Commit 0ddcab7e authored by Carlos GO's avatar Carlos GO
Browse files

vernal done

parent 82302472
Figs/3d.png

90.4 KB

File added
File added
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -1542,9 +1542,9 @@
inkscape:window-height="780"
id="namedview836"
showgrid="false"
inkscape:zoom="0.5"
inkscape:cx="736.25099"
inkscape:cy="443.35693"
inkscape:zoom="2"
inkscape:cx="-133.83424"
inkscape:cy="436.19371"
inkscape:window-x="62"
inkscape:window-y="33"
inkscape:window-maximized="0"
......@@ -2011,7 +2011,15 @@
inkscape:connector-curvature="0"
id="path938"
style="fill:#dff3d1;fill-opacity:1;fill-rule:nonzero;stroke:none"
d="m 0,0 c 0,-45.938 -157.779,-83.175 -352.409,-83.175 -194.63,0 -352.408,37.237 -352.408,83.175 0,45.936 157.778,83.174 352.408,83.174 C -157.779,83.174 0,45.936 0,0" /></g></g></g></g><g
d="m 0,0 c 0,-45.938 -157.779,-83.175 -352.409,-83.175 -194.63,0 -352.408,37.237 -352.408,83.175 0,45.936 157.778,83.174 352.408,83.174 C -157.779,83.174 0,45.936 0,0" /></g></g></g><path
style="fill:none;stroke:#000000;stroke-width:3.77952756;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none"
d="m -343,787.94531 310.5,-0.5"
id="path4046"
inkscape:connector-curvature="0" /><path
style="fill:none;stroke:#1312f0;stroke-width:3.77952756;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none"
d="m -201,520.94531 h 46"
id="path4055"
inkscape:connector-curvature="0" /></g><g
id="g842"
inkscape:groupmode="layer"
inkscape:label="maternal"
......@@ -4417,6 +4425,7 @@
<text
y="-639.5882"
x="1225.7279"
......@@ -4436,6 +4445,7 @@
<text
y="-631.09167"
x="1259.4304"
......@@ -4460,6 +4470,7 @@
<text
y="-630.79077"
x="1282.3422"
......@@ -4482,6 +4493,7 @@
<text
y="-614.90045"
x="1268.9631"
......@@ -4502,6 +4514,7 @@
<text
y="-614.2041"
x="1274.188"
......@@ -4521,6 +4534,7 @@
</g><path
style="fill:none;stroke:#000000;stroke-width:3.16443801;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:3.16443807, 3.16443807;stroke-dashoffset:0;stroke-opacity:1"
d="m 285.29004,292.34058 c -68.81022,109.29181 -71.94978,115.38457 -71.94978,115.38457 v 0"
......@@ -4815,4 +4829,64 @@
id="path22978"
d="m 482.23,440.23 v -1.55 h 1.18 c 3.85,0 3.94,-0.54 3.94,-2.34 v -26.25 c 0,-1.8 -0.09,-2.34 -3.94,-2.34 h -1.18 v -1.55 h 18.23 l -1.34,1.55 h -5.05 c -2.33,0 -2.44,0.34 -2.44,1.98 v 26.95 c 0,1.66 0.11,2 2.44,2 h 4.98 c 3.1,0 6.54,-1.09 9.08,-4.64 2.14,-2.93 2.58,-7.22 2.58,-11.11 0,-5.53 -0.94,-8.51 -2.73,-10.95 -1,-1.34 -3.83,-4.23 -8.86,-4.23 l 1.34,-1.55 c 8.36,0 15.24,7.37 15.24,16.73 0,9.47 -6.72,17.3 -15.24,17.3 z"
inkscape:connector-curvature="0"
style="fill:#000000;stroke-width:0" /></g></g></g></svg>
\ No newline at end of file
style="fill:#000000;stroke-width:0" /></g></g><path
inkscape:connector-curvature="0"
id="path14436-8-8-7"
style="fill:#a2eeae;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -343.99747,801.22739 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70598,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17484,3.89472 -2.70596,2.46139 -4.2149,5.86531 -4.2149,9.37054 0,3.52856 1.50894,6.90132 4.2149,9.40172 2.69755,2.49258 6.35614,3.89466 10.17484,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-9"
style="fill:#a2eeae;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -284.59748,801.22739 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70598,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17484,3.89472 -2.70596,2.46139 -4.2149,5.86531 -4.2149,9.37054 0,3.52856 1.50894,6.90132 4.2149,9.40172 2.69755,2.49258 6.35614,3.89466 10.17484,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-3"
style="fill:#6baff7;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -225.19747,801.22739 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70598,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17485,3.89472 -2.70595,2.46139 -4.21489,5.86531 -4.21489,9.37054 0,3.52856 1.50894,6.90132 4.21489,9.40172 2.69756,2.49258 6.35615,3.89466 10.17485,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-8"
