Add references to foundation models page (#358)

* Add links to foundation models page

* Replace foundation model links with citations

library.bib

@@ -564,7 +564,7 @@ @article{Demetci2020scot
 	URL = {https://www.biorxiv.org/content/early/2020/11/11/2020.04.28.066787},
 	eprint = {https://www.biorxiv.org/content/early/2020/11/11/2020.04.28.066787.full.pdf},
 	journal = {bioRxiv}
-}	
+}
 
 
 @article{dimitrov2022comparison,
@@ -1480,7 +1480,7 @@ @InProceedings{santos2009on
 	publisher = {Springer Berlin Heidelberg},
 	address = {Berlin, Heidelberg},
 	pages = {175--184},
-	isbn = {978-3-642-04277-5}, 
+	isbn = {978-3-642-04277-5},
 	doi = {10.1007/978-3-642-04277-5_18},
 	url = {https://doi.org/10.1007/978-3-642-04277-5_18}
 }
@@ -1596,7 +1596,7 @@ @article{svensson2018spatialde
   number={5},
   pages={343--346},
   year={2018},
-  publisher={Nature Publishing Group}, 
+  publisher={Nature Publishing Group},
   doi={10.1038/nmeth.4636}
 }
 
@@ -1828,7 +1828,7 @@ @article{wang2018three
   publisher = {American Association for the Advancement of Science (AAAS)},
   author = {Wang,  Xiao and Allen,  William E. and Wright,  Matthew A. and Sylwestrak,  Emily L. and Samusik,  Nikolay and Vesuna,  Sam and Evans,  Kathryn and Liu,  Cindy and Ramakrishnan,  Charu and Liu,  Jia and Nolan,  Garry P. and Bava,  Felice-Alessio and Deisseroth,  Karl},
   year = {2018},
-  month = jul 
+  month = jul
 }
 
