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[feat] Reorganize CV to highlight patents and NeurIPS acceptance
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3 files changed

+210
-43
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‎assets/data/publications.json‎

Lines changed: 87 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,23 +1,106 @@
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{
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"lastUpdated": "2025-10-27",
3+
"patents": [
4+
{
5+
"title": "TxPert: AI-Driven Perturbation Prediction System",
6+
"authors": "Russell, C.T., et al.",
7+
"year": 2025,
8+
"venue": "Patent Pending",
9+
"link": "#",
10+
"doi": null,
11+
"citations": 0
12+
},
13+
{
14+
"title": "HOOK-1: Novel Therapeutic Target Discovery Platform",
15+
"authors": "Russell, C.T., et al.",
16+
"year": 2025,
17+
"venue": "Patent Pending",
18+
"link": "#",
19+
"doi": null,
20+
"citations": 0
21+
}
22+
],
323
"publications": [
424
{
525
"title": "TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Perturbation Prediction",
626
"authors": "Russell, C.T., et al.",
727
"year": 2025,
8-
"venue": "arXiv preprint",
9-
"link": "https://arxiv.org/abs/2505.14919",
28+
"venue": "NeurIPS 2025",
29+
"link": "https://neurips.cc/virtual/2025/loc/san-diego/poster/116558",
1030
"doi": null,
1131
"citations": 0
1232
},
1333
{
1434
"title": "DL4MicEverywhere: Deep learning for microscopy made flexible, shareable and reproducible",
15-
"authors": "G\u00f3mez-de-Mariscal, E., Russell, C.T., et al.",
35+
"authors": "Gómez-de-Mariscal, E., Russell, C.T., et al.",
1636
"year": 2024,
1737
"venue": "Nature Methods",
1838
"link": "https://doi.org/10.1038/s41592-024-02295-6",
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"doi": "10.1038/s41592-024-02295-6",
2040
"citations": 12
41+
},
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{
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"title": "The BioImage Archive–building a home for life-sciences microscopy data",
44+
"authors": "Hartley, M., Gault, D., Donovan, C., Mahood, R., Oyetunde, A., Russell, C.T., et al.",
45+
"year": 2023,
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"venue": "Nucleic Acids Research",
47+
"link": "https://doi.org/10.1093/nar/gkac1072",
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"doi": "10.1093/nar/gkac1072",
49+
"citations": 15
50+
},
51+
{
52+
"title": "The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing",
53+
"authors": "Harrison, P.W., Lopez, R., Rahman, N., Russell, C.T., et al.",
54+
"year": 2021,
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"venue": "Nucleic Acids Research",
56+
"link": "https://doi.org/10.1093/nar/gkab417",
57+
"doi": "10.1093/nar/gkab417",
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"citations": 89
59+
},
60+
{
61+
"title": "Frame localisation optical projection tomography",
62+
"authors": "Russell, C.T., Vallejo Ramirez, P.P., Rees, E.J.",
63+
"year": 2021,
64+
"venue": "Scientific Reports",
65+
"link": "https://doi.org/10.1038/s41598-021-84002-5",
66+
"doi": "10.1038/s41598-021-84002-5",
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"citations": 3
68+
},
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{
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"title": "mmSIM: An open toolbox for accessible structured illumination microscopy",
71+
"authors": "Russell, C.T., Shaw, M.",
72+
"year": 2021,
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"venue": "Philosophical Transactions A",
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"link": "https://doi.org/10.1098/rsta.2020.0353",
75+
"doi": "10.1098/rsta.2020.0353",
76+
"citations": 7
77+
},
78+
{
79+
"title": "An open-hardware sample mounting solution for inverted lightsheet microscopes",
80+
"authors": "Russell, C.T., Rees, E.J.",
81+
"year": 2020,
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"venue": "Journal of Microscopy",
83+
"link": "https://doi.org/10.1111/jmi.12935",
84+
"doi": "10.1111/jmi.12935",
85+
"citations": 4
86+
},
87+
{
88+
"title": "Helminth Defense Molecules as Design Templates for Membrane Active Antibiotics",
89+
"authors": "Hammond, K., Lewis, H., Faruqui, N., Russell, C.T., et al.",
90+
"year": 2019,
91+
"venue": "ACS Infectious Diseases",
92+
"link": "https://doi.org/10.1021/acsinfecdis.9b00157",
93+
"doi": "10.1021/acsinfecdis.9b00157",
94+
"citations": 21
95+
},
96+
{
97+
"title": "Homographically generated light sheets for the microscopy of large specimens",
98+
"authors": "Russell, C.T., Rees, E.J., Kaminski, C.F.",
99+
"year": 2018,
100+
"venue": "Optics Letters",
101+
"link": "https://doi.org/10.1364/OL.43.000663",
102+
"doi": "10.1364/OL.43.000663",
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"citations": 8
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}
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]
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}
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}

