240605: add publication

_bibliography/papers.bib

@@ -1,113 +1,61 @@
----
----
-
-@string{aps = {American Physical Society,}}
-
-@book{einstein1920relativity,
-  title={Relativity: the Special and General Theory},
-  author={Einstein, Albert},
-  year={1920},
-  publisher={Methuen & Co Ltd},
-  html={relativity.html}
-}
-
-@book{einstein1956investigations,
-  bibtex_show={true},
-  title={Investigations on the Theory of the Brownian Movement},
-  author={Einstein, Albert},
-  year={1956},
-  publisher={Courier Corporation},
-  preview={brownian-motion.gif}
-}
-
-@article{einstein1950meaning,
-  abbr={AJP},
-  bibtex_show={true},
-  title={The meaning of relativity},
-  author={Einstein, Albert and Taub, AH},
-  journal={American Journal of Physics},
-  volume={18},
-  number={6},
-  pages={403--404},
-  year={1950},
-  publisher={American Association of Physics Teachers}
-}
-
-@article{PhysRev.47.777,
-  abbr={PhysRev},
-  title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
-  author={Einstein, A. and Podolsky, B. and Rosen, N.},
-  abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.},
-  journal={Phys. Rev.},
-  location={New Jersey},
-  volume={47},
-  issue={10},
-  pages={777--780},
-  numpages={0},
-  year={1935},
-  month={May},
-  publisher=aps,
-  doi={10.1103/PhysRev.47.777},
-  url={http://link.aps.org/doi/10.1103/PhysRev.47.777},
-  html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777},
-  pdf={example_pdf.pdf},
-  altmetric={248277},
-  dimensions={true},
-  google_scholar_id={qyhmnyLat1gC},
-  video={https://www.youtube-nocookie.com/embed/aqz-KE-bpKQ},
-  additional_info={. *More Information* can be [found here](https://github.com/alshedivat/al-folio/)},
-  selected={true}
-}
-
-@article{einstein1905molekularkinetischen,
-  title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen},
-  author={Einstein, A.},
-  journal={Annalen der physik},
-  volume={322},
-  number={8},
-  pages={549--560},
-  year={1905},
-  publisher={Wiley Online Library}
-}
-
-@article{einstein1905movement,
-  abbr={Ann. Phys.},
-  title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat},
-  author={Einstein, A.},
-  journal={Ann. Phys.},
-  volume={17},
-  pages={549--560},
-  year={1905}
-}
-
-@article{einstein1905electrodynamics,
-  title={On the electrodynamics of moving bodies},
-  author={Einstein, A.},
-  year={1905}
-}
-
-@Article{einstein1905photoelectriceffect,
-  bibtex_show={true},
-  abbr={Ann. Phys.},
-  title="{{\"U}ber einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt}",
-  author={Albert Einstein},
-  abstract={This is the abstract text.},
-  journal={Ann. Phys.},
-  volume={322},
-  number={6},
-  pages={132--148},
-  year={1905},
-  doi={10.1002/andp.19053220607},
-  award={Albert Einstein receveid the **Nobel Prize in Physics** 1921 *for his services to Theoretical Physics, and especially for his discovery of the law of the photoelectric effect*},
-  award_name={Nobel Prize}
-}
-
-@book{przibram1967letters,
-  bibtex_show={true},
-  title={Letters on wave mechanics},
-  author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl},
-  year={1967},
-  publisher={Vision},
-  preview={wave-mechanics.gif},
-  abbr={Vision}
+@article{li2023comparative,
+  title={A comparative atlas of single-cell chromatin accessibility in the human brain},
+  author={Li, Yang Eric and Preissl, Sebastian and Miller, Michael and Johnson, Nicholas D and Wang, Zihan and Jiao, Henry and Zhu, Chenxu and Wang, Zhaoning and Xie, Yang and Poirion, Olivier and others},
+  journal={Science},
+  volume={382},
+  number={6667},
+  pages={eadf7044},
+  year={2023},
+  publisher={American Association for the Advancement of Science}
+
+  link={https://www.science.org/doi/full/10.1126/science.adf7044}
+}
+
+@article{xie2023droplet,
+  title={Droplet-based single-cell joint profiling of histone modifications and transcriptomes},
+  author={Xie, Yang and Zhu, Chenxu and Wang, Zhaoning and Tastemel, Melodi and Chang, Lei and Li, Yang Eric and Ren, Bing},
+  journal={Nature Structural \& Molecular Biology},
+  volume={30},
+  number={10},
+  pages={1428--1433},
+  year={2023},
+  publisher={Nature Publishing Group US New York}
+
+  link={https://www.nature.com/articles/s41594-023-01060-1}
+}
+
+@article{zu2023single,
+  title={Single-cell analysis of chromatin accessibility in the adult mouse brain},
+  author={Zu, Songpeng and Li, Yang Eric and Wang, Kangli and Armand, Ethan J and Mamde, Sainath and Amaral, Maria Luisa and Wang, Yuelai and Chu, Andre and Xie, Yang and Miller, Michael and others},
+  journal={Nature},
+  volume={624},
+  number={7991},
+  pages={378--389},
+  year={2023},
+  publisher={Nature Publishing Group UK London}
+
+  link={https://www.nature.com/articles/s41586-023-06824-9}
+}
+
+@article{zemke2023conserved,
+  title={Conserved and divergent gene regulatory programs of the mammalian neocortex},
+  author={Zemke, Nathan R and Armand, Ethan J and Wang, Wenliang and Lee, Seoyeon and Zhou, Jingtian and Li, Yang Eric and Liu, Hanqing and Tian, Wei and Nery, Joseph R and Castanon, Rosa G and others},
+  journal={Nature},
+  volume={624},
+  number={7991},
+  pages={390--402},
+  year={2023},
+  publisher={Nature Publishing Group UK London}
+
+  link={https://www.nature.com/articles/s41586-023-06819-6}
+}
+
+@article{chang2024droplet,
+  title={Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells},
+  author={Chang, Lei and Xie, Yang and Taylor, Brett and Wang, Zhaoning and Sun, Jiachen and Tan, Tuyet R and Bejar, Rafael and Chen, Clark C and Furnari, Frank B and Hu, Ming and others},
+  journal={bioRxiv},
+  year={2024},
+  publisher={Cold Spring Harbor Laboratory Preprints}
+
+ link={https://www.biorxiv.org/content/10.1101/2024.04.18.590148v1}
 }