style="fill:#6baff7;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -165.79746,801.22739 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70599,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17485,3.89472 -2.70595,2.46139 -4.21489,5.86531 -4.21489,9.37054 0,3.52856 1.50894,6.90132 4.21489,9.40172 2.69756,2.49258 6.35615,3.89466 10.17485,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-0"
style="fill:#6baff7;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -106.39746,801.22739 c 3.8187,0 7.468829,-1.40208 10.174799,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.705985,-2.50038 -6.356099,-3.89472 -10.174799,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17484,3.89472 -2.70596,2.46139 -4.2149,5.86531 -4.2149,9.37054 0,3.52856 1.50894,6.90132 4.2149,9.40172 2.69755,2.49258 6.35614,3.89466 10.17484,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-2"
style="fill:#ee6669;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -46.997467,801.22739 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.705985,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.174845,3.89472 -2.705955,2.46139 -4.214895,5.86531 -4.214895,9.37054 0,3.52856 1.50894,6.90132 4.214895,9.40172 2.697555,2.49258 6.356145,3.89466 10.174845,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-7-4"
style="fill:#a2eeae;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -214.80383,533.98898 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70598,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17484,3.89472 -2.70596,2.46139 -4.2149,5.86531 -4.2149,9.37054 0,3.52856 1.50894,6.90132 4.2149,9.40172 2.69755,2.49258 6.35614,3.89466 10.17484,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-9-8"
style="fill:#a2eeae;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -259.70512,475.65267 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87315 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70598,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17484,3.89472 -2.70596,2.46139 -4.2149,5.86531 -4.2149,9.37054 0,3.52857 1.50894,6.90132 4.2149,9.40172 2.69755,2.49258 6.35614,3.89466 10.17484,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-3-3"
style="fill:#6baff7;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -214.80383,416.96281 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70598,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17485,3.89472 -2.70595,2.46139 -4.21489,5.86531 -4.21489,9.37054 0,3.52856 1.50894,6.90132 4.21489,9.40172 2.69756,2.49258 6.35615,3.89466 10.17485,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-8-9"
style="fill:#6baff7;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -139.45665,416.96281 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70599,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17485,3.89472 -2.70595,2.46139 -4.21489,5.86531 -4.21489,9.37054 0,3.52856 1.50894,6.90132 4.21489,9.40172 2.69756,2.49258 6.35615,3.89466 10.17485,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-0-0"
style="fill:#6baff7;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -96.676691,475.65267 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87315 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70599,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.818699,0 -7.477289,1.39434 -10.174839,3.89472 -2.70596,2.46139 -4.2149,5.86531 -4.2149,9.37054 0,3.52857 1.50894,6.90132 4.2149,9.40172 2.69755,2.49258 6.35614,3.89466 10.174839,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /><path
inkscape:connector-curvature="0"
id="path14436-8-8-2-5"
style="fill:#ee6669;fill-opacity:1;fill-rule:nonzero;stroke:#06060b;stroke-width:5.6692915;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:6.94000006;stroke-dasharray:none;stroke-opacity:1"
d="m -139.45665,533.98898 c 3.8187,0 7.46883,-1.40208 10.1748,-3.89466 2.6976,-2.50038 4.21494,-5.87316 4.21494,-9.40172 0,-3.5052 -1.51737,-6.90915 -4.21494,-9.37054 -2.70598,-2.50038 -6.3561,-3.89472 -10.1748,-3.89472 -3.8187,0 -7.47729,1.39434 -10.17484,3.89472 -2.70596,2.46139 -4.2149,5.86531 -4.2149,9.37054 0,3.52856 1.50894,6.90132 4.2149,9.40172 2.69755,2.49258 6.35614,3.89466 10.17484,3.89466 z"
transform="matrix(0.75000002,0,0,-0.75000002,0,684.33401)" /></g></svg>
\ No newline at end of file
File added
No preview for this file type
This diff is collapsed.