‎assets/js/publications.js‎

Lines changed: 112 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -8,105 +8,162 @@ class PublicationsLoader {
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this.userGoogleScholarId = 'XVt7BYQAAAAJ';
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this.cacheKey = 'scholar_publications';
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this.publicationsJsonUrl = '/assets/data/publications.json';
11+
this.fallbackPatents = [
12+
{
13+
title: "TxPert: AI-Driven Perturbation Prediction System",
14+
authors: "Russell, C.T., et al.",
15+
year: 2025,
16+
venue: "Patent Pending",
17+
link: "#",
18+
doi: null,
19+
citations: 0
20+
},
21+
{
22+
title: "HOOK-1: Novel Therapeutic Target Discovery Platform",
23+
authors: "Russell, C.T., et al.",
24+
year: 2025,
25+
venue: "Patent Pending",
26+
link: "#",
27+
doi: null,
28+
citations: 0
29+
}
30+
];
1131
this.fallbackPublications = [
1232
{
1333
title: "TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Perturbation Prediction",
1434
authors: "Russell, C.T., et al.",
1535
year: 2025,
16-
venue: "arXiv preprint",
17-
link: "https://arxiv.org/abs/2505.14919",
18-
doi: null
36+
venue: "NeurIPS 2025",
37+
link: "https://neurips.cc/virtual/2025/loc/san-diego/poster/116558",
38+
doi: null,
39+
citations: 0
1940
},
2041
{
2142
title: "DL4MicEverywhere: Deep learning for microscopy made flexible, shareable and reproducible",
2243
authors: "Gómez-de-Mariscal, E., Russell, C.T., et al.",
2344
year: 2024,
2445
venue: "Nature Methods",
2546
link: "https://doi.org/10.1038/s41592-024-02295-6",
26-
doi: "10.1038/s41592-024-02295-6"
47+
doi: "10.1038/s41592-024-02295-6",
48+
citations: 12
49+
},
50+
{
51+
title: "The BioImage Archive–building a home for life-sciences microscopy data",
52+
authors: "Hartley, M., Gault, D., Donovan, C., Mahood, R., Oyetunde, A., Russell, C.T., et al.",
53+
year: 2023,
54+
venue: "Nucleic Acids Research",
55+
link: "https://doi.org/10.1093/nar/gkac1072",
56+
doi: "10.1093/nar/gkac1072",
57+
citations: 15
2758
},
2859
{
2960
title: "The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing",
3061
authors: "Harrison, P.W., Lopez, R., Rahman, N., Russell, C.T., et al.",
3162
year: 2021,
3263
venue: "Nucleic Acids Research",
3364
link: "https://doi.org/10.1093/nar/gkab417",
34-
doi: "10.1093/nar/gkab417"
65+
doi: "10.1093/nar/gkab417",
66+
citations: 89
3567
},
3668
{
3769
title: "Frame localisation optical projection tomography",
3870
authors: "Russell, C.T., Vallejo Ramirez, P.P., Rees, E.J.",
3971
year: 2021,
4072
venue: "Scientific Reports",
4173
link: "https://doi.org/10.1038/s41598-021-84002-5",
42-
doi: "10.1038/s41598-021-84002-5"
74+
doi: "10.1038/s41598-021-84002-5",
75+
citations: 3
4376
},
4477
{
4578
title: "mmSIM: An open toolbox for accessible structured illumination microscopy",
4679
authors: "Russell, C.T., Shaw, M.",
4780
year: 2021,
4881
venue: "Philosophical Transactions A",
4982
link: "https://doi.org/10.1098/rsta.2020.0353",
50-
doi: "10.1098/rsta.2020.0353"
83+
doi: "10.1098/rsta.2020.0353",
84+
citations: 7
5185
},
5286
{
5387
title: "An open-hardware sample mounting solution for inverted lightsheet microscopes",
5488
authors: "Russell, C.T., Rees, E.J.",
5589
year: 2020,
5690
venue: "Journal of Microscopy",
5791
link: "https://doi.org/10.1111/jmi.12935",
58-
doi: "10.1111/jmi.12935"
92+
doi: "10.1111/jmi.12935",
93+
citations: 4
5994
},
6095
{
6196
title: "Helminth Defense Molecules as Design Templates for Membrane Active Antibiotics",
6297
authors: "Hammond, K., Lewis, H., Faruqui, N., Russell, C.T., et al.",
6398
year: 2019,
6499
venue: "ACS Infectious Diseases",
65100
link: "https://doi.org/10.1021/acsinfecdis.9b00157",
66-
doi: "10.1021/acsinfecdis.9b00157"
101+
doi: "10.1021/acsinfecdis.9b00157",
102+
citations: 21
67103
},
68104
{
69105
title: "Homographically generated light sheets for the microscopy of large specimens",
70106
authors: "Russell, C.T., Rees, E.J., Kaminski, C.F.",
71107
year: 2018,
72108
venue: "Optics Letters",
73109
link: "https://doi.org/10.1364/OL.43.000663",
74-
doi: "10.1364/OL.43.000663"
110+
doi: "10.1364/OL.43.000663",
111+
citations: 8
75112
}
76113
];
77114
this.corsProxy = 'https://api.allorigins.win/raw?url=';
78115
}
79116

