diff --git a/docs/Bibliography.org b/docs/Bibliography.org
index 5aeb15d..ce05521 100644
--- a/docs/Bibliography.org
+++ b/docs/Bibliography.org
@@ -7,7 +7,7 @@
* Deep Learning
** Attention is All You Need
#+begin_src bibtex
-@article{https://doi.org/10.48550/arxiv.1706.03762,
+@article{Vaswani2017,
doi = {10.48550/ARXIV.1706.03762},
url = {https://arxiv.org/abs/1706.03762},
author = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and
@@ -178,7 +178,7 @@ A masked language model (MLM) randomly masks some of the tokens from the input,
* Deep Learning + Biology
** CpG Transformer for imputation of single-cell methylomes
#+begin_src bibtex
-@article{10.1093/bioinformatics/btab746,
+@article{DeWaele2021,
author = {De Waele, Gaetan and Clauwaert, Jim and Menschaert, Gerben
and Waegeman, Willem},
title = "{CpG Transformer for imputation of single-cell methylomes}",
@@ -214,7 +214,7 @@ A masked language model (MLM) randomly masks some of the tokens from the input,
#+end_src
** MSA Transformer
#+begin_src bibtex
-@article {Rao2021.02.12.430858,
+@article {Rao2021,
author = {Rao, Roshan and Liu, Jason and Verkuil, Robert and Meier,
Joshua and Canny, John F. and Abbeel, Pieter and Sercu, Tom
and Rives, Alexander},
@@ -443,3 +443,50 @@ A masked language model (MLM) randomly masks some of the tokens from the input,
challenges associated with running the competition.}
}
#+end_src
+** Eleven grand challenges in single-cell data science
+#+begin_src bibtex
+@article{Lähnemann2020,
+ author = {L{\"a}hnemann, David and K{\"o}ster, Johannes and Szczurek,
+ Ewa and McCarthy, Davis J. and Hicks, Stephanie C. and
+ Robinson, Mark D. and Vallejos, Catalina A. and Campbell,
+ Kieran R. and Beerenwinkel, Niko and Mahfouz, Ahmed and
+ Pinello, Luca and Skums, Pavel and Stamatakis, Alexandros and
+ Attolini, Camille Stephan-Otto and Aparicio, Samuel and
+ Baaijens, Jasmijn and Balvert, Marleen and Barbanson, Buys de
+ and Cappuccio, Antonio and Corleone, Giacomo and Dutilh, Bas
+ E. and Florescu, Maria and Guryev, Victor and Holmer, Rens and
+ Jahn, Katharina and Lobo, Thamar Jessurun and Keizer, Emma M.
+ and Khatri, Indu and Kielbasa, Szymon M. and Korbel, Jan O.
+ and Kozlov, Alexey M. and Kuo, Tzu-Hao and Lelieveldt,
+ Boudewijn P.F. and Mandoiu, Ion I. and Marioni, John C. and
+ Marschall, Tobias and M{\"o}lder, Felix and Niknejad, Amir and
+ Raczkowski, Lukasz and Reinders, Marcel and Ridder, Jeroen de
+ and Saliba, Antoine-Emmanuel and Somarakis, Antonios and
+ Stegle, Oliver and Theis, Fabian J. and Yang, Huan and
+ Zelikovsky, Alex and McHardy, Alice C. and Raphael, Benjamin
+ J. and Shah, Sohrab P. and Sch{\"o}nhuth, Alexander},
+ title = {Eleven grand challenges in single-cell data science},
+ journal = {Genome Biology},
+ year = 2020,
+ month = {Feb},
+ day = 07,
+ volume = 21,
+ number = 1,
+ pages = 31,
+ abstract = {The recent boom in microfluidics and combinatorial indexing
+ strategies, combined with low sequencing costs, has empowered
+ single-cell sequencing technology. Thousands---or even
+ millions---of cells analyzed in a single experiment amount to
+ a data revolution in single-cell biology and pose unique data
+ science problems. Here, we outline eleven challenges that will
+ be central to bringing this emerging field of single-cell data
+ science forward. For each challenge, we highlight motivating
+ research questions, review prior work, and formulate open
+ problems. This compendium is for established researchers,
+ newcomers, and students alike, highlighting interesting and