No preview for this file type
......@@ -6,6 +6,34 @@
\usepackage{xspace}
\usepackage{subcaption}
\usepackage{tikz}
\usetikzlibrary{shadows}
\usepackage{etoolbox}
\usepackage{pifont}% http://ctan.org/pkg/pifont
\newcommand{\cmark}{\ding{51}}%
\newcommand{\xmark}{\ding{55}}%
%% tags
\AtBeginEnvironment{quote}{\small}
\tikzstyle{greentagstyle} = [rectangle, fill = green!30, draw = black, drop shadow, font={\sffamily\bfseries}, text=black]
\tikzstyle{redtagstyle} = [rectangle, fill = red!30, draw = black, drop shadow, font={\sffamily\bfseries}, text=black]
\newcommand{\ideatag}{\tikz{\node[greentagstyle] {Idea};}\xspace}
\newcommand{\problemtag}{\tikz{\node[redtagstyle] {Problem};}\xspace}
\newcommand{\maternal}{\texttt{mateRNAl}\xspace}
\newcommand{\rnamigos}{\texttt{RNAmigos}\xspace}
......@@ -17,6 +45,8 @@
\setbeamerfont{footnote}{size=\tiny}
\footnotesize \let\tiny\footnotesize
\graphicspath{{Figs/}}
\title{Computational Tools for Studying Complex RNA Structures}
......@@ -33,49 +63,30 @@
\begin{frame}
\frametitle{Timeline}
\begin{figure}[h]
\setupchronology{startyear=2016,color=blue,stopyear=2021,dates=false,arrow=false}
\setupchronoevent{textstyle=\it,date=false}
\setupchronoperiode{dates=false,textdepth=-15pt}
\startchronology
\chronograduation{1}
\chronoevent[markdepth=70pt]{8/2019}{Proposal}
\chronoevent[markdepth=30pt]{6/8/2019}{\maternal Accepted}
\chronoevent[markdepth=30pt]{1/1/2017}{\maternal Submitted}
\chronoevent[markdepth=45pt]{1/2019}{\rnamigos Submitted}
\chronoevent[markdepth=70pt]{9/2017}{Comprehensive}
\chronoevent[markdepth=70pt]{9/2020}{Defense}
\chronoperiode[dates=false]{2016}{2017}{\maternal}
\chronoperiode{2017}{2019}{\rnamigos}
\chronoperiode{2019}{2020}{\vernal}
\chronoperiode{2020}{2021}{\garl}
\stopchronology
\caption{Timeline for my PhD.}
\label{fig:timeline}
\end{figure}
%\begin{itemize}
% \item {\bf Oliver, C. G.,} Reinharz, V., \& Waldisphl, J. (2019). {\it The necessary emergence of structural complexity in self-replicating RNA populations.} bioRxiv, 218990. (Accepted for publication at the RNA Journal) ~\cite{oliver2017necessary}
% \item {\bf Oliver, C. G.,} Gendron, R. S., Moitessier, N., Mallet, V., Reinharz, V., \& Waldisphl, J. (2019). {\it Extended RNA base pairing networks imprint small molecule binding preferences.} bioRxiv, 701326. (Submitted for publication at PNAS) ~\cite{oliver2019extended}
% \item Sarrazin-Gendron, R., Reinharz, V., {\bf Oliver, C. G.,} Moitessier, N., \& Waldisphl, J. (2019). {\it Automated, customizable and efficient identification of 3D base pair modules with BayesPairing.} Nucleic acids research, 47(7), 3321-3332. ~\cite{sarrazin2019automated}
