diff --git a/Gemfile b/Gemfile index 348718f..76c5219 100644 --- a/Gemfile +++ b/Gemfile @@ -1,3 +1,5 @@ source 'https://rubygems.org' gem 'github-pages' gem 'jekyll-paginate' + +gem "webrick", "~> 1.8" diff --git a/_data/publications.yml b/_data/publications.yml index 339692c..3a4dcc8 100644 --- a/_data/publications.yml +++ b/_data/publications.yml @@ -1,3 +1,97 @@ +- title: "Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline." + citation: '**Barad BA†**, Medina M†, Fuentes D, Wiseman, RL, Grotjahn DA. *Journal of Cell Biology* 2023 †Equal contribution' + date: "2023-02-14" + image: '/static/img/pub/surfacemorphometrics-01.png' + biorxiv: 2022.01.23.477440 + pmid: 36786771 + pdf: '/static/pdf/Barad_Medina_Membrane_Morphometrics_Final.pdf' + links: + - name: "Surface Morphometrics on Github" + url: 'https://github.com/GrotjahnLab/surface_morphometrics/' + - name: "EMPIAR Deposition (Tilt Series, Tomograms, Segmentations, and Surfaces)" + url: 'https://www.ebi.ac.uk/empiar/EMPIAR-11370/' + - name: "Zenodo Deposition (Quantifications and Statistics)" + url: 'https://zenodo.org/record/7510830' + - name: "Review Commons Reviews" + url: "https://www.biorxiv.org/content/10.1101/2022.01.23.477440v3#review" + - name: "Wiseman Lab @ Scripps Research" + url: 'http://www.wiseman.scripps.edu/' + - name: "Preprint Tweetorial" + url: 'https://twitter.com/benjaminbarad/status/1485829710533693443' + - name: "Journal Tweetorial" + url: 'https://twitter.com/benjaminbarad/status/1625573810249555968' + +- title: "Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography" + citation: "Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, **Barad BA**, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O'Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC. (2022) *bioRxiv*." + date: 202206 + image: '/static/img/pub/wolff_2022.jpeg' + pmid: + pmcid: + biorxiv: '2022.06.10.495662' + pdf: '/static/pdf/wolff_2022_biorxiv.pdf' + pdbs: + - 8CVU + - 8CVV + - 8CVW + - 8CW0 + - 8CW1 + - 8CW3 + - 8CW5 + - 8CW6 + - 8CW7 + - 8CW8 + - 8CWB + - 8CWC + - 8CWD + - 8CWE + - 8CWF + - 8CWG + - 8CWH + data: + - '10.11577/1873469' + links: + - name: Temperature Analysis on Github + url: https://github.com/mthompson-lab/Temperature-Jump-Crystallography_Analysis-for-Paper/ + - name: Nango lab @ Tohoku University + url: http://www2.tagen.tohoku.ac.jp/lab/nango/html/ + - name: Fraser lab @ UC San Francisco + url: http://www.fraserlab.com/ + - name: Thompson Lab @ UC Merced + url: https://thompsonlab.science + - name: SACLA XFEL + url: http://xfel.riken.jp/eng/ + - name: BioSciences @ LBNL + url: https://biosciences.lbl.gov/ + - name: Preprint Tweetstorm + url: https://twitter.com/MThompsonLab/status/1536365959174234112 + + +- title: "Nanoscale details of mitochondrial fission revealed by cryo-electron tomography." + citation: 'Mageswaran, SK†, Grotjahn DA†§, Zeng X, **Barad BA**, Medina M, Hoang MH, Dobro MJ, Chang YW, Xu M, Yang WY, Jensen, GJ§. *bioRxiv* 2021 †Equal contribution §Corresponding authors' + image: '/static/img/pub/Apr20_TS02_ModelMT.png' + biorxiv: 2021.12.13.472487 + pdf: '/static/pdf/Mageswaran_Grotjahn_MitochondrialFission-CryoET_biorxiv.pdf' + links: + - name: "Filament Architecture on Github" + url: 'https://github.com/GrotjahnLab/measure_models/' + - name: "Jensen Lab" + url: 'http://www.jensenlab.caltech.edu/' + +- title: "CellPAINT: Turnkey illustration of molecular cell biology" + citation: "Gardner A, Ludovic A, Fuentes D, Maritan M, **Barad BA**, Medina, M, Olson AJ, Grotjahn DA, Goodsell DS. *Front. Bioinform.* 2021." + image: "/static/img/pub/gardner_2021.jpg" + date: "2020-03-29" + pmid: "34790910" + pmcid: "PMC8594902" + pdf: "https://www.frontiersin.org/articles/10.3389/fbinf.2021.660936/pdf" + zenodo: + - code: "4606923" + description: "Tomogram used for CellPAINT hypothesis generation" + links: + - name: "Molecular Graphics Laboratory" + url: "https://ccsb.scripps.edu/goodsell/" + + - title: "Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge." citation: "Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, **Barad BA**, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Jr. MAH, Hoh SW, Hou J, Hung L, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. *Nature Methods*. 2021." date: '2020-06-19' @@ -11,7 +105,7 @@ url: https://challenges.emdataresource.org/?q=model-metrics-challenge-2019 - title: "Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates" - citation: "**Barad BA, Liu L, Diaz RE, Basillo R**, Van Dyken SJ, Locksley RM, **Fraser JS**. *Protein Science*. 2020." + citation: "**Barad BA**, Liu L, Diaz RE, Basillo R, Van Dyken SJ, Locksley RM, Fraser JS. *Protein Science*. 2020." date: '2020-01-12' image: '/static/img/pub/chitin_2019.jpg' pmid: '31930591' @@ -50,9 +144,6 @@ - name: 'Paper Submission Celebration Tweetstorm' url: 'https://twitter.com/fraser_lab/status/1067213167367905280' - - url: https://twitter.com/benjaminbarad/status/1171091343789056000 - - title: "Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers" citation: 'Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, **Barad BA**, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG. *Cell Reports.* 2019.' date: 201810 diff --git a/_includes/footer.html b/_includes/footer.html index 9ae879d..a3f94c4 100644 --- a/_includes/footer.html +++ b/_includes/footer.html @@ -2,12 +2,13 @@
diff --git a/_includes/header.html b/_includes/header.html index 32bcfd8..72797b4 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -9,7 +9,8 @@ - + + diff --git a/index.md b/index.md index 181b034..651a8ed 100644 --- a/index.md +++ b/index.md @@ -7,9 +7,21 @@ group: home Giving a talk about recent developments in electron crystallography, February 2014

