diff --git a/_data/people.yml b/_data/people.yml index 73df7e6..dbd54d6 100644 --- a/_data/people.yml +++ b/_data/people.yml @@ -262,12 +262,6 @@ id: BlakeBunney alum: false -- name: Haarika Kathi - pos: Technician - email: hkathi@wi.mit.edu - id: HaarikaKathi - alum: false - - name: Emily He pos: Technician email: ehe@wi.mit.edu @@ -736,7 +730,8 @@ pos: Post-doc id: Gene-WeiLi alum: true - now: PI & Associate Professor of Biology | Massachusetts Institute of Technology + now: PI, Associate Professor of Biology & HHMI Investigator | Massachusetts Institute + of Technology & HHMI - name: Han Li pos: Technician diff --git a/_data/publications.yml b/_data/publications.yml index 9ed6af2..34f1a5d 100644 --- a/_data/publications.yml +++ b/_data/publications.yml @@ -1,3 +1,71 @@ +- title: High-quality peptide evidence for annotating non-canonical open reading frames + as human proteins. + authors: + - Eric W Deutsch + - Leron W Kok + - Jonathan M Mudge + - Jorge Ruiz-Orera + - Ivo Fierro-Monti + - Zhi Sun + - Jennifer G Abelin + - M Mar Alba + - Julie L Aspden + - Ariel A Bazzini + - Elspeth A Bruford + - Marie A Brunet + - Lorenzo Calviello + - Steven A Carr + - Anne-Ruxandra Carvunis + - Sonia Chothani + - Jim Clauwaert + - Kellie Dean + - Pouya Faridi + - Adam Frankish + - Norbert Hubner + - Nicholas T Ingolia + - Michele Magrane + - Maria Jesus Martin + - Thomas F Martinez + - Gerben Menschaert + - Uwe Ohler + - Sandra Orchard + - Owen Rackham + - Xavier Roucou + - Sarah A Slavoff + - Eivind Valen + - Aaron Wacholder + - Jonathan S Weissman + - Wei Wu + - Zhi Xie + - Jyoti Choudhary + - Michal Bassani-Sternberg + - "Juan Antonio Vizca\xEDno" + - Nicola Ternette + - Robert L Moritz + - John R Prensner + - Sebastiaan van Heesch + publication_date: 24/09/24 + publication_year: '2024' + pubmed_id: '39314370' + abstract: 'A major scientific drive is to characterize the protein-coding genome + as it provides the primary basis for the study of human health. But the fundamental + question remains: what has been missed in prior genomic analyses? Over the past + decade, the translation of non-canonical open reading frames (ncORFs) has been + observed across human cell types and disease states, with major implications for + proteomics, genomics, and clinical science. However, the impact of ncORFs has + been limited by the absence of a large-scale understanding of their contribution + to the human proteome. Here, we report the collaborative efforts of stakeholders + in proteomics, immunopeptidomics, Ribo-seq ORF discovery, and gene annotation, + to produce a consensus landscape of protein-level evidence for ncORFs. We show + that at least 25% of a set of 7,264 ncORFs give rise to translated gene products, + yielding over 3,000 peptides in a pan-proteome analysis encompassing 3.8 billion + mass spectra from 95,520 experiments. With these data, we developed an annotation + framework for ncORFs and created public tools for researchers through GENCODE + and PeptideAtlas. This work will provide a platform to advance ncORF-derived proteins + in biomedical discovery and, beyond humans, diverse animals and plants where ncORFs + are similarly observed.' + doi: 10.1101/2024.09.09.612016 + journal: biorxiv - title: Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling. authors: diff --git a/compile_info.ipynb b/compile_info.ipynb index c4e875e..cab966b 100644 --- a/compile_info.ipynb +++ b/compile_info.ipynb @@ -62,7 +62,7 @@ { "data": { "text/plain": [ - "266" + "268" ] }, "execution_count": 2, @@ -199,6 +199,28 @@ "
\n", "263 rows × 8 columns
\n", + "266 rows × 8 columns
