Merge pull request #11 from aristoteleo/dev

Create individual pages for people and publications.

_config.yml

@@ -33,6 +33,14 @@ theme: minima
 plugins:
   - jekyll-feed
 
+collections:
+  papers:
+    output: true
+    permalink: /papers/:path/
+  people:
+    output: true
+    permalink: /people/:path/
+
 sass:
   sass_dir: _sass
   style: compressed

_includes/footer.html

@@ -93,7 +93,7 @@ <h3>Qiu Lab @ Stanford</h3>
       <ul class="social-icons">
         <li><a href="https://github.com/aristoteleo" target="_blank"><i class="fab fa-xxx"></i></a></li>  <!-- Fake to ensure the symbols are centered below the text above -->
         <li><a href="https://github.com/aristoteleo" target="_blank"><i class="fab fa-xxx"></i></a></li>  <!-- Fake to ensure the symbols are centered below the text above -->
-        <li><img src="assets/images/qiu_lab_logo_transparent_processed.png" alt="QIU Lab Logo" style="width: 33px;"> </li> <!-- Adjust width as needed -->
+        <li><img src="{{ site.baseurl }}/assets/images/qiu_lab_logo_transparent_processed.png" alt="QIU Lab Logo" style="width: 33px;"> </li> <!-- Adjust width as needed -->
         <li><a href="https://github.com/aristoteleo" target="_blank"><i class="fab fa-github"></i></a></li>
         <li><a href="https://twitter.com/Xiaojie_Qiu" target="_blank"><i class="fab fa-twitter"></i></a></li>
         <li><a href="https://scholar.google.com/citations?user=XlMd8TAAAAAJ&hl=en" target="_blank"><i class="fab fa-google"></i></a></li>

_includes/header.html

@@ -7,12 +7,12 @@
         <div class="logo-container">
           <img
             class="lab-logo-top"
-            src="assets/images/qiu_lab_logo_transparent_processed.png"
+            src="{{ site.baseurl }}/assets/images/qiu_lab_logo_transparent_processed.png"
             alt="Qiu lab logo"
           />
           <img
             class="lab-logo-bottom"
-            src="assets/images/Stanford_logo.png"
+            src="{{ site.baseurl }}/assets/images/Stanford_logo.png"
             alt="Stanford University logo"
           />
         </div>
@@ -46,7 +46,7 @@
             <a class="nav-link" href="/research">Research</a>
           </li>
           <li class="nav-item">
-            <a class="nav-link" href="/publications">Papers</a>
+            <a class="nav-link" href="/papers">Papers</a>
           </li>
           <li class="nav-item">
             <a class="nav-link" href="/news">News</a>

_layouts/paper.html

@@ -0,0 +1,68 @@
+---
+layout: "wrapper"
+---
+
+<div class="bigspacer"></div>
+
+<div class="row">
+    <div class="col-lg-8 paperbox offset-lg-2 paperbox">
+        <div class="media d-flex">
+
+            <img class="pad-right media-object" src="{{ page.image_url }}" style="max-width: 160px; max-height: 200px;">
+
+            <div class="media-body">
+                <h3>{{ page.paper_title }}</h3>
+                {% if page.paper_subtitle %}
+                <div class="smallhead" style="text-align: right; margin-right: 60px;">{{ page.paper_subtitle }}</div>
+                {% endif %}
+                <p></p>
+                <div class="smallsubhead">{{ page.author_list }}</div>
+                <div class="bigspacer"></div>
+                <div class="smallsubhead">
+                    {{ page.journal }}
+                    ({{ page.year }})
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+
+<div class="bigspacer"></div>
+
+<div class="row">
+    <div class="col-lg-2 offset-lg-2">
+        <div class="bigspacer"></div>
+        <div class="glyphbox note">
+            <div class="bigspacer"></div>
+            <div class="smallhead">
+                PDF
+            </div>
+            <div class="pad-left note">
+                <i class="far fa-file"></i>
+                <a class="off" href="{{ site.baseurl }}{{ page.pdf_url }}">
+                    {{ page.pdf_url | split: '/' | last | split: '.' | first }}.pdf
+                </a>
+            </div>
+
+            <div class="bigspacer"></div>
+            <div class="smallhead">
+                DOI
+            </div>
+            <div class="pad-left note" style="display: flex; align-items: center;">
+                <p></p>
+                <i class="fas fa-link"></i>
+                <a class="off" href="https://doi.org/{{ page.doi }}">{{ page.doi }}</a>
+            </div>
+            <div class="bigspacer"></div>
+
+            </div>
+    </div>
+    <div class="col-lg-5">
+        <div class="post">
+            <h3 id="abstract">Abstract</h3>
+        </div>
+        <div class="justified-paragraph">
+            {{ content }}
+        </div>
+    </div>
+</div>