+ rewarding problems for the coming years.},
+ issn = {1474-760X},
+ doi = {10.1186/s13059-020-1926-6},
+ url = {https://doi.org/10.1186/s13059-020-1926-6}
+}
+#+end_src
diff --git a/docs/bibliography.bib b/docs/bibliography.bib
index 0102fcd..17153e3 100644
--- a/docs/bibliography.bib
+++ b/docs/bibliography.bib
@@ -1,4 +1,4 @@
-@article{https://doi.org/10.48550/arxiv.1706.03762,
+@article{Vaswani2017,
doi = {10.48550/ARXIV.1706.03762},
url = {https://arxiv.org/abs/1706.03762},
author = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and
@@ -148,7 +148,7 @@
copyright = {arXiv.org perpetual, non-exclusive license}
}
-@article{10.1093/bioinformatics/btab746,
+@article{DeWaele2021,
author = {De Waele, Gaetan and Clauwaert, Jim and Menschaert, Gerben
and Waegeman, Willem},
title = "{CpG Transformer for imputation of single-cell methylomes}",
@@ -182,7 +182,7 @@
{https://academic.oup.com/bioinformatics/article-pdf/38/3/597/42167564/btab746.pdf},
}
-@article {Rao2021.02.12.430858,
+@article {Rao2021,
author = {Rao, Roshan and Liu, Jason and Verkuil, Robert and Meier,
Joshua and Canny, John F. and Abbeel, Pieter and Sercu, Tom
and Rives, Alexander},
@@ -399,3 +399,48 @@
describe trends of well performing approaches, and discuss
challenges associated with running the competition.}
}
+
+@article{Lähnemann2020,
+ author = {L{\"a}hnemann, David and K{\"o}ster, Johannes and Szczurek,
+ Ewa and McCarthy, Davis J. and Hicks, Stephanie C. and
+ Robinson, Mark D. and Vallejos, Catalina A. and Campbell,
+ Kieran R. and Beerenwinkel, Niko and Mahfouz, Ahmed and
+ Pinello, Luca and Skums, Pavel and Stamatakis, Alexandros and
+ Attolini, Camille Stephan-Otto and Aparicio, Samuel and
+ Baaijens, Jasmijn and Balvert, Marleen and Barbanson, Buys de
+ and Cappuccio, Antonio and Corleone, Giacomo and Dutilh, Bas
+ E. and Florescu, Maria and Guryev, Victor and Holmer, Rens and
+ Jahn, Katharina and Lobo, Thamar Jessurun and Keizer, Emma M.
+ and Khatri, Indu and Kielbasa, Szymon M. and Korbel, Jan O.
+ and Kozlov, Alexey M. and Kuo, Tzu-Hao and Lelieveldt,
+ Boudewijn P.F. and Mandoiu, Ion I. and Marioni, John C. and
+ Marschall, Tobias and M{\"o}lder, Felix and Niknejad, Amir and
+ Raczkowski, Lukasz and Reinders, Marcel and Ridder, Jeroen de
+ and Saliba, Antoine-Emmanuel and Somarakis, Antonios and
+ Stegle, Oliver and Theis, Fabian J. and Yang, Huan and
+ Zelikovsky, Alex and McHardy, Alice C. and Raphael, Benjamin
+ J. and Shah, Sohrab P. and Sch{\"o}nhuth, Alexander},
+ title = {Eleven grand challenges in single-cell data science},
+ journal = {Genome Biology},
+ year = 2020,
+ month = {Feb},
+ day = 07,
+ volume = 21,
+ number = 1,
+ pages = 31,
+ abstract = {The recent boom in microfluidics and combinatorial indexing
+ strategies, combined with low sequencing costs, has empowered
+ single-cell sequencing technology. Thousands---or even
+ millions---of cells analyzed in a single experiment amount to
+ a data revolution in single-cell biology and pose unique data
+ science problems. Here, we outline eleven challenges that will
+ be central to bringing this emerging field of single-cell data
+ science forward. For each challenge, we highlight motivating
+ research questions, review prior work, and formulate open
+ problems. This compendium is for established researchers,
+ newcomers, and students alike, highlighting interesting and
+ rewarding problems for the coming years.},
+ issn = {1474-760X},
+ doi = {10.1186/s13059-020-1926-6},
+ url = {https://doi.org/10.1186/s13059-020-1926-6}
+}