Update HIDIVE Papers (#540)

Co-authored-by: manzt <24403730+manzt@users.noreply.github.com>

assets/papers/preprints.csv

@@ -1,11 +1,8 @@
 Month,Year,Citation,PubMed ID,DOI
 10,2024,"S L'Yi, HG Zhang, AP Mar, TC Smits, L Weru, S Rojas, A Lex, N Gehlenborg, ""A comprehensive evaluation of life sciences data resources reveals significant accessibility barriers"", OSF Preprints (2024).",,10.31219/osf.io/5v98j
 10,2024,"J Kubica, S Korsak, AB Clerkin, D Kouřil, D Schirman, AD Yadavalli, K Banecki, M Kadlof, B Busby, D Plewczynski, ""The‬‭ challenge‬‭ of‬‭ chromatin‬‭ model‬‭ comparison‬‭ and‬‭ validation‬‭ a‬‭ project‬‭ from‬‭ the‬ first international 4D Nucleome Hackathon‬"", bioRxiv (2024).",,10.1101/2024.10.02.616241
-9,2024,"4D Nucleome Consortium, J Dekker, BA Oksuz, Y Zhang, Y Wang, MK Minsk, S Kuang, L Yang, JH Gibcus, N Krietenstein, OJ Rando, J Xu, DH Janssens, S Henikoff, A Kukalev, A Willemin, W Winick-Ng, R Kempfer, A Pombo, M Yu, P Kumar, L Zhang, AS Belmont, T Sasaki, T Van Schaik, L Brueckner, D Peric-Hupkes, B Van Steensel, P Wang, H Chai, M Kim, Y Ruan, R Zhang, SA Quinodoz, P Bhat, M Guttman, W Zhao, S Chien, Y Liu, SV Venev, D Plewczynski, I Irastorza Azcarate, D Szabó, CJ Thieme, T Szczepińska, M Chiliński, K Sengupta, M Conte, A Esposito, A Abraham, R Zhang, Y Wang, X Wen, Q Wu, Y Yang, J Liu, L Boninsegna, A Yildirim, Y Zhan, AM Chiariello, S Bianco, L Lee, M Hu, Y Li, RJ Barnett, AL Cook, DJ Emerson, C Marchal, P Zhao, P Park, BH Alver, A Schroeder, R Navelkar, C Bakker, W Ronchetti, S Ehmsen, A Veit, N Gehlenborg, T Wang, D Li, X Wang, M Nicodemi, B Ren, S Zhong, JE Phillips-Cremins, DM Gilbert, KS Pollard, F Alber, J Ma, WS Noble, F Yue, ""An integrated view of the structure and function of the human 4D nucleome"", bioRxiv (2024).",,10.1101/2024.09.17.613111
+9,2024,"4D Nucleome Consortium, J Dekker, BA Oksuz, Y Zhang, Y Wang, MK Minsk, S Kuang, L Yang, JH Gibcus, N Krietenstein, OJ Rando, J Xu, DH Janssens, S Henikoff, A Kukalev, A Willemin, W Winick-Ng, R Kempfer, A Pombo, M Yu, P Kumar, L Zhang, AS Belmont, T Sasaki, T Van Schaik, L Brueckner, D Peric-Hupkes, B Van Steensel, P Wang, H Chai, M Kim, Y Ruan, R Zhang, SA Quinodoz, P Bhat, M Guttman, W Zhao, S Chien, Y Liu, SV Venev, D Plewczynski, I Irastorza Azcarate, D Szabó, CJ Thieme, T Szczepińska, M Chiliński, K Sengupta, M Conte, A Esposito, A Abraham, R Zhang, Y Wang, X Wen, Q Wu, Y Yang, J Liu, L Boninsegna, A Yildirim, Y Zhan, AM Chiariello, S Bianco, L Lee, M Hu, Y Li, RJ Barnett, AL Cook, DJ Emerson, C Marchal, P Zhao, P Park, BH Alver, A Schroeder, R Navelkar, C Bakker, W Ronchetti, S Ehmsen, A Veit, N Gehlenborg, T Wang, D Li, X Wang, M Nicodemi, B Ren, S Zhong, JE Phillips-Cremins, DM Gilbert, KS Pollard, F Alber, J Ma, WS Noble, F Yue, ""An integrated view of the structure and function of the human 4D nucleome"", bioRxiv (2024).",39484446,10.1101/2024.09.17.613111
