetic analysis of synaptonemal complex dynamics during meiosis of yeast Saccharomyces cerevisiae reveals biphasic growth and abortive disassembly.
  Frontiers in cell and developmental biology 2023 Pollard MG, Rockmill B, Oke A, Anderson CM, Fung JC
• Modeling cell biological features of meiotic chromosome pairing to study interlock resolution.
  PLoS computational biology 2022 Navarro EJ, Marshall WF, Fung JC
• A Role for Synaptonemal Complex in Meiotic Mismatch Repair.
  Genetics 2021 Karen Voelkel-Meiman, Ashwini Oke, Arden Feil, Alexander Shames, Jennifer Fung, Amy J MacQueen
• Steroid hormones regulate genome-wide epigenetic programming and gene transcription in human endometrial cells with marked aberrancies in endometriosis.
  PLoS genetics 2020 Houshdaran S, Oke AB, Fung JC, Vo KC, Nezhat C, Giudice LC
• Network Rewiring of Homologous Recombination Enzymes during Mitotic Proliferation and Meiosis.
  Molecular cell 2019 Wild P, Susperregui A, Piazza I, Dörig C, Oke A, Arter M, Yamaguchi M, Hilditch AT, Vuina K, Chan KC, Gromova T, Haber JE, Fung JC, Picotti P, Matos J
• Modeling meiotic chromosome pairing: a tug of war between telomere forces and a pairing-based Brownian ratchet leads to increased pairing fidelity.
  Physical biology 2019 Marshall WF, Fung JC
• Regulated Crossing-Over Requires Inactivation of Yen1/GEN1 Resolvase during Meiotic Prophase I.
  Developmental cell 2018 Arter M, Hurtado-Nieves V, Oke A, Zhuge T, Wettstein R, Fung JC, Blanco MG, Matos J
• Kinetochores: Importance of Being Fashionably Late.
  Cell systems 2017 Fung JC
• In Vivo Imaging of Budding Yeast Meiosis.
  Methods in molecular biology (Clifton, N.J.) 2017 Pollard MG, Fung JC
• Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion.
  Physical biology 2016 Marshall WF, Fung JC
• DAZL and CPEB1 regulate mRNA translation synergistically during oocyte maturation.
  Development 2016 Joao P. Sousa Martins, Xueqing Liu, Ashwini Oke, Ripla Arora, Federica Franciosi, Stephan Viville, Diana J. Laird, Jennifer C. Fung, Marco Conti
• DAZL and CPEB1 regulate mRNA translation synergistically during oocyte maturation.
  Journal of cell science 2016 Sousa Martins JP, Liu X, Oke A, Arora R, Franciosi F, Viville S, Laird DJ, Fung JC, Conti M
• Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion
  Journal of Physical Biology 2016 Marshall WM, Fung JC
• The kinetochore prevents centromere-proximal crossover recombination during meiosis.
  eLife 2015 Vincenten N, Kuhl LM, Lam I, Oke A, Kerr AR, Hochwagen A, Fung J, Keeney S, Vader G, Marston AL
• Reduced Crossover Interference and Increased ZMM-Independent Recombination in the Absence of Tel1/ATM.
  PLoS genetics 2015 Anderson CM, Oke A, Yam P, Zhuge T, Fung JC
• Follicle dynamics and global organization in the intact mouse ovary.
  Developmental biology 2015 Faire M, Skillern A, Arora R, Nguyen DH, Wang J, Chamberlain C, German MS, Fung JC, Laird DJ
• Controlling meiotic recombinational repair - specifying the roles of ZMMs, Sgs1 and Mus81/Mms4 in crossover formation.
  PLoS genetics 2014 Oke A, Anderson CM, Yam P, Fung JC
• Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks.
  PLoS genetics 2014 Liu Y, Gaines WA, Callender T, Busygina V, Oke A, Sung P, Fung JC, Hollingsworth NM
• High throughput sequencing reveals alterations in the recombination signatures with diminishing Spo11 activity.
  PLoS genetics 2013 Rockmill B, Lefrançois P, Voelkel-Meiman K, Oke A, Roeder GS, Fung JC
• High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Arigovindan M, Fung JC, Elnatan D, Mennella V, Chan YH, Pollard M, Branlund E, Sedat JW, Agard DA
• Mitochondrial network size scaling in budding yeast.
  Science (New York, N.Y.) 2012 Rafelski SM, Viana MP, Zhang Y, Chan YH, Thorn KS, Yam P, Fung JC, Li H, Costa Lda F, Marshall WF
• ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets.
  PloS one 2011 Anderson CM, Chen SY, Dimon MT, Oke A, DeRisi JL, Fung JC
• Mapping of crossover sites using DNA microarrays.