_layouts/people.html

@@ -0,0 +1,94 @@
+---
+layout: "wrapper"
+---
+
+<div class="container mt-4">
+        <div class="bigspacer"></div>
+        <div class="row">
+            <div class="col-lg-12">
+                <div class="media">
+                    <img class="pull-left pad-right media-object" width="160" src="{{ site.baseurl }}/assets/images/headshots/{% if page.headshot %}{{ page.headshot }}{% else %}placeholder-headshot.png{% endif %}">
+                    <div class="media-body">
+                        <h2>
+                            {{ page.name }}
+                        </h2>
+                        <p>
+                            <div class="smallhead">
+                                {{ page.position }}
+                            </div>
+                        </p>
+                    </div>
+                </div>
+            </div>
+        </div>
+        <div class="bigspacer"></div>
+        <div class="row">
+            <div class="col-lg-3">
+                {% if page.cv_url %}
+                <div class="smallhead">
+                    CV
+                </div>
+                <div class="pad-left note">
+                    <div class="smallspacer"></div>
+                    <i class="far fa-file"></i>
+                    <a class="off" href="{{ site.baseurl }}/{{ page.cv_url }}">cv.pdf</a>
+                </div>
+                <div class="bigspacer"></div>
+                {% endif %}
+                {% if page.GitHub %}
+                <div class="smallhead">
+                    GitHub
+                </div>
+                <div class="pad-left note">
+                    <div class="smallspacer"></div>
+                    <i class="fab fa-github"></i>
+                    <a class="off" href="{{ page.GitHub }}">{{ page.name }}</a>
+                </div>
+                <div class="bigspacer"></div>
+                {% endif %}
+                {% if page.google_scholar %}
+                <div class="smallhead">
+                    Google Scholar
+                </div>
+                <div class="pad-left note">
+                    <div class="smallspacer"></div>
+                    <i class="fa fa-book fa-fw"></i>
+                    <a class="off" href="{{ page.google_scholar }}">{{ page.name }}</a>
+                </div>
+                <div class="bigspacer"></div>
+                {% endif %}
+                {% if page.twitter %}
+                <div class="smallhead">
+                    Twitter
+                </div>
+                <div class="pad-left note">
+                    <div class="smallspacer"></div>
+                    <i class="fab fa-twitter"></i>
+                    <a class="off" href={{ page.twitter }}>{{ page.name }}</a>
+                </div>
+                <div class="bigspacer"></div>
+                {% endif %}
+                {% if page.email %}
+                <div class="smallhead">
+                    Email
+                </div>
+                <div class="pad-left note">
+                    <div class="smallspacer"></div>
+                    <i class="fa fa-inbox fa-fw"></i>
+                    {{ page.email }}
+                </div>
+                <div class="bigspacer"></div>
+                {% endif %}
+            </div>
+            <div class="col-lg-8">
+                <h3>Bio</h3>
+                <div class="justified-paragraph">
+                  {{ page.bio }}
+                </div>
+                <div class="bigspacer"></div>
+                <div class="justified-paragraph">
+                    {{ content }}
+                </div>
+            </div>
+        </div>
+    </div>

_papers/Bing_hccnet_2010.md

@@ -0,0 +1,27 @@
+---
+layout: paper
+title: "Read our work"
+type: previous involved work
+paper_title: "HCCNet: an integrated network database of hepatocellular carcinoma"
+author_list: Bing He, Xiaojie Qiu, Peng Li, Lishan Wang, Qi Lv, Tieliu Shi+.
+journal: Cell Research
+doi: 10.1038/cr.2010.67
+year: 2010
+pdf_url: /assets/PDFs/Bing_hccnet_2010.pdf
+image_url: /assets/images/papers/Bing_hccnet_2010.png
+paper_alt: Bing_hccnet_2010 Paper Image
+rank: 10
+---
+
+As a complex disease, the development and progression of hepatocellular carcinoma (HCC) involves the interactions of 
+multiple proteins, genes and miRNAs in various biological pathways, and it has been extensively studied with different 
+high-throughput techniques. However, efforts to integrate multiple data sources at different levels, especially with 
+regard to biological pathways and interaction networks, are still negligible in the HCC research field. We have built 
+a database of the HCC network (HCCNet) by integrating interactions of multiple proteins, genes and miRNAs in biological 
+pathways, and manually collecting all of the HCC-related genes and miRNAs from the literature in combination with 
+a bioinformatic analysis of the collected HCC expression data (Supplementary information, Data S1). Currently, there 
+are 37 811 experimentally confirmed protein-protein interactions (PPIs), 9 148 experimentally confirmed transcriptional 
+regulatory interactions (TRIs), 114 miRNA-target gene interactions, 2 234 high-confidence HCC-related genes and 160 
+HCC-related miRNAs available in the database. The database also provides an online graphic analysis tool to view 
+the interactions among HCC-related proteins, genes and miRNAs. HCCNet is a helpful platform to explore the molecular 
+mechanisms that underlie human HCC. The database can be accessed at http://www.megabionet.org/hcc.