Benjamin Barad, Ph.D.

+

New Faculty at OHSU

-I am a structural biologist with a special interest in emerging computational and experimental methods in electron microscopy. I am working as a postdoc with [Danielle Grotjahn](https://www.scripps.edu/faculty/grotjahn/), using cryo-electron tomography of focused ion beam-thinned cells to quantify mitochondrial morphology and solve _in situ_ protein structures. In particular, I am excited about the power of electron tomography to contextualize the structure, dynamics, and interactions of proteins as they perform their physiolocal function in the cell. -I received my PhD in biophysics from UCSF in the lab of [James Fraser](http://fraserlab.com), where I developed methods for the building and validating atomic models generated from single particle electron microscopy, as well as investigating the mechanisms of activity of mammalian chitinases. Before that, I was an undergraduate at Stanford University studying Biological Chemistry, where I worked with [Elizabeth Sattely](http://www.stanford.edu/group/sattelygroup/cgi-bin/wordpress/) investigating bacterial degradation of the plant polymer lignin. + +I am a structural biologist with a special interest in emerging computational and experimental methods in electron microscopy. In January 2024, I will be starting my lab at [Oregon Health & Science University](https://www.ohsu.edu/school-of-medicine/chemical-physiology-and-biochemistry) in Portland, OR. The focus of my lab will be leveraging cryo-electron tomography as well as novel computational analyses developed in the lab to study the remodeling of mammalian organelles by intracellular bacteria and their effector proteins. Cryo-electron tomography has the capacity to reveal both protein localization and structure at the same time as cytoskeletal and membrane ultrastructure within cells within a single dataset, and the long term goal of my lab is to build workflows that unify and contextualize protein structure and cellular ultrastructure into a multi-scale understanding of cellular function and regulation.

+ + +I completed my undergraduate degree in Biological Chemistry at Stanford University, where I worked with [Elizabeth Sattely](http://www.stanford.edu/group/sattelygroup/cgi-bin/wordpress/) investigating bacterial degradation of the plant polymer lignin. While there, I grew to love the collective regulation of large-scale ultrastructural features of organisms (such as the plant cell wall) by individual enzymes. This is a passion that has continue to fuel my scientific path to this day.
+ + +I received my PhD in biophysics from UCSF in the lab of [James Fraser](http://fraserlab.com), where I developed methods for the [building](https://elifesciences.org/articles/17219) and [validating atomic models](https://www.nature.com/articles/nmeth.3541) generated from single particle electron microscopy. I also developed [novel computational analysis tools for time-resolved x-ray scattering experiments](https://www.nature.com/articles/s41557-019-0329-3) as well as investigating the [mechanisms of activity of mammalian chitinases](https://onlinelibrary.wiley.com/doi/10.1002/pro.3822).

+ + +Previous to starting my lab, I worked as a postdoc with [Danielle Grotjahn](https://www.scripps.edu/faculty/grotjahn/), using cryo-electron tomography of focused ion beam-thinned cells to quantify mitochondrial morphology and solve _in situ_ protein structures. While there, I developed the [Surface Morphometrics Pipeline](https://github.com/GrotjahnLab/surface_morphometrics), the ongoing development of which will continue in the Barad lab. I also developed automation advances that allowed the collection and processing of hundreds of tilt series, and used these advances to study changes to the architecture and regulation of mitochondrial fission in response to varied chemical and genetic perturbations. Some of that work is ongoing!

+ + Beyond my scientific interests, I am excited about food and cooking, coffee, 3D printing, and games.

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