% \item Mallet, V., {\bf Oliver, C. G.,} Moitessier, N., \& Waldispuhl, J. (2019). {\it Leveraging binding-site structure for drug discovery with point-cloud methods.} arXiv preprint arXiv:1905.12033. (In preparation for resubmission) ~\cite{mallet2019leveraging}
%\end{itemize}
%\begin{frame}
% \frametitle{Courses Taken \& Contributions}
%
% Courses
%
% \begin{itemize}
% \item Courses: COMP 551, 561, 598, 652, 680, 762, 767
% \end{itemize}
%
% Contributions
%
% {\fontsize{9}{5}
% \begin{itemize}
% \item {\bf Oliver, C. G.,} Reinharz, V., \& Waldisphl, J. (2019). {\it The necessary emergence of structural complexity in self-replicating RNA populations.} bioRxiv, 218990. (Accepted for publication at the RNA Journal)
% \item {\bf Oliver, C. G.,} Gendron, R. S., Moitessier, N., Mallet, V., Reinharz, V., \& Waldisphl, J. (2019). {\it Extended RNA base pairing networks imprint small molecule binding preferences.} bioRxiv, 701326. (Submitted for publication at PNAS)
% \item {\bf Oliver, C. G}., Ricottone, A., \& Philippopoulos, P. (2017). {\it Proposal for a fully decentralized blockchain and proof-of-work algorithm for solving NP-complete problems.} arXiv preprint arXiv:1708.09419.
% \item Sarrazin-Gendron, R., Reinharz, V., {\bf Oliver, C. G.,} Moitessier, N., \& Waldisphl, J. (2019). {\it Automated, customizable and efficient identification of 3D base pair modules with BayesPairing.} Nucleic acids research, 47(7), 3321-3332.
% \item Mallet, V., {\bf Oliver, C. G.,} Moitessier, N., \& Waldispuhl, J. (2019). {\it Leveraging binding-site structure for drug discovery with point-cloud methods.} arXiv preprint arXiv:1905.12033. (In preparation for resubmission)
%\end{itemize}}
\end{frame}
%\end{frame}
\section{Backgound}
......@@ -95,18 +106,29 @@
\frametitle{3D interactions}
\begin{figure}
\centering
\includegraphics[width=0.8\textwidth]{lws.png}
\footnote{Leontis et.al, 2010}
\end{figure}
\begin{itemize}
\item Looking closer at looping regions we see more pairwise interactions.
\end{itemize}
\begin{columns}
\begin{column}{0.2\textwidth}
\begin{centering}
\includegraphics[width=\textwidth]{3d}
\end{centering}
\end{column}
\begin{column}{0.7\textwidth}
\includegraphics[width=\textwidth]{lws.png}
\end{column}
\end{columns}
\end{frame}
\begin{frame}
\frametitle{Overview of Projects}
\begin{figure}
\includegraphics[width=\textwidth]{phd.pdf}
\includegraphics[width=\textwidth]{phd_s.pdf}
\end{figure}
\end{frame}
......@@ -115,20 +137,25 @@
\begin{frame}
\frametitle{{\bf Project I:} \maternal, How do complex structures evolve?}
\begin{itemize}
\item \problemtag How can energetically unfavorable structures appear?
\item \ideatag Model the distribution of mutants.