_config.yml

@@ -9,7 +9,6 @@ last_name: Xie
 email: [email protected]
 description: > # the ">" symbol means to ignore newlines until "footer_text:"
   A simple, whitespace theme for academics. Based on [*folio](https://github.com/bogoli/-folio) design.
-  Photos from <a href="https://unsplash.com" target="_blank">Unsplash</a>.
 footer_text: >
   Powered by <a href="https://jekyllrb.com/" target="_blank">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio">al-folio</a> theme.
   Hosted by <a href="https://pages.github.com/" target="_blank">GitHub Pages</a>.

_pages/about.md

@@ -19,9 +19,9 @@ Hi there! My name is Yang Xie (谢旸). I am currently a Ph.D. candidate in [Ren
 
 Our body is a complex system. Each cell in our body can have different roles and developmental trajetories, even though they usually have the same genes. The diversity is mainly driven by the way genes are turned on and off in specific places and times. This precious regulation process is controlled by different elements in our genome, through various chemical modifications and conformation changes in DNA or associated proteins, all of which make up what we call the epigenome.  
 
-During my graduate studies, I focused on developing high-throughput, multi-modal single-cell sequencing techniques to investigate epigenomic diversity in mammalian brains, and study how does the dysregulation contribute to diseases including glioblastoma, a type of malignant brain tumor. 
+During my graduate studies, I focused on developing high-throughput, multi-modal single-cell sequencing techniques to capture the epigenomic diversity in mammalian brains, and study how does the dysregulation contribute to diseases including glioblastoma, a type of malignant brain tumor. 
 
-I completed my BSc in Biological Sciences from Fudan University, China, with Guodong Ren as my undergraduate thesis advisor. Before joing Ren lab, I worked in [O'Shea lab](https://www.salk.edu/scientist/clodagh-oshea/) at Salk Institute, where I studied how DNA folds using electron microscope and live-cell imaging. 
+I grew up in Shantou, a charming coastal city known for its delicious food. I completed my BSc in Biological Sciences from Fudan University, Shanghai, with Guodong Ren as my undergraduate thesis advisor. Before joing Ren lab, I worked in [O'Shea lab](https://www.salk.edu/scientist/clodagh-oshea/) at Salk Institute, where I studied how DNA folds using electron microscope and live-cell imaging. 
 