  Methods in molecular biology (Clifton, N.J.) 2011 Chen SY, Fung JC
• Global analysis of the meiotic crossover landscape.
  Developmental cell 2008 Chen SY, Tsubouchi T, Rockmill B, Sandler JS, Richards DR, Vader G, Hochwagen A, Roeder GS, Fung JC
• Imposition of crossover interference through the nonrandom distribution of synapsis initiation complexes.
  Cell 2004 Fung JC, Rockmill B, Odell M, Roeder GS
• The Sgs1 helicase regulates chromosome synapsis and meiotic crossing over.
  Current biology : CB 2003 Rockmill B, Fung JC, Branda SS, Roeder GS
• Homologous DNA Interactions in Interphase: Spatial Organization of Interphase Nucleus.
  Encyclopedia of Life Sciences 2001 Jennifer C Fung, John W Sedat, Wallace F Marshall
• Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations.
  The Journal of cell biology 1998 Fung JC, Marshall WF, Dernburg A, Agard DA, Sedat JW
• New Insights Into the Three-Dimensional Structure of the Nucleus and Chromosomes.
  Microscopy and Microanalysis 1997 J. Sedat, W. Marshall, A. Dernburg, J. Fung, D. Agard
• Microstructural Analysis of a Cubic Bicontinuous Morphology in a Neat SIS Triblock Copolymer.
  Macromolecules 1997 Jonathan H. Laurer, Damian A. Hajduk, Jennifer C. Fung, John W. Sedat, Steven D. Smith, Sol M. Gruner, David A. Agard, Richard J. Spontak
• Deconstructing the nucleus: global architecture from local interactions.
  Current opinion in genetics & development 1997 Marshall WF, Fung JC, Sedat JW
• From Micelles to Randomly Connected, Bilayered Membranes in Dilute Block Copolymer Blends.
  Langmuir 1997 Jonathan H. Laurer, Jennifer C. Fung, John W. Sedat, Steven D. Smith, Jon Samseth, Kell Mortensen, David A. Agard, Richard J. Spontak
• Phase Behavior of Complex Diblock Copolymer Blends: A Transmission Electron Microscopy Study.
  1997 J.C. Fung, L. Kane, S.D. Smith, J.W. Sedat, D.A. Agard, R.J. Spontak
• Direct measurement of chromatin diffusion and constraint in living cells using a gfp-lac repressor fusion protein.
  Microscopy and Microanalysis 1996 W.F. Marshall, A.F. Straight, A. Murray, J.C. Fung, J. Marko, D.A. Agard, J.W. Sedat
• Perturbation of nuclear architecture by long-distance chromosome interactions.
  Cell 1996 Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J, Agard DA, Sedat JW
• Architecture-Induced Phase Immiscibility in a Diblock/Multiblock Copolymer Blend.
  Macromolecules 1996 Richard J. Spontak, Jennifer C. Fung, Michael B. Braunfeld, John W. Sedat, David A. Agard, Arman Ashraf, Steven D. Smith
• Phase Behavior of Ordered Diblock Copolymer Blends:  Effect of Compositional Heterogeneity.
  Macromolecules 1996 Richard J. Spontak, Jennifer C. Fung, Michael B. Braunfeld, John W. Sedat, David A. Agard, Lisaleigh Kane, Steven D. Smith, Michael M. Satkowski, Arman Ashraf, Damian A. Hajduk, Sol M. Gruner
• Toward fully automated high-resolution electron tomography
  Journal of Structural Biology 1996 Fung JC, Liu W, de Ruijter WJ, Chen H, Abbey CK, Sedat JW, Agard DA
• Three-dimensional structural characterization of centrosomes from early Drosophila embryos.
  The Journal of cell biology 1995 Moritz M, Braunfeld MB, Fung JC, Sedat JW, Alberts BM, Agard DA
• Automated electron tomography: from data collection to image processing.
  Microscopy and Microanalysis 1995 Weiping Liu, Jennifer Fung, W.J. de Ruijter, Hans Chen, John W. Sedat, David A. Agard
• Automatic/interactive bead alignment in electron tomographic image processing.
  Microscopy and Microanalysis 1994 Weiping Liu, Jennifer Fung, Craig Abbey, John W. Sedat, David A. Agard
• Three-Dimensional reconstruction of the synaptonemal complex from high-pressure frozen maize meiocytes using IVEM Tomography.
  Microscopy and Microanalysis 1994 Jennifer C. Fung, David A. Agard, John W. Sedat
• Three-Dimensional reconstruction of the synaptonemal complex from pachytene maize meiocytes using Electron Microscopy tomography.
  Microscopy and Microanalysis 1993 Jennifer C. Fung, Bethe A. Scalettar, David A. Agard, John W. Sedat