update published papers

Author: mjke

_data/papers.csv

@@ -1,17 +1,17 @@
 id,title,journal,date,authors,link,doi_suffix,preprint_url,preprint_journal,jekyll_date,type
+10.1021.acs.jcim.4c01876,Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation,J Chem Inf Model,2025 Feb 24,"Nogueira VHR, Sharma R, Guido RVC, Keiser MJ",https://doi.org/10.1021/acs.jcim.4c01876,10.1021/acs.jcim.4c01876,https://doi.org/10.26434/chemrxiv-2024-ffcrs,chemRxiv,2025-02-24,ncbi
 bioRxiv.2025.02.04.636489,Network-aware self-supervised learning enables high-content phenotypic screening for genetic modifiers of neuronal activity dynamics,bioRxiv,2025 Feb 05,"Grosjean P, Shevade K, Nguyen C, Ancheta S, Mader K, Franco I, Heo SJ, Lewis G, Boggess S, De Domenico A, Ullian E, Shafer S, Litterman A, Przybyla L, Keiser MJ, Ifkovits J, Yala A, Kampmann N",,10.1101/2025.02.04.636489,https://doi.org/10.1101/2025.02.04.636489,bioRxiv,2025-02-05,preprint
+10.1371.journal.pcbi.1012841,ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization,PLoS Comput Biol,2025 Feb,"Gunsalus LM, Keiser MJ, Pollard KS",https://doi.org/10.1371/journal.pcbi.1012841,10.1371/journal.pcbi.1012841,https://doi.org/10.1101/2023.11.22.568268,bioRxiv,2025-02-01,ncbi
 chemRxiv.chemrxiv-2024-7p4ws,Autoparty: Machine learning-guided visual inspection of molecular docking results,chemRxiv,2024 Dec 09,"Shub L, Korczynska M, Muir DF, Lin F-Y, Mathiowetz AM, Keiser MJ",,10.26434/chemrxiv-2024-7p4ws,https://doi.org/10.26434/chemrxiv-2024-7p4ws,chemRxiv,2024-12-09,preprint
 10.1038.s41467-024-54375-y,Deep phenotypic profiling of neuroactive drugs in larval zebrafish,Nat Commun,2024 Nov 17,"Gendelev L, Taylor J, Myers-Turnbull D, Chen S, McCarroll MN, Arkin MR, Kokel D, Keiser MJ",https://doi.org/10.1038/s41467-024-54375-y,10.1038/s41467-024-54375-y,https://doi.org/10.1101/2024.02.22.581657,bioRxiv,2024-11-17,ncbi
 bioRxiv.2024.10.23.619915,Evolutionary-scale enzymology enables biochemical constant prediction across a multi-peaked catalytic landscape,bioRxiv,2024 Oct 25,"Muir DF, Asper GPR, Notin P, Posner JA, Marks DS, Keiser MJ, Pinney MM",,10.1101/2024.10.23.619915,https://doi.org/10.1101/2024.10.23.619915,bioRxiv,2024-10-25,preprint
 10.1021.acs.jcim.4c00683,Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds,J Chem Inf Model,2024 Oct 14,"Hall BW, Keiser MJ",https://doi.org/10.1021/acs.jcim.4c00683,10.1021/acs.jcim.4c00683,https://doi.org/10.26434/chemrxiv-2024-qsdd1,chemRxiv,2024-10-14,ncbi
 10.1038.s42003-024-06865-4,Learning chemical sensitivity reveals mechanisms of cellular response,Commun Biol,2024 Sep 15,"Connell W, Garcia K, Goodarzi H, Keiser MJ",https://doi.org/10.1038/s42003-024-06865-4,10.1038/s42003-024-06865-4,https://doi.org/10.1101/2023.08.26.554851,bioRxiv,2024-09-15,ncbi
 bioRxiv.2024.09.12.612732,Machine-learning convergent melanocytic morphology despite noisy archival slides,bioRxiv,2024 Sep 12,"Tada M, Gaskins G, Ghandian S, Mew N, Keiser MJ, Keiser ES",,10.1101/2024.09.12.612732,https://doi.org/10.1101/2024.09.12.612732,bioRxiv,2024-09-12,preprint