\end{itemize}
\begin{figure}
\includegraphics[width=\textwidth]{ml.pdf}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Related Work}
\begin{itemize}
\item Presence of polymerases, cellular barriers
\item Adaptation to target
\item Very short sequences (20 nt)
\item No GC content
\end{itemize}
\end{frame}
%\begin{frame}
% \frametitle{Related Work}
% \begin{itemize}
% \item Presence of polymerases, cellular barriers
% \item Adaptation to target
% \item Very short sequences (20 nt)
% \item No GC content
% \end{itemize}
%\end{frame}
\begin{frame}
\frametitle{Sampling methods.}
......@@ -180,12 +207,19 @@
\begin{frame}
\frametitle{{\bf Project II:} \rnamigos functional roles for complex structures}
\begin{itemize}
\item RNA function can be modulated through binding with small organic compounds (ligands).
\end{itemize}
\begin{columns}
\begin{column}{\textwidth}
\begin{centering}
\begin{figure}
\includegraphics[height=0.35\textheight]{rna1.png}
\includegraphics[height=0.35\textheight]{rna2.png}
\includegraphics[height=0.3\textheight]{rna10.png}
\caption{3D crystal structure}
\end{figure}
\end{centering}
\end{column}
\end{columns}
......@@ -219,8 +253,13 @@
\begin{frame}
\frametitle{Pipeline}
\frametitle{RNAMIGOS}
\begin{itemize}
\item \problemtag given a new RNA, what drugs would likely bind to it?
\item \problemtag we don't have an energy model for non-canonical interactions.
\item \ideatag treat RNA and ligand as input-output pair for ML.
\end{itemize}
\begin{figure}
\includegraphics[width=\textwidth]{rnamigos.pdf}
\end{figure}
......@@ -241,7 +280,7 @@
\caption{Per-ligand score}
\label{fig:violin-lig}
\end{subfigure}
\caption{Performance over each binding site during cross-validation {\bf Fig. ~\ref{fig:violin}}. Each point represents an input pocket and its corresponding enrichment score for the observed ligand. Shuffled control is denoted as `shuffle' and a single-feature encoding of just the size of the pocket is denoted by `size'. In {\bf Fig. ~\ref{fig:violin-lig}} we show performance averaged by ligand class.}
\label{fig:worms}
\end{figure}
......@@ -253,7 +292,7 @@
\begin{figure}
\centering
\includegraphics[width=\textwidth]{tree_ligs.pdf}
\caption{Performance of \rnamigos on different ligand classes. The tree represents a hierarchical clustering over the ligands in the dataset to visualize similarity relationships. Performance on each class is shown with a colored tiled at the leaves of the tree.}
\caption{Performance of \rnamigos on different ligand classes. The tree represents a hierarchical clustering over the ligands in the dataset to visualize similarity relationships. Performance on each class is shown with a colored tile at the leaves of the tree.}
\label{fig:tree}
\end{figure}
......@@ -269,7 +308,7 @@
\end{itemize}
\item Next Steps
\begin{itemize}
\item ... holds promise, and the method introduced did seem innovative. Without more detailed retrospective studies for ligand enrichment,..., and without prospective prediction and testing for new, non-trivial ligands, the manuscript will not command the attention of the broad audience that PNAS attracts. In its current form, the manuscript may be better suited to a more specialized journal, such as JCIM.
\item \begin{quote} ... holds promise, and the method introduced did seem innovative. Without more detailed retrospective studies for ligand enrichment,..., and without prospective prediction and testing for new, non-trivial ligands, the manuscript will not command the attention of the broad audience that PNAS attracts. In its current form, the manuscript may be better suited to a more specialized journal, such as JCIM. \end{quote}
\item Validate signal with {\bf computational docking}.
\end{itemize}
\end{itemize}
......@@ -290,8 +329,8 @@
\frametitle{{\bf Project III:} \vernal, discovering new functional structures}
\begin{itemize}
\item Novel functional RNA sites can be found in crystal structures
\item Idea: represent crystal structures as graphs and identify recurrent subgraphs.
\item \problemtag Novel functional RNA sites can be found in crystal structures
\item \ideatag: represent crystal structures as graphs and identify recurrent subgraphs.