 7,2024,"L Weru, S L'Yi, TC Smits, N Gehlenborg, ""Using OpenKeyNav to Enhance the Keyboard-Accessibility of Web-based Data Visualization Tools"", OSF Preprints (2024).",,10.31219/osf.io/3wjsa
-7,2024,"TC Smits, S L'Yi, HN Nguyen, AP Mar, N Gehlenborg, ""Explaining Unfamiliar Genomics Data Visualizations to a Blind Individual through Transitions"", OSF Preprints (2024).",,10.31219/osf.io/v7mxz
-6,2024,"TC Smits, S L'Yi, AP Mar, N Gehlenborg, ""AltGosling: Automatic Generation of Text Descriptions for Accessible Genomics Data Visualization"", OSF Preprints (2024).",,10.31219/osf.io/26jvr
-6,2024,"T Manz, N Abdennur, N Gehlenborg, ""anywidget: reusable widgets for interactive analysis and visualization in computational notebooks"", OSF Preprints (2024).",,10.31219/osf.io/tw9sg
 5,2024,"V Stoiber, N Gehlenborg, W Aigner, M Streit, ""time-i-gram: A Grammar for Interactive Visualization of Time-based Data"", OSF Preprints (2024).",,10.31219/osf.io/m9ubg
 4,2024,"E Mörth, C Nielsen, M Turner, L Xianhao, MS Keller, J Beyer, H Pfister, C Zhu-Tian, N Gehlenborg, ""A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps"", OSF Preprints (2024).",,10.31219/osf.io/zka2j
 4,2024,"MS Keller, T Manz, N Gehlenborg, ""Use-Coordination: Model, Grammar, and Library for Implementation of Coordinated Multiple Views"", OSF Preprints (2024).",,10.31219/osf.io/vhs7m

assets/papers/pubs.csv

@@ -1,11 +1,14 @@
 Month,Year,Citation,PubMed ID,DOI
+11,2024,"TC Smits, S L’Yi, AP Mar, N Gehlenborg, ""AltGosling: Automatic Generation of Text Descriptions for Accessible Genomics Data Visualization"", Bioinformatics btae670 (2024).",,10.1093/bioinformatics/btae670
+10,2024,"TC Smits, S L’Yi, HN Nguyen, AP Mar, N Gehlenborg, ""Explaining Unfamiliar Genomics Data Visualizations to a Blind Individual through Transitions"", 2024 1st Workshop on Accessible Data Visualization (AccessViz) (2024).",,10.1109/AccessViz64636.2024.00010
 9,2024,"K Huang, P Chandak, Q Wang, S Havaldar, A Vaid, J Leskovec, GN Nadkarni, BS Glicksberg, N Gehlenborg, M Zitnik, ""A foundation model for clinician-centered drug repurposing"", Nature Medicine (2024).",,10.1038/s41591-024-03233-x
 9,2024,"MS Keller, I Gold, C McCallum, T Manz, PV Kharchenko, N Gehlenborg, ""Vitessce: integrative visualization of multimodal and spatially resolved single-cell data"", Nature Methods 1-5 (2024).",,10.1038/s41592-024-02436-x
 8,2024,"I Sarfraz, Y Wang, A Shastry, WK Teh, A Sokolov, BR Herb, HH Creasy, I Virshup, R Dries, K Degatano, A Mahurkar, DJ Schnell, P Madrigal, J Hilton, N Gehlenborg, T Tickle, JD Campbell, ""MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data"", Genome Biology 25(1):205 (2024).",39090672,10.1186/s13059-024-03349-w
 7,2024,"T Manz, N Gehlenborg, N Abdennur, ""Any notebook served: authoring and sharing reusable interactive widgets"", Proceedings of the 23rd Python in Science Conference (2024).",,10.25080/NRPV2311