 10.1021.acs.jcim.4c00311,Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks,J Chem Inf Model,2024 Jul 22,"Gale-Day ZJ, Shub L, Chuang KV, Keiser MJ",https://doi.org/10.1021/acs.jcim.4c00311,10.1021/acs.jcim.4c00311,https://doi.org/10.26434/chemrxiv-2024-hznxh,chemRxiv,2024-07-22,ncbi
-chemRxiv.chemrxiv-2024-ffcrs,Fuzz testing molecular representation using deep variational anomaly generation,chemRxiv,2024 Jul 11,"Nogueira VHR, Sharma R, Guido RVC, Keiser MJ",,10.26434/chemrxiv-2024-ffcrs,https://doi.org/10.26434/chemrxiv-2024-ffcrs,chemRxiv,2024-07-11,preprint
 bioRxiv.2024.05.15.594372,Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations,bioRxiv,2024 May 15,"Ghandian S, Albarghouthi L, Nava K, Sharma SRR, Minaud L, Beckett L, Saito N, DeCarli C, Rissman RA, Teich AF, Jin LW, Dugger BN, Keiser MJ",,10.1101/2024.05.15.594372,https://doi.org/10.1101/2024.05.15.594372,bioRxiv,2024-05-15,preprint
 bioRxiv.024.03.18.585639,Metric Ion Classification (MIC): A deep learning tool for assigning ions and waters in cryo-EM and x-ray crystallography structures,bioRxiv,2024 Mar 19,"Shub L, Liu W, Skiniotis G, Keiser MJ, Robertson MJ",,10.1101/2024.03.18.585639,https://doi.org/10.1101/2024.03.18.585639,bioRxiv,2024-03-19,preprint
 10.1186.s40478-023-01691-x,Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles,Acta Neuropathol Commun,2023 Dec 18,"Vizcarra JC, Pearce TM, Dugger BN, Keiser MJ, Gearing M, Crary JF, Kiely EJ, Morris M, White B, Glass JD, Farrell K, Gutman DA",https://doi.org/10.1186/s40478-023-01691-x,10.1186/s40478-023-01691-x,,,2023-12-18,ncbi
-bioRxiv.2023.11.22.568268,ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization,bioRxiv,2023 Nov 22,"Gunsalus LM, Keiser MJ, Pollard KS",,10.1101/2023.11.22.568268,https://doi.org/10.1101/2023.11.22.568268,bioRxiv,2023-11-22,preprint
 arXiv_-_NeurIPS_GenBio.2401.05370,Autoregressive fragment-based diffusion for pocket-aware ligand design,arXiv - NeurIPS GenBio,2023 Nov 2,"Ghorbani M, Gendelev L, Beroza P, Keiser MJ",,10.48550/arXiv.2401.05370,https://arxiv.org/abs/2401.05370,arXiv - NeurIPS GenBio,2023-11-02,preprint
 10.1016.j.xgen.2023.100410,In silico discovery of repetitive elements as key sequence determinants of 3D genome folding,Cell Genom,2023 Oct 11,"Gunsalus LM, Keiser MJ, Pollard KS",https://doi.org/10.1016/j.xgen.2023.100410,10.1016/j.xgen.2023.100410,https://doi.org/10.1101/2022.08.11.503410,bioRxiv,2023-10-11,ncbi
 10.1038.s42003-023-05031-6,Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels,Commun Biol,2023 Jun 24,"Wong DR, Magaki SD, Vinters HV, Yong WH, Monuki ES, Williams CK, Martini AC, DeCarli C, Khacherian C, Graff JP, Dugger BN, Keiser MJ",https://doi.org/10.1038/s42003-023-05031-6,10.1038/s42003-023-05031-6,https://www.biorxiv.org/content/10.1101/2023.01.13.524019,bioRxiv,2023-06-24,ncbi