_papers/Qiu_etal_Scribe_CellSys_2020.md

@@ -0,0 +1,27 @@
+---
+layout: paper
+title: "Read our work"
+type: selected work
+paper_title: Inferring causal gene regulatory networks from coupled single-cell expression dynamics using scribe
+author_list: Xiaojie Qiu*, Arman Rahimzamani*, Li Wang, Bingcheng Ren, Qi Mao, Timothy Durham, José L McFaline-Figueroa, 
+    Lauren Saunders, Cole Trapnell+, Sreeram Kannan+.
+journal: Cell Systems
+doi: 10.1016/j.cels.2020.02.003
+year: 2020
+pdf_url: /assets/PDFs/Qiu_etal_Scribe_CellSys_2020.pdf
+image_url: /assets/images/papers/Qiu_etal_Scribe_CellSys_2020.png
+paper_alt: Census Paper Image
+rank: 5
+---
+
+Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal 
+regulatory interactions between genes and explore the potential for single-cell experiments to power network 
+reconstruction. Scribe employs restricted directed information to determine causality by estimating the strength of 
+information transferred from a potential regulator to its downstream target. We apply Scribe and other leading 
+approaches for causal network reconstruction to several types of single-cell measurements and show that there is a 
+dramatic drop in performance for ‘‘pseudotime’’-ordered single-cell data compared with true time-series data. We 
+demonstrate that performing causal inference requires temporal coupling between measurements. We show that methods 
+such as ‘‘RNA velocity’’ restore some degree of coupling through an analysis of chromaffin cell fate commitment. These 
+analyses highlight a shortcoming in experimental and computational methods for analyzing gene regulation at single-cell 
+resolution and suggest ways of overcoming it.
+

_papers/Saunders_elife_2019.md

@@ -0,0 +1,26 @@
+---
+layout: paper
+title: "Read our work"
+type: previous involved work
+paper_title: Thyroid hormone regulates distinct paths to maturation in pigment cell lineages
+author_list: Lauren M Saunders, Abhishek K Mishra, Andrew J Aman, Victor M Lewis, Matthew B Toomey, Jonathan S Packer, 
+    Xiaojie Qiu, Jose L McFaline-Figueroa, Joseph C Corbo, Cole Trapnell+, David M Parichy+.
+journal: eLife
+doi: 10.7554/eLife.45181
+year: 2019
+pdf_url: /assets/PDFs/Saunders_elife_2019.pdf
+image_url: /assets/images/papers/Saunders_elife_2019.png
+paper_alt: Saunders_elife_2019 Paper Image
+rank: 4
+---
+
+Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, 
+TH has opposite effects on neural crest derived pigment cells of the adult stripe pattern, limiting melanophore 
+population expansion, yet increasing yellow/orange xanthophore numbers. To learn how TH elicits seemingly opposite 
+responses in cells having a common embryological origin, we analyzed individual transcriptomes from thousands of 
+neural crest-derived cells, reconstructed developmental trajectories, identified pigment cell-lineage specific 
+responses to TH, and assessed roles for TH receptors. We show that TH promotes maturation of both cell types but 
+in distinct ways. In melanophores, TH drives terminal differentiation, limiting final cell numbers. In xanthophores, 
+TH promotes accumulation of orange carotenoids, making the cells visible. TH receptors act primarily to repress these 
+programs when TH is limiting. Our findings show how a single endocrine factor integrates very different cellular 
+activities during the generation of adult form.