\n", "" ], "text/plain": [ " title \\\n", - "0 Transcriptome-wide characterization of genetic... \n", - "1 Brainwide silencing of prion protein by AAV-me... \n", - "2 Nucleotide depletion promotes cell fate transi... \n", - "3 CRISPRi screens identify the lncRNA, LOUP, as ... \n", - "4 Triaging of α-helical proteins to the mitochon... \n", + "0 Robustness and reliability of single-cell regu... \n", + "1 Multi-species genome-wide CRISPR screens ident... \n", + "2 Transcriptome-wide characterization of genetic... \n", + "3 Brainwide silencing of prion protein by AAV-me... \n", + "4 Nucleotide depletion promotes cell fate transi... \n", ".. ... \n", - "258 Generation of prion transmission barriers by m... \n", - "259 Directed evolution of substrate-optimized GroE... \n", - "260 The FAD- and O(2)-dependent reaction cycle of ... \n", - "261 Origins and kinetic consequences of diversity ... \n", - "262 The utility of prions. \n", + "261 Generation of prion transmission barriers by m... \n", + "262 Directed evolution of substrate-optimized GroE... \n", + "263 The FAD- and O(2)-dependent reaction cycle of ... \n", + "264 Origins and kinetic consequences of diversity ... \n", + "265 The utility of prions. \n", "\n", " authors publication_date \\\n", - "0 [Ajay Nadig, Joseph M Replogle, Angela N Pogso... 15/07/24 \n", - "1 [Edwin N Neumann, Tessa M Bertozzi, Elaine Wu,... 27/06/24 \n", - "2 [Brian T Do, Peggy P Hsu, Sidney Y Vermeulen, ... 02/06/24 \n", - "3 [Haley Halasz, Eric Malekos, Sergio Covarrubia... 23/05/24 \n", - "4 [Gayathri Muthukumar, Taylor A Stevens, Alison... 02/03/24 \n", + "0 [Chen Weng, Jonathan S Weissman, Vijay G Sanka... 04/09/24 \n", + "1 [Breanna Lam, Kathrin M Kajderowicz, Heather R... 02/08/24 \n", + "2 [Ajay Nadig, Joseph M Replogle, Angela N Pogso... 15/07/24 \n", + "3 [Edwin N Neumann, Tessa M Bertozzi, Elaine Wu,... 27/06/24 \n", + "4 [Brian T Do, Peggy P Hsu, Sidney Y Vermeulen, ... 02/06/24 \n", ".. ... ... \n", - "258 [Peter Chien, Angela H DePace, Sean R Collins,... 22/08/03 \n", - "259 [Jue D Wang, Christophe Herman, Kimberly A Tip... 01/01/03 \n", - "260 [Benjamin P Tu, Jonathan S Weissman] 28/11/02 \n", - "261 [Angela H DePace, Jonathan S Weissman] 09/04/02 \n", - "262 [Lev Z Osherovich, Jonathan S Weissman] 08/02/02 \n", + "261 [Peter Chien, Angela H DePace, Sean R Collins,... 22/08/03 \n", + "262 [Jue D Wang, Christophe Herman, Kimberly A Tip... 01/01/03 \n", + "263 [Benjamin P Tu, Jonathan S Weissman] 28/11/02 \n", + "264 [Angela H DePace, Jonathan S Weissman] 09/04/02 \n", + "265 [Lev Z Osherovich, Jonathan S Weissman] 08/02/02 \n", "\n", " publication_year pubmed_id \\\n", - "0 2024 39005298 \n", - "1 2024 38935715 \n", - "2 2024 38823395 \n", - "3 2024 38781216 \n", - "4 2024 38428433 \n", + "0 2024 39229039 \n", + "1 2024 39091747 \n", + "2 2024 39005298 \n", + "3 2024 38935715 \n", + "4 2024 38823395 \n", ".. ... ... \n", - "258 2003 12931190 \n", - "259 2003 12507429 \n", - "260 2002 12453408 \n", - "261 2002 11938354 \n", - "262 2002 11832240 \n", + "261 2003 12931190 \n", + "262 2003 12507429 \n", + "263 2002 12453408 \n", + "264 2002 11938354 \n", + "265 2002 11832240 \n", "\n", " abstract \\\n", - "0 Single cell CRISPR screens such as Perturb-seq... \n", - "1 Prion disease is caused by misfolding of the p... \n", - "2 Control of cellular identity requires coordina... \n", - "3 Long noncoding RNAs (lncRNAs) account for the ... \n", - "4 Mitochondrial outer membrane ⍺-helical protein... \n", + "0 The detection of mitochondrial DNA (mtDNA) mut... \n", + "1 Cells must adapt to environmental changes to m... \n", + "2 Single cell CRISPR screens such as Perturb-seq... \n", + "3 Prion disease is caused by misfolding of the p... \n", + "4 Control of cellular identity requires coordina... \n", ".. ... \n", - "258 Self-propagating beta-sheet-rich protein