Publications

 




  1. Nguyen TM, Pombumpa N, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Harmon-Smithm M, Eloe-Fadrosh EA, Pietrasiak N, Stajich JE, and Hom EFY (2024)

  2. “Whole Community Shotgun Metagenomes of Two Biological Soil Crust Types from the Mojave Desert.”

  3. Microbiology Resource Announcements e00980-23 [DOI: 10.1128/mra.00980-23]



  1. Nguyen TM, Pombumpa N, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Harmon-Smithm M, Eloe-Fadrosh EA, Pietrasiak N, Stajich JE, and Hom EFY (2024)

  2. “Metatranscriptomes of Two Biological Soil Crust Types from Mojave Desert in Response to Wetting.”

  3. Microbiology Resource Announcements e01080-23 [DOI: 10.1128/mra.01080-23]



  1. Calatrava V, Hom EFY, Guan Q, Llamas A, Fernández E, and Galván A (2024)

  2. “Genetic Evidence for Algal Auxin Production in Chlamydomonas and Its Role in an Inter-Kingdom Mutualism with a Plant Growth-Promoting Bacterium.”

  3. iScience 27:108762 [DOI: 10.1016/j.isci.2023.108762]



  1. Jurburg SD, Hom EFY, and Chatzinotas A (2023)

  2. “Beyond Pathogenesis: Detecting the Full Spectrum of Ecological Interactions in the Virosphere.”

  3. PLoS Biology 21:e3002109 [DOI: 10.1371/journal.pbio.3002109]



  1. Venkataram S, Kuo H-Y, Hom EFY, and Kryazhimskiy S (2023)

  2. “Mutualism-enhancing Mutations Dominate Early Adaptation in a Microbial Community.”

  3. Nature Ecology & Evolution 7:143-154 [DOI: 10.1038/s41559-022-01923-8]



  1. Keel LL, Platt B, Gifford J, Muir C, and Hom EFY (2022)

  2. “Living off the Land: Soil Health Maintenance Through Sustainable Farming/'Agro-ecology' Practices at a Tea Farm in Hawaii.”

  3. Geological Society of America Abstracts with Programs, 54 (GSA 2022 Annual Conference) [DOI: 10.1130/abs/2022am-381948]



  1. Jurburg SD, Buscot F, Chatzinotas A, Chaudhari NM, Clark AT, Garbowski M, Grenié M, Hom EFY, Karakoç C, Marr S, Neumann S, Tarkka M, van Dam NM, Weinhold A, and Heintz‑Buschart A (2022)

  2. “The Community Ecology Perspective of Omics Data.”

  3. Microbiome, 10:225 [DOI: 10.1186/s40168-022-01423-8]



  1. Hom EFY and Penn AS (2021)

  2. “Symbiosis and the Anthropocene.”

  3. Symbiosis, 84:239-270 [DOI: 10.1007/s13199-021-00794-0]



  1. Kaup M, Trull S, and Hom EFY (2021)

  2. “Of Sloths and Their Symbionts.”

  3. Biological Reviews, 96:2638-2660 [DOI: 10.1111/brv.12773]



  1. Nazem-Bokaee H, Hom EFY, Warden AC, Mathews S, and Gueidan C (2021)

  2. “Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling.”

  3. Frontiers in Microbiology 12:667864 [DOI: 10.3389/fmicb.2021.667864]



  1. Oita S, Ibáñez A, Lutzoni F, Miadlikowska J, Geml J, Lewis LA, Hom EFY, Carbone I, and Arnold AE (2021)

  2. “Climate and Seasonality Drive the Richness and Composition of Tropical Fungal Endophytes at a Landscape Scale.”

  3. Communication Biology 4:313 [DOI: 10.1038/s42003-021-01826-7]



  1. Oita S, Carey J, Kline I, Ibáñez A, Yang N, Hom EFY, Carbone I, U’Ren JM, and Arnold AE (2021)

  2. “Methodological Approaches Frame Insights into Endophyte Richness and Community Composition.”