\end{itemize}
......@@ -304,60 +343,99 @@
\frametitle{Related work}
\begin{itemize}
\item rna3dmotif -- exact matching, only local interactions
\item carnaval -- exact matching, long range interactions
\item nar thing -- not graph-based, only local interactions
\item We want a motif finding tool that works on graphs and is inductive.
\end{itemize}
\begin{table}[]
\resizebox{\textwidth}{!}{%
\begin{tabular}{lllll}
\hline
& flexible motifs & all ss & graph-based & inductive \\ \hline
rna3dmotif & \xmark & \xmark & \cmark & \xmark \\ \hline
3d motif atlas & \xmark\cmark & \xmark & \xmark\cmark & \xmark \\ \hline
carnaval & \xmark & \xmark & \cmark & \xmark \\ \hline
RNAMSC & \cmark & \xmark & \xmark & \xmark \\ \hline
{\bf VERNAL} & \cmark & \cmark & \cmark & \cmark
\end{tabular}%
}
\end{table}
\end{frame}
\begin{frame}
\frametitle{VERNAL}
\begin{itemize}
\item Idea: encode graph structure in vector space
\item Perform clustering over all nodes to retrieve motifs.
\item \problemtag Quickly identify similar subgraphs from a large set of large graphs.
\item \ideatag Encode each node's structure in vector space and cluster.
\item $Z \in \mathbb{R}^{n \times d}$ embedding matrix.
\item $K \in \mathbb{R}^{n \times n}$ similarity matrix.
\end{itemize}
\begin{figure}
\includegraphics[width=\textwidth]{vernal_0.pdf}
\end{figure}
\end{frame}
\begin{frame}
\begin{figure}
\centering
\includegraphics[width=\textwidth]{motif_1.pdf}
\begin{frame}{Picking $d$: Edge histogram distance}
Idea: similar rings will have similar distributions of edge types.
\begin{equation}
k_L(u,v) := \sum_{l=0}^{L-1} \lambda^{l} d(R_u^l, R_v^l)
\end{equation}
\begin{equation}
d(R, R') := \frac{f_R \cap f_R'}{f_R \cup f_R'}
\end{equation}
Where $R$ and $R'$ are node rings and $f_R$ is a histogram of counts for each edge type.
\begin{figure}
\centering
\includegraphics[width=0.4\textwidth]{k.pdf}
\end{figure}
\end{frame}
\begin{frame}
\begin{figure}
\centering
\includegraphics[width=\textwidth]{motif_6.pdf}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Preliminary Results on Chemical Compounds}
\begin{itemize}
\item \problemtag Finds similar nodes, but not always similar subgraphs
\end{itemize}
\begin{figure}
\centering
\includegraphics[width=\textwidth]{motif_3.pdf}
\includegraphics[height=0.8\textheight]{motifs_nice.pdf}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Motif learning}
\begin{itemize}
\item Idea: assign each node to $m << n$ `motif' centers.
\end{itemize}
\begin{itemize}
\item \ideatag assign each node to $m << n$ `motif' centers.
\item $\Sigma \in [0,1]^{n \times m}$ soft assignment of each node ($n$) to a motif ($m$)
\item $E \in [0,1]^{m \times d}$ dictionary matrix.
\item $\Sigma^T Z \in \mathbb{R}^{m \times d}$ at cluster $i$ and dimension $d$ is an average embedding weighted by motif attribution.