_papers/anika_pnas.md

@@ -0,0 +1,29 @@
+---
+layout: paper
+title: "Read our work"
+type: previous involved work
+paper_title: Inferring gene regulation from stochastic transcriptional variation across single cells at steady state
+author_list: Anika Gupta*, Jorge D Martin-Rufino*, Thouis R Jones, Vidya Subramanian, Xiaojie Qiu, Emanuelle I Grody, 
+    Alex Bloemendal, Chen Weng, Sheng-Yong Niu, Kyung Hoi Min, Arnav Mehta, Kaite Zhang, Layla Siraj, Aziz Al'Khafaji, 
+    Vijay G Sankaran, Soumya Raychaudhuri, Brian Cleary, Sharon Grossman, Eric S Lander+.
+journal: PNAS
+doi: 10.1073/pnas.2207392119
+year: 2022
+pdf_url: /assets/PDFs/anika_pnas.pdf
+image_url: /assets/images/papers/anika_pnas.png
+paper_alt: anika_pnas Paper Image
+rank: 3
+---
+
+Regulatory relationships between transcription factors (TFs) and their target genes lie at the heart of cellular 
+identity and function; however, uncovering these relationships is often labor-intensive and requires perturbations. 
+Here, we propose a principled framework to systematically infer gene regulation for all TFs simultaneously in cells 
+at steady state by leveraging the intrinsic variation in the transcriptional abundance across single cells. Through 
+modeling and simulations, we characterize how transcriptional bursts of a TF gene are propagated to its target genes, 
+including the expected ranges of time delay and magnitude of maximum covariation. We distinguish these temporal trends 
+from the time-invariant covariation arising from cell states, and we delineate the experimental and technical 
+requirements for leveraging these small but meaningful cofluctuations in the presence of measurement noise. While 
+current technology does not yet allow adequate power for definitively detecting regulatory relationships for all TFs 
+simultaneously in cells at steady state, we investigate a small-scale dataset to inform future experimental design. 
+This study supports the potential value of mapping regulatory connections through stochastic variation, and it 
+motivates further technological development to achieve its full potential.

_papers/cacchiarelli-hsmm.md

@@ -0,0 +1,28 @@
+---
+layout: paper
+title: "Read our work"
+type: previous involved work
+paper_title: Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of myogenic reprogramming outcome
+author_list: Davide Cacchiarelli, Xiaojie Qiu, Sanjay Srivatsan, Anna Manfredi, Michael Ziller, Eliah Overbey,
+    Antonio Grimaldi, Jonna Grimsby, Prapti Pokharel, Kenneth J Livak, Shuqiang Li, Alexander Meissner,
+    Tarjei S Mikkelsen, John L Rinn, Cole Trapnell+.
+journal: Cell Systems
+doi: 10.1016/j.cels.2018.07.006
+year: 2018
+pdf_url: /assets/PDFs/cacchiarelli-hsmm.pdf
+image_url: /assets/images/papers/cacchiarelli-hsmm.png
+paper_alt: cacchiarelli-hsmm Paper Image
+rank: 5
+---
+
+Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell 
+types needed for use in therapy and for revealing principles of gene regulation. However, most reprogramming systems 
+are inefficient, converting only a fraction of cells to the desired state. Here, we analyze MYOD-mediated reprogramming 
+of human fibroblasts to myotubes, a well-characterized model system for direct conversion by defined factors, at 
+pseudotemporal resolution using single-cell RNA-seq. To expose barriers to efficient conversion, we introduce a novel 
+analytic technique, trajectory alignment, which enables quantitative comparison of gene expression kinetics across two 
+biological processes. Reprogrammed cells navigate a trajectory with branch points that correspond to two alternative 
+decision points, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. 
+Analysis of these branch points revealed insulin and BMP signaling as crucial molecular determinants of reprogramming. 
+Single-cell trajectory alignment enables rigorous quantitative comparisons between biological trajectories found in 
+diverse processes in development, reprogramming, and other contexts.

_papers/cao-combinatorial-indexing.md

@@ -0,0 +1,24 @@
+---
+layout: paper
+title: "Read our work"
+type: selected work
+paper_title: Comprehensive single-cell transcriptional profiling of a multicellular organism
+author_list: Junyue Cao*, Jonathan S Packer*, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, 
+    Choli Lee, Scott N Furlan, Frank J Steemers, Andrew Adey, Robert H Waterston+, Cole Trapnell+, Jay Shendure+.
+journal: Science
+doi: 10.1126/science.aam8940
+year: 2017
+pdf_url: /assets/PDFs/cao-combinatorial-indexing.pdf
+image_url: /assets/images/papers/cao-combinatorial-indexing.png
+paper_alt: cao-combinatorial-indexing Paper Image
+rank: 7
+---
+
+To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of 
+single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing RNA sequencing). We applied sci-RNA-seq 
+to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 larval stage, which provided >50-fold 
+“shotgun” cellular coverage of its somatic cell composition. From these data, we defined consensus expression profiles 
+for 27 cell types and recovered rare neuronal cell types corresponding to as few as one or two cells in the L2 worm. We 
+integrated these profiles with whole-animal chromatin immunoprecipitation sequencing data to deconvolve the cell 
+type–specific effects of transcription factors. The data generated by sci-RNA-seq constitute a powerful resource for 
+nematode biology and foreshadow similar atlases for other organisms.