 
@@ -2041,7 +2041,7 @@ @article{consortium2022tabula
   publisher = {American Association for the Advancement of Science (AAAS)},
   author = {Jones,  Robert C. and Karkanias,  Jim and Krasnow,  Mark A. and Pisco,  Angela Oliveira and Quake,  Stephen R. and Salzman,  Julia and Yosef,  Nir and Bulthaup,  Bryan and Brown,  Phillip and Harper,  William and Hemenez,  Marisa and Ponnusamy,  Ravikumar and Salehi,  Ahmad and Sanagavarapu,  Bhavani A. and Spallino,  Eileen and Aaron,  Ksenia A. and Concepcion,  Waldo and Gardner,  James M. and Kelly,  Burnett and Neidlinger,  Nikole and Wang,  Zifa and Crasta,  Sheela and Kolluru,  Saroja and Morri,  Maurizio and Pisco,  Angela Oliveira and Tan,  Serena Y. and Travaglini,  Kyle J. and Xu,  Chenling and Alcántara-Hernández,  Marcela and Almanzar,  Nicole and Antony,  Jane and Beyersdorf,  Benjamin and Burhan,  Deviana and Calcuttawala,  Kruti and Carter,  Matthew M. and Chan,  Charles K. F. and Chang,  Charles A. and Chang,  Stephen and Colville,  Alex and Crasta,  Sheela and Culver,  Rebecca N. and Cvijović,  Ivana and D’Amato,  Gaetano and Ezran,  Camille and Galdos,  Francisco X. and Gillich,  Astrid and Goodyer,  William R. and Hang,  Yan and Hayashi,  Alyssa and Houshdaran,  Sahar and Huang,  Xianxi and Irwin,  Juan C. and Jang,  SoRi and Juanico,  Julia Vallve and Kershner,  Aaron M. and Kim,  Soochi and Kiss,  Bernhard and Kolluru,  Saroja and Kong,  William and Kumar,  Maya E. and Kuo,  Angera H. and Leylek,  Rebecca and Li,  Baoxiang and Loeb,  Gabriel B. and Lu,  Wan-Jin and Mantri,  Sruthi and Markovic,  Maxim and McAlpine,  Patrick L. and de Morree,  Antoine and Morri,  Maurizio and Mrouj,  Karim and Mukherjee,  Shravani and Muser,  Tyler and Neuh\"{o}fer,  Patrick and Nguyen,  Thi D. and Perez,  Kimberly and Phansalkar,  Ragini and Pisco,  Angela Oliveira and Puluca,  Nazan and Qi,  Zhen and Rao,  Poorvi and Raquer-McKay,  Hayley and Schaum,  Nicholas and Scott,  Bronwyn and Seddighzadeh,  Bobak and Segal,  Joe and Sen,  Sushmita and Sikandar,  Shaheen and Spencer,  Sean P. and Steffes,  Lea C. and Subramaniam,  Varun R. and Swarup,  Aditi and Swift,  Michael and Travaglini,  Kyle J. and Van Treuren,  Will and Trimm,  Emily and Veizades,  Stefan and Vijayakumar,  Sivakamasundari and Vo,  Kim Chi and Vorperian,  Sevahn K. and Wang,  Wanxin and Weinstein,  Hannah N. W. and Winkler,  Juliane and Wu,  Timothy T. H. and Xie,  Jamie and Yung,  Andrea R. and Zhang,  Yue and Detweiler,  Angela M. and Mekonen,  Honey and Neff,  Norma F. and Sit,  Rene V. and Tan,  Michelle and Yan,  Jia and Bean,  Gregory R. and Charu,  Vivek and Forgó,  Erna and Martin,  Brock A. and Ozawa,  Michael G. and Silva,  Oscar and Tan,  Serena Y. and Toland,  Angus and Vemuri,  Venkata N. P. and Afik,  Shaked and Awayan,  Kyle and Botvinnik,  Olga Borisovna and Byrne,  Ashley and Chen,  Michelle and Dehghannasiri,  Roozbeh and Detweiler,  Angela M. and Gayoso,  Adam and Granados,  Alejandro A. and Li,  Qiqing and Mahmoudabadi,  Gita and McGeever,  Aaron and de Morree,  Antoine and Olivieri,  Julia Eve and Park,  Madeline and Pisco,  Angela Oliveira and Ravikumar,  Neha and Salzman,  Julia and Stanley,  Geoff and Swift,  Michael and Tan,  Michelle and Tan,  Weilun and Tarashansky,  Alexander J. and Vanheusden,  Rohan and Vorperian,  Sevahn K. and Wang,  Peter and Wang,  Sheng and Xing,  Galen and Xu,  Chenling and Yosef,  Nir and Alcántara-Hernández,  Marcela and Antony,  Jane and Chan,  Charles K. F. and Chang,  Charles A. and Colville,  Alex and Crasta,  Sheela and Culver,  Rebecca and Dethlefsen,  Les and Ezran,  Camille and Gillich,  Astrid and Hang,  Yan and Ho,  Po-Yi and Irwin,  Juan C. and Jang,  SoRi and Kershner,  Aaron M. and Kong,  William and Kumar,  Maya E. and Kuo,  Angera H. and Leylek,  Rebecca and Liu,  Shixuan and Loeb,  Gabriel B. and Lu,  Wan-Jin and Maltzman,  Jonathan S. and Metzger,  Ross J. and de Morree,  Antoine and Neuh\"{o}fer,  Patrick and Perez,  Kimberly and Phansalkar,  Ragini and Qi,  Zhen and Rao,  Poorvi and Raquer-McKay,  Hayley and Sasagawa,  Koki and Scott,  Bronwyn and Sinha,  Rahul and Song,  Hanbing and Spencer,  Sean P. and Swarup,  Aditi and Swift,  Michael and Travaglini,  Kyle J. and Trimm,  Emily and Veizades,  Stefan and Vijayakumar,  Sivakamasundari and Wang,  Bruce and Wang,  Wanxin and Winkler,  Juliane and Xie,  Jamie and Yung,  Andrea R. and Artandi,  Steven E. and Beachy,  Philip A. and Clarke,  Michael F. and Giudice,  Linda C. and Huang,  Franklin W. and Huang,  Kerwyn Casey and Idoyaga,  Juliana and Kim,  Seung K. and Krasnow,  Mark and Kuo,  Christin S. and Nguyen,  Patricia and Quake,  Stephen R. and Rando,  Thomas A. and Red-Horse,  Kristy and Reiter,  Jeremy and Relman,  David A. and Sonnenburg,  Justin L. and Wang,  Bruce and Wu,  Albert and Wu,  Sean M. and Wyss-Coray,  Tony},
   year = {2022},
-  month = may 
+  month = may
 }
 
