From 8be295ab52ae18ba1c239a56d90ef22578595fe6 Mon Sep 17 00:00:00 2001 From: coolneng Date: Mon, 31 Oct 2022 12:38:27 +0100 Subject: [PATCH] Use human readable keys for the bibliography --- docs/Bibliography.org | 53 ++++++++++++++++++++++++++++++++++++++++--- docs/bibliography.bib | 51 ++++++++++++++++++++++++++++++++++++++--- 2 files changed, 98 insertions(+), 6 deletions(-) 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} +}