_pages/publications.md

@@ -11,6 +11,23 @@ intro:
     - title: Publications
 feature_row0:
 
+  - image_path: /assets/images/papers/10.1021.acs.jcim.4c01876.jpg
+    alt: >-
+        Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation
+    title: >-
+        <span itemprop="name">Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation</span>
+    excerpt: >-
+        <span itemprop="isPartOf" itemscope itemtype="http://schema.org/Periodical"><strong>J Chem Inf Model</strong></span>. <span itemprop="datePublished">2025 Feb 24</span>. <span itemprop="author">Nogueira VHR, Sharma R, Guido RVC, Keiser MJ</span>.
+    url: "https://doi.org/10.1021/acs.jcim.4c01876"
+    doi: "10.1021/acs.jcim.4c01876"
+    btn_label: >-
+        doi &nbsp; <i class="fas fa-external-link-alt"></i>
+    btn_class: "btn--primary"
+    url2: "https://doi.org/10.26434/chemrxiv-2024-ffcrs"
+    btn2_label: >-
+        chemRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
+    btn2_class: "btn--info"
+
   - image_path: /assets/images/papers/bioRxiv.2025.02.04.636489.jpg
     alt: >-
         Network-aware self-supervised learning enables high-content phenotypic screening for genetic modifiers of neuronal activity dynamics
@@ -28,6 +45,25 @@ feature_row0:
         bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
     btn2_class: "btn--info"
 
+  - image_path: /assets/images/papers/10.1371.journal.pcbi.1012841.jpg
+    alt: >-
+        ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization
+    title: >-
+        <span itemprop="name">ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization</span>
+    excerpt: >-
+        <span itemprop="isPartOf" itemscope itemtype="http://schema.org/Periodical"><strong>PLoS Comput Biol</strong></span>. <span itemprop="datePublished">2025 Feb</span>. <span itemprop="author">Gunsalus LM, Keiser MJ, Pollard KS</span>.
+    url: "https://doi.org/10.1371/journal.pcbi.1012841"
+    doi: "10.1371/journal.pcbi.1012841"
+    btn_label: >-
+        doi &nbsp; <i class="fas fa-external-link-alt"></i>
+    btn_class: "btn--primary"
+    url2: "https://doi.org/10.1101/2023.11.22.568268"
+    btn2_label: >-
+        bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
+    btn2_class: "btn--info"
+
+feature_row1:
+
   - image_path: /assets/images/papers/chemRxiv.chemrxiv-2024-7p4ws.jpg
     alt: >-
         Autoparty: Machine learning-guided visual inspection of molecular docking results
@@ -62,8 +98,6 @@ feature_row0:
         bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
     btn2_class: "btn--info"
 
-feature_row1:
-
   - image_path: /assets/images/papers/bioRxiv.2024.10.23.619915.jpg
     alt: >-
         Evolutionary-scale enzymology enables biochemical constant prediction across a multi-peaked catalytic landscape
@@ -81,6 +115,8 @@ feature_row1:
         bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
     btn2_class: "btn--info"
 
+feature_row2:
+
   - image_path: /assets/images/papers/10.1021.acs.jcim.4c00683.jpg
     alt: >-
         Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds
@@ -115,8 +151,6 @@ feature_row1:
         bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
     btn2_class: "btn--info"
 
-feature_row2:
-
   - image_path: /assets/images/papers/bioRxiv.2024.09.12.612732.jpg
     alt: >-
         Machine-learning convergent melanocytic morphology despite noisy archival slides
@@ -134,6 +168,8 @@ feature_row2:
         bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
     btn2_class: "btn--info"
 
+feature_row3:
+
   - image_path: /assets/images/papers/10.1021.acs.jcim.4c00311.jpg
     alt: >-
         Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks
@@ -151,25 +187,6 @@ feature_row2:
         chemRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
     btn2_class: "btn--info"
 
-  - image_path: /assets/images/papers/chemRxiv.chemrxiv-2024-ffcrs.jpg
-    alt: >-
-        Fuzz testing molecular representation using deep variational anomaly generation
-    title: >-
-        <span itemprop="name">Fuzz testing molecular representation using deep variational anomaly generation</span>
-    excerpt: >-
-        <span itemprop="isPartOf" itemscope itemtype="http://schema.org/Periodical"><strong>chemRxiv</strong></span>. <span itemprop="datePublished">2024 Jul 11</span>. <span itemprop="author">Nogueira VHR, Sharma R, Guido RVC, Keiser MJ</span>.
-    url: ""
-    doi: "10.26434/chemrxiv-2024-ffcrs"
-    btn_label: >-
-        doi &nbsp; <i class="fas fa-external-link-alt"></i>
-    btn_class: "btn--primary"
-    url2: "https://doi.org/10.26434/chemrxiv-2024-ffcrs"
-    btn2_label: >-
-        chemRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
-    btn2_class: "btn--info"
-
-feature_row3:
-
   - image_path: /assets/images/papers/bioRxiv.2024.05.15.594372.jpg
     alt: >-
         Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations
@@ -204,6 +221,8 @@ feature_row3:
         bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
     btn2_class: "btn--info"
 