\begin{equation}
(\Sigma^T Z)_{ij} = \frac{\sum_{k=1}^{n} \sigma_{ik} z_{jk}}{\norm{\sigma_i}}
\end{equation}
\end{itemize}
\begin{figure}
\includegraphics[width=\textwidth]{vernal_1.pdf}
\includegraphics[width=0.65\textwidth]{motif_illustration.pdf}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Full}
......@@ -373,21 +451,32 @@
\begin{itemize}
\item Nodes belonging to motif $\mathcal{\mu} \in \mathcal{M}$ should get the same `label' across all graphs
\item i.e. distribution over labels inside motif instances should have zero entropy
\item Let $P = \mathbb{P}[\Phi(v) \vert \Phi, v \in \mu]$
\item Let $\bar{P} = \mathbb{P}[\Phi(v) \vert \Phi, v \notin \mu]$
\item Let $P = \mathbb{P}[\Phi(v) \vert \Phi, v \in \mu]$, $\bar{P} = \mathbb{P}[\Phi(v) \vert \Phi, v \notin \mu]$
\begin{equation}
\frac{1}{\vert \mathcal{M} \vert \log m} \sum_{\mu \in \mathcal{M}} [H(P) + JSD(P, \bar{P})]
\end{equation}
\item $m$ is the number of `clusters' in model
\item $\Phi(v)$ is the motif assignment given by model $\Phi$ on node $v$
\item $H =1$ means motif assignment uniform (\textcolor{red}{bad})
\item $H = 0$ means motif assignment consistent (\textcolor{green}{good})
\item $\Phi(v)$ is the motif assignment given by model $\Phi$ on node $v$
\end{itemize}
\begin{figure}
\centering
\includegraphics[width=0.5\textwidth]{carnvalidate.pdf}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{First Look At Motif Learning}
\begin{itemize}
\item \problemtag Always assigning the same motif
\end{itemize}
\begin{figure}
\includegraphics[width=0.8\textwidth]{attr.pdf}
\end{figure}
\end{frame}
\section{{\bf Project IV:} \garl}
......@@ -404,8 +493,11 @@
\begin{itemize}
\item Once we've identified related structures we need to align them to build:
\item Statistical models from consensus graphs (\texttt{BayesPairing})
\item Predictive models from distances (\rnamigos)
\begin{itemize}
\item Analysis of conserved (functional) interactions.
\item Statistical models from consensus (\texttt{BayesPairing})
\item Predictive models from distances (\rnamigos)
\end{itemize}
\item Graph alignment $\sim$ sequential graph editing or node matching.
\end{itemize}
......@@ -416,7 +508,7 @@
\begin{frame}
\frametitle{RNA-specific considerations}
\frametitle{Some RNA-specific considerations}
\begin{figure}
\includegraphics[width=\textwidth]{align.pdf}
......@@ -451,8 +543,61 @@
\begin{frame}
\frametitle{Conclusion}
Structural complexity in RNA poses many computational challenges which we addressed with the following:
\begin{enumerate}
\item \maternal lets us explore evolutionary scenarios that can permit the formation of complex structures
\item \rnamigos shows that graphical representations of RNA structure holds important functional signals
\item \vernal helps us identify potentially novel related or functional RNAs
\item \garl can highlight key interactions in groups of related RNA.
\end{enumerate}
\end{frame}
\begin{frame}
\frametitle{Timeline}
\begin{figure}[h]
\setupchronology{startyear=2016,color=blue,stopyear=2021,dates=false,arrow=false}
\setupchronoevent{textstyle=\it,date=false}
\setupchronoperiode{dates=false,textdepth=-15pt}
\startchronology
\chronograduation{1}
\chronoevent[markdepth=70pt]{8/2019}{Proposal}
\chronoevent[markdepth=30pt]{6/8/2019}{\maternal Accepted}
\chronoevent[markdepth=30pt]{1/1/2017}{\maternal Submitted}
\chronoevent[markdepth=45pt]{1/2019}{\rnamigos Submitted}
\chronoevent[markdepth=70pt]{9/2017}{Comprehensive}
\chronoevent[markdepth=70pt]{9/2020}{Defense}
\chronoperiode[dates=false]{2016}{2017}{\maternal}
\chronoperiode{2017}{2019}{\rnamigos}
\chronoperiode{2019}{2020}{\vernal}
\chronoperiode{2020}{2021}{\garl}
\stopchronology
\caption{Timeline for my PhD.}
\label{fig:timeline}
\end{figure}