aggre... \n", - "259 GroEL/S chaperonin ring complexes fold many un... \n", - "260 The endoplasmic reticulum (ER) supports disulf... \n", - "261 A remarkable feature of prions is that infecti... \n", - "262 Infectious, self-propagating protein aggregate... \n", + "261 Self-propagating beta-sheet-rich protein aggre... \n", + "262 GroEL/S chaperonin ring complexes fold many un... \n", + "263 The endoplasmic reticulum (ER) supports disulf... \n", + "264 A remarkable feature of prions is that infecti... \n", + "265 Infectious, self-propagating protein aggregate... \n", "\n", " doi journal \n", - "0 10.1101/2024.07.03.601903 biorxiv \n", - "1 10.1126/science.ado7082 Science \n", - "2 10.1016/j.devcel.2024.05.010 Developmental cell \n", - "3 10.1073/pnas.2322524121 PNAS \n", - "4 10.1016/j.molcel.2024.01.028 Molecular cell \n", + "0 10.1101/2024.08.23.609473 biorxiv \n", + "1 10.1101/2024.07.25.605098 biorxiv \n", + "2 10.1101/2024.07.03.601903 biorxiv \n", + "3 10.1126/science.ado7082 Science \n", + "4 10.1016/j.devcel.2024.05.010 Developmental cell \n", ".. ... ... \n", - "258 10.1038/nature01894 Nature \n", - "259 10.1016/s0092-8674(02)01198-4 Cell \n", - "260 10.1016/s1097-2765(02)00696-2 Molecular cell \n", - "261 10.1038/nsb786 Nature structural biology \n", - "262 10.1016/s1534-5807(02)00118-1 Developmental cell \n", + "261 10.1038/nature01894 Nature \n", + "262 10.1016/s0092-8674(02)01198-4 Cell \n", + "263 10.1016/s1097-2765(02)00696-2 Molecular cell \n", + "264 10.1038/nsb786 Nature structural biology \n", + "265 10.1016/s1534-5807(02)00118-1 Developmental cell \n", "\n", - "[263 rows x 8 columns]" + "[266 rows x 8 columns]" ] }, "execution_count": 8, @@ -451,17 +451,17 @@ " \n", "104 rows × 9 columns
\n", + "106 rows × 9 columns
\n", "" ], "text/plain": [ " title \\\n", - "93 Combinatorial genetics in liver repopulation a... \n", - "355 Combinatorial genetics in liver repopulation a... \n", - "122 Targeting the AAA ATPase p97 as an Approach to... \n", - "384 Targeting the AAA ATPase p97 as an Approach to... \n", - "428 Ribosome profiling provides evidence that larg... \n", + "361 Combinatorial genetics in liver repopulation a... \n", + "96 Combinatorial genetics in liver repopulation a... \n", + "390 Targeting the AAA ATPase p97 as an Approach to... \n", + "125 Targeting the AAA ATPase p97 as an Approach to... \n", + "434 Ribosome profiling provides evidence that larg... \n", ".. ... \n", - "390 Pharmacological dimerization and activation of... \n", - "124 Paradoxical resistance of multiple myeloma to ... \n", - "386 Paradoxical resistance of multiple myeloma to ... \n", - "354 The Human Cell Atlas. \n", - "92 The Human Cell Atlas. \n", + "131 Pharmacological dimerization and activation of... \n", + "127 Paradoxical resistance of multiple myeloma to ... \n", + "392 Paradoxical resistance of multiple myeloma to ... \n", + "95 The Human Cell Atlas. \n", + "360 The Human Cell Atlas. \n", "\n", " authors publication_date \\\n", - "93 [Kirk J Wangensteen, Yue J Wang, Zhixun Dou, A... 02/11/17 \n", - "355 [Kirk J Wangensteen, Yue J Wang, Zhixun Dou, A... 02/11/17 \n", - "122 [Daniel J Anderson, Ronan Le Moigne, Stevan Dj... 12/11/15 \n", - "384 [Daniel J Anderson, Ronan Le Moigne, Stevan Dj... 12/11/15 \n", - "428 [Mitchell Guttman, Pamela Russell, Nicholas T ... 03/07/13 \n", + "361 [Kirk J Wangensteen, Yue J Wang, Zhixun Dou, A... 02/11/17 \n", + "96 [Kirk J Wangensteen, Yue J Wang, Zhixun Dou, A... 02/11/17 \n", + "390 [Daniel J Anderson, Ronan Le Moigne, Stevan Dj... 12/11/15 \n", + "125 [Daniel J Anderson, Ronan Le Moigne, Stevan Dj... 12/11/15 \n", + "434 [Mitchell Guttman, Pamela Russell, Nicholas T ... 