+feature_row4:
+
   - image_path: /assets/images/papers/10.1186.s40478-023-01691-x.jpg
     alt: >-
         Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles
@@ -217,25 +236,6 @@ feature_row3:
         doi &nbsp; <i class="fas fa-external-link-alt"></i>
     btn_class: "btn--primary"
 
-feature_row4:
-
-  - image_path: /assets/images/papers/bioRxiv.2023.11.22.568268.jpg
-    alt: >-
-        ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization
-    title: >-
-        <span itemprop="name">ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization</span>
-    excerpt: >-
-        <span itemprop="isPartOf" itemscope itemtype="http://schema.org/Periodical"><strong>bioRxiv</strong></span>. <span itemprop="datePublished">2023 Nov 22</span>. <span itemprop="author">Gunsalus LM, Keiser MJ, Pollard KS</span>.
-    url: ""
-    doi: "10.1101/2023.11.22.568268"
-    btn_label: >-
-        doi &nbsp; <i class="fas fa-external-link-alt"></i>
-    btn_class: "btn--primary"
-    url2: "https://doi.org/10.1101/2023.11.22.568268"
-    btn2_label: >-
-        bioRxiv &nbsp; <i class="fas fa-external-link-alt"></i>
-    btn2_class: "btn--info"
-
   - image_path: /assets/images/papers/arXiv_-_NeurIPS_GenBio.2401.05370.jpg
     alt: >-
         Autoregressive fragment-based diffusion for pocket-aware ligand design

assets/images/papers/chemRxiv.chemrxiv-2024-ffcrs.jpg renamed to assets/images/papers/10.1021.acs.jcim.4c01876.jpg

@@ -10,9 +10,9 @@ excerpt: "Grad Student; ARCS Scholar in Bioinformatics, 2018-2023. Laura was an
 header:
   teaser: /assets/images/people/bio-gunsalus.jpg
 papers: 
-    - title: ChromaFactor- deconvolution of single-molecule chromatin organization with non-negative matrix factorization
-      excerpt: <u>Gunsalus LM</u>, Keiser MJ, Pollard KS. __bioRxiv__. 2023 Nov 22.
-      link: "https://doi.org/10.1101/2023.11.22.568268"
+    - title: ChromaFactor- Deconvolution of single-molecule chromatin organization with non-negative matrix factorization
+      excerpt: <u>Gunsalus LM</u>, Keiser MJ, Pollard KS. __PLoS Comput Biol__. 2025 Feb.
+      link: "https://doi.org/10.1371/journal.pcbi.1012841"
 
     - title: In silico discovery of repetitive elements as key sequence determinants of 3D genome folding
       excerpt: <u>Gunsalus LM</u>, Keiser MJ, Pollard KS. __Cell Genom__. 2023 Oct 11.

assets/images/papers/bioRxiv.2023.11.22.568268.jpg renamed to assets/images/papers/10.1371.journal.pcbi.1012841.jpg

@@ -10,10 +10,18 @@ excerpt: "<p>Michael is a Chan Zuckerberg Initiative Ben Barres Investigator and
 header:
   teaser: /assets/images/people/bio-keiser.jpg
 papers: 
+    - title: Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation
+      excerpt: Nogueira VHR, Sharma R, Guido RVC, <u>Keiser MJ</u>. __J Chem Inf Model__. 2025 Feb 24.
+      link: "https://doi.org/10.1021/acs.jcim.4c01876"
+
     - title: Network-aware self-supervised learning enables high-content phenotypic screening for genetic modifiers of neuronal activity dynamics
       excerpt: Grosjean P, Shevade K, Nguyen C, Ancheta S, Mader K, Franco I, Heo SJ, Lewis G, Boggess S, De Domenico A, Ullian E, Shafer S, Litterman A, Przybyla L, <u>Keiser MJ</u>, Ifkovits J, Yala A, Kampmann N. __bioRxiv__. 2025 Feb 05.
       link: "https://doi.org/10.1101/2025.02.04.636489"
 