  3. Microbial Ecology 82:21-34 [DOI: 10.1007/s00248-020-01654-y]



  1. Clear MR and Hom EFY (2019)

  2. “The Evolution of Symbiotic Plant-Microbe Signaling.”

  3. Annual Plant Reviews 2:1-52 [DOI: 10.1002/9781119312994.apr0684]



  1. Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker A, Yarden O, and Gladfelter AS (2019)

  2. “Fungi in the Marine Environment: Open Questions and Unsolved Problems.”

  3. mBio 10:e01189-18 [DOI: 10.1128/mBio.01189-18]



  1. Calatrava V, Hom EFY, Llamas A, Fernández F, and Galván A (2019)

  2. “Nitrogen Scavenging from Amino Acids and Peptides in the Model Alga, Chlamydomonas reinhardtii and the Role of Extracellular L-Amino Oxidase.”

  3. Algal Research 38:101395 [DOI: 10.1016/j.algal.2018.101395]



  1. Cheng Q, Hill-Cunningham PR, Moore J, Hom EFY (2018)

  2. “STEM in Hawaii: Exploring the Impact of an Innovative Field Trip Experience on Pre-Service Teachers.”

  3. International Journal of Innovative Research and Knowledge 3:238-252. [http://ijirk.com/upload/IJIRK-3.06.18.pdf]



  1. Calatrava V, Hom EFY, Llamas A, Fernández F, and Galván A (2018)

  2. “OK, Thanks! A New Mutualism Between Chlamydomonas and Methylobacteria Facilitates Growth on Amino Acids and Peptides.”

  3. FEMS Microbiology Letters 365:fny021. [DOI: 10.1093/femsle/fny021]



  1. Khona DK, Shirolikar SM, Gawde KK, Hom EFY, Deodhar MA, and D'Souza JS (2016)

  2. “Characterization of salt stress-induced palmelloids in the green alga, Chlamydomonas reinhardtii.”

  3. Algal Research 16:434-448. [DOI: 10.1016/j.algal.2016.03.035]



  1. Hom EFY, Aiyar P, Schaeme D, Mittag M, and Sasso S (2015)

  2. “A Chemical Perspective on Microalgal-Microbial Interactions.”

  3. Trends in Plant Sciences 20:689-693. [DOI: 10.1016/j.tplants.2015.09.004]



  1. Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Harris EH, Lefebvre, Hom EFY, Salehi-Ashtiani K, and Purugganan MD (2015)

  2. “Whole Genome Re-sequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.”

  3. The Plant Cell 27:2353-2369. [PMCID: PMC4815094]



  1. Hom EFY and Murray AW (2014)

  2. “Niche Engineering Demonstrates a Latent Capacity for Fungal-Algal Mutualism.”

  3. Science 345:94-98. [Supplemental] [PMCID: PMC4409001]



  1. Blaby IK, Blaby-Haas C, Tourasse N, Hom EFY, Lopez D, Aksoy M, Grossman A, Umen J, Dutcher J, Porter M, King S, Witman G, Stanke M, Harris EH, Goodstein D, Grimwood J, Schmutz J, Vallon O, Merchant SS, and Prochnik S (2014)

  2. “The Chlamydomonas Genome Project: A Decade On.”

  3. Trends in Plant Sciences 19:672-680. [PMCID: PMC4185214].



  1. Patel-King RS, Gilberti RM, Hom EFY, and King SM (2013)

  2. “WD60/FAP163 is a Dynein Intermediate Chain Required for Retrograde Intraflagellar Transport in Cilia.”

  3. Molecular Biology of the Cell 24:2668-77. [PMCID: PMC3756919]



  1. Hom EFY, Witman GB, Harris EH, Dutcher SK, Kamiya R, Mitchell DR, Pazour GJ, Porter ME, Sale WS, Wirschell M, Yagi T, and King SM (2011)

  2. “A Unified Taxonomy for Ciliary Dyneins.”