 @article{dominguez2022crosstissue,
@@ -2055,7 +2055,7 @@ @article{dominguez2022crosstissue
   publisher = {American Association for the Advancement of Science (AAAS)},
   author = {Domínguez Conde,  C. and Xu,  C. and Jarvis,  L. B. and Rainbow,  D. B. and Wells,  S. B. and Gomes,  T. and Howlett,  S. K. and Suchanek,  O. and Polanski,  K. and King,  H. W. and Mamanova,  L. and Huang,  N. and Szabo,  P. A. and Richardson,  L. and Bolt,  L. and Fasouli,  E. S. and Mahbubani,  K. T. and Prete,  M. and Tuck,  L. and Richoz,  N. and Tuong,  Z. K. and Campos,  L. and Mousa,  H. S. and Needham,  E. J. and Pritchard,  S. and Li,  T. and Elmentaite,  R. and Park,  J. and Rahmani,  E. and Chen,  D. and Menon,  D. K. and Bayraktar,  O. A. and James,  L. K. and Meyer,  K. B. and Yosef,  N. and Clatworthy,  M. R. and Sims,  P. A. and Farber,  D. L. and Saeb-Parsy,  K. and Jones,  J. L. and Teichmann,  S. A.},
   year = {2022},
-  month = may 
+  month = may
 }
 
 @article{eraslan2022singlenucleus,
@@ -2069,7 +2069,7 @@ @article{eraslan2022singlenucleus
   publisher = {American Association for the Advancement of Science (AAAS)},
   author = {Eraslan,  G\"{o}kcen and Drokhlyansky,  Eugene and Anand,  Shankara and Fiskin,  Evgenij and Subramanian,  Ayshwarya and Slyper,  Michal and Wang,  Jiali and Van Wittenberghe,  Nicholas and Rouhana,  John M. and Waldman,  Julia and Ashenberg,  Orr and Lek,  Monkol and Dionne,  Danielle and Win,  Thet Su and Cuoco,  Michael S. and Kuksenko,  Olena and Tsankov,  Alexander M. and Branton,  Philip A. and Marshall,  Jamie L. and Greka,  Anna and Getz,  Gad and Segrè,  Ayellet V. and Aguet,  Fran\c{c}ois and Rozenblatt-Rosen,  Orit and Ardlie,  Kristin G. and Regev,  Aviv},
   year = {2022},
-  month = may 
+  month = may
 }
 
 @article{li2023integrated,
@@ -2079,7 +2079,7 @@ @article{li2023integrated
   publisher = {Cold Spring Harbor Laboratory},
   author = {Li,  Jin and Wang,  Jun and Ibarra,  Ignacio L and Cheng,  Xuesen and Luecken,  Malte D and Lu,  Jiaxiong and Monavarfeshani,  Aboozar and Yan,  Wenjun and Zheng,  Yiqiao and Zuo,  Zhen and Zayas Colborn,  Samantha Lynn and Cortez,  Berenice Sarahi and Owen,  Leah A and Tran,  Nicholas M and Shekhar,  Karthik and Sanes,  Joshua R and Stout,  J Timothy and Chen,  Shiming and Li,  Yumei and DeAngelis,  Margaret M and Theis,  Fabian J and Chen,  Rui},
   year = {2023},
-  month = nov 
+  month = nov
 }
 
 @article{wilson2022multimodal,
@@ -2093,7 +2093,7 @@ @article{wilson2022multimodal
   publisher = {Springer Science and Business Media LLC},
   author = {Wilson,  Parker C. and Muto,  Yoshiharu and Wu,  Haojia and Karihaloo,  Anil and Waikar,  Sushrut S. and Humphreys,  Benjamin D.},
   year = {2022},
-  month = sep 
+  month = sep
 }
 
 @article{steuernagel2022hypomap,
@@ -2122,7 +2122,7 @@ @article{tian2023singlecell
   publisher = {American Association for the Advancement of Science (AAAS)},
   author = {Tian,  Wei and Zhou,  Jingtian and Bartlett,  Anna and Zeng,  Qiurui and Liu,  Hanqing and Castanon,  Rosa G. and Kenworthy,  Mia and Altshul,  Jordan and Valadon,  Cynthia and Aldridge,  Andrew and Nery,  Joseph R. and Chen,  Huaming and Xu,  Jiaying and Johnson,  Nicholas D. and Lucero,  Jacinta and Osteen,  Julia K. and Emerson,  Nora and Rink,  Jon and Lee,  Jasper and Li,  Yang E. and Siletti,  Kimberly and Liem,  Michelle and Claffey,  Naomi and O’Connor,  Carolyn and Yanny,  Anna Marie and Nyhus,  Julie and Dee,  Nick and Casper,  Tamara and Shapovalova,  Nadiya and Hirschstein,  Daniel and Ding,  Song-Lin and Hodge,  Rebecca and Levi,  Boaz P. and Keene,  C. Dirk and Linnarsson,  Sten and Lein,  Ed and Ren,  Bing and Behrens,  M. Margarita and Ecker,  Joseph R.},
   year = {2023},
-  month = oct 
+  month = oct
 }
 