+    - title: ChromaFactor- Deconvolution of single-molecule chromatin organization with non-negative matrix factorization
+      excerpt: Gunsalus LM, <u>Keiser MJ</u>, Pollard KS. __PLoS Comput Biol__. 2025 Feb.
+      link: "https://doi.org/10.1371/journal.pcbi.1012841"
+
     - title: Autoparty- Machine learning-guided visual inspection of molecular docking results
       excerpt: Shub L, Korczynska M, Muir DF, Lin F-Y, Mathiowetz AM, <u>Keiser MJ</u>. __chemRxiv__. 2024 Dec 09.
       link: "https://doi.org/10.26434/chemrxiv-2024-7p4ws"
@@ -42,10 +50,6 @@ papers:
       excerpt: Gale-Day ZJ, Shub L, Chuang KV, <u>Keiser MJ</u>. __J Chem Inf Model__. 2024 Jul 22.
       link: "https://doi.org/10.1021/acs.jcim.4c00311"
 
-    - title: Fuzz testing molecular representation using deep variational anomaly generation
-      excerpt: Nogueira VHR, Sharma R, Guido RVC, <u>Keiser MJ</u>. __chemRxiv__. 2024 Jul 11.
-      link: "https://doi.org/10.26434/chemrxiv-2024-ffcrs"
-
     - title: Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations
       excerpt: Ghandian S, Albarghouthi L, Nava K, Sharma SRR, Minaud L, Beckett L, Saito N, DeCarli C, Rissman RA, Teich AF, Jin LW, Dugger BN, <u>Keiser MJ</u>. __bioRxiv__. 2024 May 15.
       link: "https://doi.org/10.1101/2024.05.15.594372"
@@ -58,10 +62,6 @@ papers:
       excerpt: Vizcarra JC, Pearce TM, Dugger BN, <u>Keiser MJ</u>, Gearing M, Crary JF, Kiely EJ, Morris M, White B, Glass JD, Farrell K, Gutman DA. __Acta Neuropathol Commun__. 2023 Dec 18.
       link: "https://doi.org/10.1186/s40478-023-01691-x"
 
-    - title: ChromaFactor- deconvolution of single-molecule chromatin organization with non-negative matrix factorization
-      excerpt: Gunsalus LM, <u>Keiser MJ</u>, Pollard KS. __bioRxiv__. 2023 Nov 22.
-      link: "https://doi.org/10.1101/2023.11.22.568268"
-
     - title: Autoregressive fragment-based diffusion for pocket-aware ligand design
       excerpt: Ghorbani M, Gendelev L, Beroza P, <u>Keiser MJ</u>. __arXiv - NeurIPS GenBio__. 2023 Nov 2.
       link: "https://arxiv.org/abs/2401.05370"

collections/_people/laura_gunsalus.md

@@ -11,8 +11,8 @@ excerpt: "Research Data Analyst, 2021-2023. Rish is interested in generative mod
 header:
   teaser: /assets/images/people/bio-rsharma.jpg
 papers: 
-    - title: Fuzz testing molecular representation using deep variational anomaly generation
-      excerpt: Nogueira VHR, <u>Sharma R</u>, Guido RVC, Keiser MJ. __chemRxiv__. 2024 Jul 11.
-      link: "https://doi.org/10.26434/chemrxiv-2024-ffcrs"
+    - title: Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation
+      excerpt: Nogueira VHR, <u>Sharma R</u>, Guido RVC, Keiser MJ. __J Chem Inf Model__. 2025 Feb 24.
+      link: "https://doi.org/10.1021/acs.jcim.4c01876"
 
 ---

collections/_people/michael_keiser.md

@@ -10,8 +10,8 @@ excerpt: "Visiting [CAPES Scholar](https://www.iie.org/Programs/CAPES), 2022-202
 header:
   teaser: /assets/images/people/bio-rabesquine.jpg
 papers: 
-    - title: Fuzz testing molecular representation using deep variational anomaly generation
-      excerpt: <u>Nogueira VHR</u>, Sharma R, Guido RVC, Keiser MJ. __chemRxiv__. 2024 Jul 11.
-      link: "https://doi.org/10.26434/chemrxiv-2024-ffcrs"
+    - title: Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation
+      excerpt: <u>Nogueira VHR</u>, Sharma R, Guido RVC, Keiser MJ. __J Chem Inf Model__. 2025 Feb 24.
+      link: "https://doi.org/10.1021/acs.jcim.4c01876"
 
 ---