  3. Cytoskeleton 68:555-65. [Supplemental]  [PMID: 21953912]



  1. Chang RL, Ghamsari L, Manichaikul A, Hom EFY, Balaji S, Fu W, Shen Y, Palsson BØ, Salehi-Ashtiani K, and Papin JA (2011)

  2. “Metabolic Network Reconstruction of Chlamydomonas Offers Insight Into Light-Driven Algal Metabolism.”

  3. Molecular Systems Biology 7:518. [Supplemental]  [PMID: 21811229]



  1. Specht M, Stanke M, Terashima M, Naumann-Busch B, Janßen I, Höhner R, Hom EFY, Liang C, and Hippler M (2011)

  2. “Concerted Action of the New Genomic Peptide Finder and AUGUSTUS Allows for Automated Proteogenomic Annotation of the Chlamydomonas reinhardtii Genome.”

  3. Proteomics 11:1-10.  [Supplemental]  [PMCID: PMC3145493]



  1. Manichaikul A*, Ghamsari L*, Hom EFY*, Lin C*, Murray RR*, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, and Papin JA (2009)
            (*co-first authorship)

  2. “Metabolic Network Analysis Integrated with Transcript Verification for Sequenced Genomes.”

  3. Nature Methods 185:39-63.  [Supplemental]  [PMCID: PMC3139173]



  1. Hom EFY, Marchis F, Lee TK, Haase S, Agard DA, and Sedat JW (2007)

  2. “An Adaptive Image Deconvolution Algorithm (AIDA) with Application to Multi-Frame and Three-Dimensional Data.”

  3. Journal of the Optical Society of America, A. 24:1580-1600. [PMCID: PMC3166524]



  1. Marchis F, Kaasalainen M, Hom EFY, Berthier J, Enriquez J, Hestroffer D, LeMignant D, and dePater I (2006)

  2. “Shape, Size. And Multiplicity of Main-Belt Asteroids I. Keck Adaptive Optics Survey.”

  3. Icarus (International Journal of Solar System Studies) 185:39-63. [PMCID: PMC2600456]



  1. Dix JA, Hom EFY, and Verkman AS (2006)

  2. “Fluorescence Correlation Spectroscopy Simulations for Analysis of Photophysical Phenomena and Macromolecular Interactions: A Molecular Dynamics/Monte Carlo Approach.”

  3. Journal of Physical Chemistry, B 110:1896-1906.  [PMCID: PMC3129548]



  1. Hom EFY and Verkman AS (2002)

  2. “Analysis of Coupled Bimolecular Reaction Kinetics and Diffusion by Two-Color Fluorescence Correlation Spectroscopy: Enhanced Resolution of Kinetics by Resonance Energy Transfer.”

  3. Biophysical Journal 83:533-546.  [PMCID: PMC1302167]



  1. Dayel MJ, Hom EFY, and Verkman AS (1999)

  2. “Diffusion of Green Fluorescent Protein in the Endoplasmic Reticulum.”

  3. Biophysical Journal 76:2843-2851.  [PMCID: PMC1300255]




  2. Helms V, Hom EFY, Straatsma TP, McCammon JA, and Langhoff P (1998)

  3. “Exciting Green Fluorescent Protein.”

  4. In Amer. Chem. Soc. Symp. Series v. 712: Combined Quantum Mechanical and Molecular Mechanical Methods.  (Eds. Gao J and Thompson MA).  Washington DC: American Chemical Society, pp. 288-295.



❖ ❖ ❖


Theses

  1. Hom EFY (2006), “Distilling Information from Noisy Data: Examples from Microscopy”

  2. Ph.D. Dissertation, University of California-San Francisco.




  1. Hom EFY (1995), “Cellular Rhythms of a Drosophila Clock Protein.”

  2. B.A. Honors Thesis, External Examination Program, Swarthmore College.

  3. [a blast from the past, here for archival purposes!]