-Besides research, I enjoy listening to music, exploring different food and cooking. The best part of my weekend is (currently) composed of: Asian pop, contemporary French cuisine, yakiniku, gin, and Hazy IPA.   
+Besides research, I enjoy listening to music, exploring different food and cooking. The best part of my weekend is (currently) composed of: Fuji Kaze, Yakiniku, Negori, and Hazy IPA.   
 

_pages_unused/papers.bib

@@ -0,0 +1,113 @@
+---
+---
+
+@string{aps = {American Physical Society,}}
+
+@book{einstein1920relativity,
+  title={Relativity: the Special and General Theory},
+  author={Einstein, Albert},
+  year={1920},
+  publisher={Methuen & Co Ltd},
+  html={relativity.html}
+}
+
+@book{einstein1956investigations,
+  bibtex_show={true},
+  title={Investigations on the Theory of the Brownian Movement},
+  author={Einstein, Albert},
+  year={1956},
+  publisher={Courier Corporation},
+  preview={brownian-motion.gif}
+}
+
+@article{einstein1950meaning,
+  abbr={AJP},
+  bibtex_show={true},
+  title={The meaning of relativity},
+  author={Einstein, Albert and Taub, AH},
+  journal={American Journal of Physics},
+  volume={18},
+  number={6},
+  pages={403--404},
+  year={1950},
+  publisher={American Association of Physics Teachers}
+}
+
+@article{PhysRev.47.777,
+  abbr={PhysRev},
+  title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
+  author={Einstein, A. and Podolsky, B. and Rosen, N.},
+  abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.},
+  journal={Phys. Rev.},
+  location={New Jersey},
+  volume={47},
+  issue={10},
+  pages={777--780},
+  numpages={0},
+  year={1935},
+  month={May},
+  publisher=aps,
+  doi={10.1103/PhysRev.47.777},
+  url={http://link.aps.org/doi/10.1103/PhysRev.47.777},
+  html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777},
+  pdf={example_pdf.pdf},
+  altmetric={248277},
+  dimensions={true},
+  google_scholar_id={qyhmnyLat1gC},
+  video={https://www.youtube-nocookie.com/embed/aqz-KE-bpKQ},
+  additional_info={. *More Information* can be [found here](https://github.com/alshedivat/al-folio/)},
+  selected={true}
+}
+
+@article{einstein1905molekularkinetischen,
+  title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen},
+  author={Einstein, A.},
+  journal={Annalen der physik},
+  volume={322},
+  number={8},
+  pages={549--560},
+  year={1905},
+  publisher={Wiley Online Library}
+}
+
+@article{einstein1905movement,
+  abbr={Ann. Phys.},
+  title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat},
+  author={Einstein, A.},
+  journal={Ann. Phys.},
+  volume={17},
+  pages={549--560},
+  year={1905}
+}
+
+@article{einstein1905electrodynamics,
+  title={On the electrodynamics of moving bodies},
+  author={Einstein, A.},
+  year={1905}
+}
+
+@Article{einstein1905photoelectriceffect,
+  bibtex_show={true},
+  abbr={Ann. Phys.},
+  title="{{\"U}ber einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt}",
+  author={Albert Einstein},
+  abstract={This is the abstract text.},
+  journal={Ann. Phys.},
+  volume={322},
+  number={6},
+  pages={132--148},
+  year={1905},
+  doi={10.1002/andp.19053220607},
+  award={Albert Einstein receveid the **Nobel Prize in Physics** 1921 *for his services to Theoretical Physics, and especially for his discovery of the law of the photoelectric effect*},
+  award_name={Nobel Prize}
+}
+
+@book{przibram1967letters,
+  bibtex_show={true},
+  title={Letters on wave mechanics},
+  author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl},
+  year={1967},
+  publisher={Vision},
+  preview={wave-mechanics.gif},
+  abbr={Vision}
+}