03/07/13 \n", ".. ... ... \n", - "390 [Carmela Sidrauski, Jordan C Tsai, Martin Kamp... 16/04/15 \n", - "124 [Diego Acosta-Alvear, Min Y Cho, Thomas Wild, ... 04/09/15 \n", - "386 [Diego Acosta-Alvear, Min Y Cho, Thomas Wild, ... 04/09/15 \n", - "354 [Aviv Regev, Sarah A Teichmann, Eric S Lander,... 06/12/17 \n", - "92 [Aviv Regev, Sarah A Teichmann, Eric S Lander,... 06/12/17 \n", + "131 [Carmela Sidrauski, Jordan C Tsai, Martin Kamp... 16/04/15 \n", + "127 [Diego Acosta-Alvear, Min Y Cho, Thomas Wild, ... 04/09/15 \n", + "392 [Diego Acosta-Alvear, Min Y Cho, Thomas Wild, ... 04/09/15 \n", + "95 [Aviv Regev, Sarah A Teichmann, Eric S Lander,... 06/12/17 \n", + "360 [Aviv Regev, Sarah A Teichmann, Eric S Lander,... 06/12/17 \n", "\n", " publication_year pubmed_id \\\n", - "93 2017 29091290 \n", - "355 2017 29091290 \n", - "122 2015 26555175 \n", - "384 2015 26555175 \n", - "428 2013 23810193 \n", + "361 2017 29091290 \n", + "96 2017 29091290 \n", + "390 2015 26555175 \n", + "125 2015 26555175 \n", + "434 2013 23810193 \n", ".. ... ... \n", - "390 2015 25875391 \n", - "124 2015 26327694 \n", - "386 2015 26327694 \n", - "354 2017 29206104 \n", - "92 2017 29206104 \n", + "131 2015 25875391 \n", + "127 2015 26327694 \n", + "392 2015 26327694 \n", + "95 2017 29206104 \n", + "360 2017 29206104 \n", "\n", " abstract \\\n", - "93 Clustered regularly interspaced short palindro... \n", - "355 Clustered regularly interspaced short palindro... \n", - "122 p97 is a AAA-ATPase with multiple cellular fun... \n", - "384 p97 is a AAA-ATPase with multiple cellular fun... \n", - "428 Large noncoding RNAs are emerging as an import... \n", + "361 Clustered regularly interspaced short palindro... \n", + "96 Clustered regularly interspaced short palindro... \n", + "390 p97 is a AAA-ATPase with multiple cellular fun... \n", + "125 p97 is a AAA-ATPase with multiple cellular fun... \n", + "434 Large noncoding RNAs are emerging as an import... \n", ".. ... \n", - "390 The general translation initiation factor eIF2... \n", - "124 Hallmarks of cancer, including rapid growth an... \n", - "386 Hallmarks of cancer, including rapid growth an... \n", - "354 The recent advent of methods for high-throughp... \n", - "92 The recent advent of methods for high-throughp... \n", + "131 The general translation initiation factor eIF2... \n", + "127 Hallmarks of cancer, including rapid growth an... \n", + "392 Hallmarks of cancer, including rapid growth an... \n", + "95 The recent advent of methods for high-throughp... \n", + "360 The recent advent of methods for high-throughp... \n", "\n", " doi journal update \n", - "93 10.1002/hep.29626 Hepatology (Baltimore, Md.) current \n", - "355 10.1002/hep.29626 Hepatology previous \n", - "122 10.1016/j.ccell.2015.10.002 Cancer cell current \n", - "384 10.1016/j.ccell.2015.10.002 Cancer cell previous \n", - "428 10.1016/j.cell.2013.06.009 Cell previous \n", + "361 10.1002/hep.29626 Hepatology previous \n", + "96 10.1002/hep.29626 Hepatology (Baltimore, Md.) current \n", + "390 10.1016/j.ccell.2015.10.002 Cancer cell previous \n", + "125 10.1016/j.ccell.2015.10.002 Cancer cell current \n", + "434 10.1016/j.cell.2013.06.009 Cell previous \n", ".. ... ... ... \n", - "390 10.7554/eLife.07314 eLife previous \n", - "124 10.7554/eLife.08153 eLife current \n", - "386 10.7554/eLife.08153 eLife previous \n", - "354 10.7554/eLife.27041 eLife previous \n", - "92 10.7554/eLife.27041 eLife current \n", + "131 10.7554/eLife.07314 eLife current \n", + "127 10.7554/eLife.08153 eLife current \n", + "392 10.7554/eLife.08153 eLife previous \n", + "95 10.7554/eLife.27041 eLife current \n", + "360 10.7554/eLife.27041 eLife previous \n", "\n", - "[104 rows x 9 columns]" + "[106 rows x 9 columns]" ] }, "execution_count": 11, @@ -854,7 +838,7 @@ " \n", " \n", "