 4,2024,"MR Hutch, J Son, TT Le, C Hong, X Wang, Z Shakeri Hossein Abad, M Morris, A Gutiérrez-Sacristán, JG Klann, A Spiridou, A Batugo, R Bellazzi, V Benoit, CL Bonzel, WA Bryant, L Chiudinelli, K Cho, P Das, T González González, DA Hanauer, DW Henderson, YL Ho, NHW Loh, A Makoudjou, S Makwana, A Malovini, B Moal, DL Mowery, A Neuraz, MJ Samayamuthu, FJ Sanz Vidorreta, ER Schriver, P Schubert, J Talbert, ALM Tan, BWL Tan, BWQ Tan, V Tibollo, P Tippman, G Verdy, W Yuan, P Avillach, N Gehlenborg, GS Omenn, The Consortium for Clinical Characterization of COVID-19 by EHR (4CE), S Visweswaran, T Cai, Y Luo, Z Xia, ""Neurological diagnoses in hospitalized COVID-19 patients associated with adverse outcomes: A multinational cohort study"", PLOS Digital Health 3(4):e0000484 (2024).",38620037,10.1371/journal.pdig.0000484
 1,2024,"DL Gisch, M Brennan, BB Lake, J Basta, MS Keller, R Melo Ferreira, S Akilesh, R Ghag, C Lu, YH Cheng, KS Collins, SV Parikh, BH Rovin, L Robbins, L Stout, KY Conklin, D Diep, B Zhang, A Knoten, D Barwinska, M Asghari, AR Sabo, MJ Ferkowicz, TA Sutton, KJ Kelly, IH De Boer, SE Rosas, K Kiryluk, JB Hodgin, F Alakwaa, S Winfree, N Jefferson, A Türkmen, JP Gaut, N Gehlenborg, CL Phillips, TM El-Achkar, PC Dagher, T Hato, K Zhang, J Himmelfarb, M Kretzler, S Mollah, the Kidney Precision Medicine Project (KPMP), B Lake, A Morales, I Stillman, S Lecker, S Bogen, A Verma, G Yu, I Schmidt, J Henderson, L Beck, P Yadati, S Waikar, AA Amodu, S Maikhor, T Ilori, MR Colona, A Weins, G McMahon, N Hacohen, A Greka, JL Marshall, PJ Hoover, VS Viswanathan, D Crawford, M Aulisio, W Bush, Y Chen, A Madabhushi, C O’Malley, C Gadegbeku, D Sendrey, E Poggio, J O’Toole, J Sedor, J Taliercio, L Bush, L Herlitz, E Palmer, J Nguyen, K Spates-Harden, L Cooperman, S Jolly, C Vinovskis, A Bomback, J Barasch, K Kiryluk, P Appelbaum, V D’Agati, C Berrouet, K Mehl, M Sabatello, N Shang, O Balderes, PA Canetta, S Kudose, J De Pinho Gonçalves, L Migas, R Van De Plas, R Lardenoije, L Barisoni, H Rennke, A Verdoes, A Sabo, DL Gisch, J Williams, K Kelly, K Dunn, M Eadon, M Ferkowicz, P Dagher, S Winfree, S Bledsoe, S Wofford, T Sutton, W Bowen, A Slade, E Record, Y Cheng, Y Jain, B Herr, E Quardokus, A Wang, CPC Villalobos, C Parikh, M Atta, S Menez, Y Wen, A Xu, L Bernard, C Johansen, S Chen, S Rosas, I Donohoe, J Sun, R Knight, A Shpigel, J Bebiak, J Saul, J Ardayfio, R Koewler, R Pinkeney, T Campbell, E Azeloglu, G Nadkarni, J He, J Tokita, K Campbell, M Patel, S Lefferts, SR Iyengar, S Ward, S Coca, C He, Y Xiong, P Prasad, B Rovin, JP Shapiro, S Parikh, SM Madhavan, J Lukowski, D Velickovic, L Pasa-Tolic, G Oliver, O Troyanskaya, R Sealfon, W Mao, A Wong, A Pollack, Y Goltsev, B Ginley, B Lutnick, G Nolan, K Anjani, T Mukatash, ZG Laszik, B Campos, B Thajudeen, D Beyda, E Bracamonte, F Brosius, G Woodhead, K Mendoza, N Marquez, R Scott, R Tsosie, M Saunders, A Rike, ES Woodle, PJ Lee, RR Alloway, T Shi, E Hsieh, J Kendrick, J Thurman, J Wrobel, L Pyle, P Bjornstad, N Lucarelli, P