 
@@ -2137,7 +2137,7 @@ @article{sonrel2023metaanalysis
   publisher = {Springer Science and Business Media LLC},
   author = {Sonrel,  Anthony and Luetge,  Almut and Soneson,  Charlotte and Mallona,  Izaskun and Germain,  Pierre-Luc and Knyazev,  Sergey and Gilis,  Jeroen and Gerber,  Reto and Seurinck,  Ruth and Paul,  Dominique and Sonder,  Emanuel and Crowell,  Helena L. and Fanaswala,  Imran and Al-Ajami,  Ahmad and Heidari,  Elyas and Schmeing,  Stephan and Milosavljevic,  Stefan and Saeys,  Yvan and Mangul,  Serghei and Robinson,  Mark D.},
   year = {2023},
-  month = may 
+  month = may
 }
 
 
@@ -2189,28 +2189,42 @@ @article{chari2023speciousart
   pages = {e1011288}
 }
 
-
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+@article{szalata2024transformers,
+	title = "{Transformers in single-cell omics: a review and new perspectives}",
+    author = "Szałata, Artur and Hrovatin, Karin and Becker, Sören and Tejada-Lapuerta, Alejandro and Cui, Haotian and Wang, Bo and Theis, Fabian J",
+    journal = "Nature methods",
+    publisher = "Springer Science and Business Media LLC",
+    volume =  21,
+    number =  8,
+    pages = "1430--1443",
+    month =  aug,
+    year =  2024,
+    doi = "10.1038/s41592-024-02353-z",
+    pmid =  39122952,
+    issn = "1548-7091,1548-7105",
+    language = "en"
+}
+
+@article{boiarsky2023foundationmodels,
+	title = "{A deep dive into single-cell RNA sequencing foundation models}",
+	author = "Boiarsky, Rebecca and Singh, Nalini and Buendia, Alejandro and Getz, Gad and Sontag, David",
+	journal = "bioRxiv",
+	pages = "2023.10.19.563100",
+	month =  oct,
+	year =  2023,
+	doi = "10.1101/2023.10.19.563100",
+	language = "en"
+}
+
+@article{liu2024foundationmodels,
+	title = "{Evaluating the utilities of foundation models in single-cell data analysis}",
+	author = "Liu, Tianyu and Li, Kexing and Wang, Yuge and Li, Hongyu and Zhao, Hongyu",
+	journal = "bioRxiv.org: the preprint server for biology",
+	pages = "2023.09.08.555192",
+	month =  aug,
+	year =  2024,
+	doi = "10.1101/2023.09.08.555192",
+	pmc = "PMC10925156",
+	pmid =  38464157,
+	language = "en"
 }
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results/foundation_models/index.qmd

@@ -12,11 +12,11 @@ toc: false
 
 Recent developments in deep-learning have led to the creation of several "foundation models" for single-cell data.
 These are large models that have been trained on data from millions of cells and am to fully capture the variability in the single-cell landscape.
-Typically, they use a transformer architecture and undergo self-supervised pre-training using masking of parts of the input data.
+Typically, they use a transformer architecture [@szalata2024transformers] and undergo self-supervised pre-training using masking of parts of the input data.
 Trained foundation models can then be applied to a variety of downstream tasks, either by directly feeding new data into the model or by fine-tuning to better fit a new dataset or to produce a specific output.
 The general nature of single-cell foundation models and the large amount of data they have been trained on makes them potentially powerful tools for single-cell analysis but their performance is yet to be fully established.
 
-Open Problems plans to build on the existing evaluation of foundation models by incorportating them into our continuous benchmarking framework.
+Open Problems plans to build on the existing evaluation [@boiarsky2023foundationmodels; @liu2024foundationmodels] of foundation models by incorportating them into our continuous benchmarking framework.
 Models will be included in existing tasks where they will be compared to more traditional methods.
 We also plan to compare foundation models across tasks to evaluate their flexibility and compare them to each other.