80117
async init() {
81118
try {
82-
// Try to load from JSON file first (stored in repo)
119+
let publications = null;
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let patents = null;
121+
let source = 'fallback';
122+
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// Try JSON file
83124
const jsonData = await this.loadFromJson();
84125
if (jsonData) {
85-
console.log('Loading publications from JSON file');
86-
this.renderPublications(jsonData, 'json');
87-
return;
126+
if (jsonData.publications && jsonData.publications.length > 0) {
127+
publications = jsonData.publications;
128+
source = 'json';
129+
console.log('Loaded publications from JSON file');
130+
}
131+
if (jsonData.patents && jsonData.patents.length > 0) {
132+
patents = jsonData.patents;
133+
console.log('Loaded patents from JSON file');
134+
}
88135
}
89136

90-
// Fallback to localStorage cache
91-
const cachedData = this.getCachedPublications();
92-
if (cachedData) {
93-
console.log('Loading publications from localStorage cache');
94-
this.renderPublications(cachedData.publications, 'cache');
95-
return;
137+
// Try localStorage cache if JSON failed
138+
if (!publications || !patents) {
139+
const cachedData = this.getCachedPublications();
140+
if (cachedData) {
141+
if (!publications && cachedData.publications) {
142+
publications = cachedData.publications;
143+
source = 'cache';
144+
}
145+
if (!patents && cachedData.patents) {
146+
patents = cachedData.patents;
147+
}
148+
}
96149
}
97150

98-
// Last resort: fetch from API
99-
const publications = await this.fetchPublications();
100-
if (publications && publications.length > 0) {
101-
this.cachePublications(publications);
102-
this.renderPublications(publications, 'api');
103-
} else {
104-
console.warn('No publications available from any source');
105-
this.showError();
151+
// Use fallback if we have nothing
152+
if (!publications || publications.length < this.fallbackPublications.length) {
153+
publications = this.fallbackPublications;
154+
source = 'fallback';
155+
}
156+
if (!patents || patents.length < this.fallbackPatents.length) {
157+
patents = this.fallbackPatents;
106158
}
159+
160+
this.renderPatents(patents, source);
161+
this.renderPublications(publications, source);
162+
107163
} catch (error) {
108-
console.warn('Failed to load publications:', error);
109-
this.showError();
164+
console.warn('Error in init, using fallback:', error);
165+
this.renderPatents(this.fallbackPatents, 'fallback');
166+
this.renderPublications(this.fallbackPublications, 'fallback');
110167
}
111168
}
112169

@@ -216,6 +273,24 @@ class PublicationsLoader {
216273
return yearMatch ? parseInt(yearMatch[0]) : new Date().getFullYear();
217274
}
218275

276+
renderPatents(patents, source = 'unknown') {
277+
const container = document.getElementById('patents-list');
278+
if (!container) return;
279+
280+
patents.sort((a, b) => (b.year || 0) - (a.year || 0));
281+
282+
const html = patents.map((patent, index) => {
283+
return `
284+
<div class="patent-item" data-year="${patent.year}">
285+
<p><strong>${index + 1}.</strong> ${patent.authors} (${patent.year}).
286+
"${patent.title}" <em>${patent.venue}</em>.</p>
287+
</div>
288+
`;
289+
}).join('');
290+
291+
container.innerHTML = html;
292+
}
293+
219294
renderPublications(publications, source = 'unknown') {
220295
const container = document.getElementById('publications-list');
221296
if (!container) return;
@@ -241,8 +316,9 @@ class PublicationsLoader {
241316
// Add source indicator
242317
const sourceLabels = {
243318
'json': 'repository data',
244-
'cache': 'cached data',
245-
'api': 'live API'
319+
'cache': 'cached data',
320+
'api': 'live API',
321+
'fallback': 'curated list'
246322
};
247323

248324
const updateInfo = document.createElement('p');
@@ -257,7 +333,7 @@ class PublicationsLoader {
257333
const response = await fetch(this.publicationsJsonUrl);
258334
if (response.ok) {
259335
const data = await response.json();
260-
return data.publications || data; // Handle different JSON structures
336+
return data;
261337
}
262338
} catch (error) {
263339
console.warn('Failed to load JSON file:', error);
@@ -280,14 +356,15 @@ class PublicationsLoader {
280356
}
281357
}
282358

283-
cachePublications(publications) {
359+
cachePublications(publications, patents) {
284360
try {
285361
const data = {
286362
publications: publications,
363+
patents: patents,
287364
timestamp: Date.now()
288365
};
289366
localStorage.setItem(this.cacheKey, JSON.stringify(data));
290-
console.log('Publications cached successfully');
367+
console.log('Publications and patents cached successfully');
291368
} catch (error) {
292369
console.warn('Error caching publications:', error);
293370
}

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