Sarder, A Renteria, A Ricardo, A Srivastava, D Redmond, E Carmona-Powell, J Bui, J Lash, M Fox, N Meza, R Gaba, S Setty, T Kelly, C Lienczewski, D Demeke, E Otto, H Ascani, J Hodgin, J Schaub, J Hartman, L Mariani, M Bitzer, M Rose, N Bonevich, N Conser, P McCown, R Dull, R Menon, R Reamy, S Eddy, U Balis, V Blanc, V Nair, YO He, Z Wright, B Steck, J Luo, R Frey, A Coleman, D Henderson-Brown, J Berge, ML Caramori, O Adeyi, P Nachman, S Safadi, S Flanagan, S Ma, S Klett, S Wolf, T Harindhanavudhi, V Rao, A Mottl, A Froment, E Zeitler, P Bream, S Kelley, M Rosengart, M Elder, P Palevsky, R Murugan, DE Hall, F Bender, J Winters, JA Kellum, M Gilliam, M Tublin, R Tan, G Zhang, K Sharma, M Venkatachalam, A Hendricks, A Kermani, J Torrealba, M Vazquez, N Wang, Q Cai, RT Miller, S Ma, S Hedayati, A Hoofnagle, A Wangperawong, A Berglund, AL Dighe, B Young, B Larson, B Berry, C Alpers, C Limonte, C Stutzke, G Roberts, I De Boer, J Snyder, J Phuong, J Carson, K Rezaei, K Tuttle, K Brown, K Blank, N Sarkisova, N Jefferson, R McClelland, S Mooney, Y Nam, A Wilcox, C Park, F Dowd, K Williams, SM Grewenow, S Daniel, S Shankland, A Pamreddy, H Ye, R Montellano, S Bansal, A Pillai, D Zhang, H Park, J Patel, K Sambandam, M Basit, N Wen, OW Moe, RD Toto, SC Lee, K Sharman, RM Caprioli, A Fogo, J Allen, J Spraggins, K Djambazova, M De Caestecker, M Dufresne, M Farrow, A Vijayan, B Minor, G Nwanne, J Gaut, K Conlon, M Kaushal, SM Diettman, AM Victoria Castro, D Moledina, FP Wilson, G Moeckel, L Cantley, M Shaw, V Kakade, T Arora, S Jain, M Rauchman, MT Eadon, ""The chromatin landscape of healthy and injured cell types in the human kidney"", Nature Communications 15(1):433 (2024).",38199997,10.1038/s41467-023-44467-6
 1,2024,"L Taing, A Dandawate, S L’Yi, N Gehlenborg, M Brown, CA Meyer, ""Cistrome Data Browser: integrated search, analysis and visualization of chromatin data"", Nucleic Acids Research 52(D1):D61-D66 (2024).",37971305,10.1093/nar/gkad1069
+,2024,"T Manz, N Abdennur, N Gehlenborg, ""anywidget: reusable widgets for interactive analysis and visualization in computational notebooks"", Journal of Open Source Software 9(102):6939 (2024).",,10.21105/joss.06939
 ,2024,"T Manz, F Lekschas, E Greene, G Finak, N Gehlenborg, ""A General Framework for Comparing Embedding Visualizations Across Class-Label Hierarchies"", IEEE Transactions on Visualization and Computer Graphics 1-11 (2024).",,10.1109/TVCG.2024.3456370
 ,2024,"S L'Yi, A van den Brandt, E Adams, HN Nguyen, N Gehlenborg, ""Learnable and Expressive Visualization Authoring through Blended Interfaces"", IEEE Transactions on Visualization and Computer Graphics 1-11 (2024).",,10.1109/TVCG.2024.3456598
 ,2024,"E Mörth, K Sidak, Z Maliga, T Möller, N Gehlenborg, P Sorger, H Pfister, J Beyer, R Krüger, ""Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data"", IEEE Transactions on Visualization and Computer Graphics 1-11 (2024).",,10.1109/TVCG.2024.3456406