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Alexey Sergushichev

@asergushichev.bsky.social
177 followers 253 following 140 posts

Assistant professor, WashU Pathology & Immunology Author of FGSEA and other packages for omics data analysis alserglab.wustl.edu

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Reposted by Alexey Sergushichev
Alex Rubinsteyn @alexr.bsky.social · 02/10/2026
FYI I wrapped a lot of immuno-informatics predictors so you don't have to: openvax.github.io/mhctools/ (eg NetMHCpan, MHCflurry, Pepsickle, DeepTAP, ERAMER, BigMHC, PRIME, &c)
openvax.github.io
mhctools
Run MHC binding, presentation, immunogenicity and antigen-processing predictors through one predict() call
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Reposted by Alexey Sergushichev
Ian Sudbery @iansudbery.bsky.social · 12/09/2026
Holy moly, @ensembl.org killed biomart! Hope many R scripts are there out there that depend on biomaRt? How many people have informatics practicals, or undergraduate project instructions that depend on a web interface for bulk selection of data?
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Alexey Sergushichev @asergushichev.bsky.social · 25/08/2026
New application note from the lab: "GAMclust: identification of regulated metabolic modules in bulk, single cell and spatial gene expression data" doi.org/10.1093/bioi... 🧬 🖥️ 1/5
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Reposted by Alexey Sergushichev
Reese Richardson @reeserichardson.bsky.social · 25/08/2026
A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵
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Reposted by Alexey Sergushichev
Bastian Greshake Tzovaras @gedankenstuecke.scholar.social.ap.brid.gy · 04/08/2026
Love this interactive exploration of how people approach pathfinding: «Why some people mow a lawn better than others» pudding.cool/2026/06/mow
pudding.cool
Why some people mow a lawn better than others
We analyzed 132,003 attempts to mow a virtual lawn efficiently.
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Alexey Sergushichev @asergushichev.bsky.social · 31/07/2026
Today I realized: R repository system doesn't sign the packages and there is no default way to verify the package origin? So if someone compromises one CRAN mirror and replaces a package with a malicious one, it will just get installed silently?
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Alexey Sergushichev @asergushichev.bsky.social · 31/07/2026
Now I know about three ports of fgsea from R/C++ to Python+Rust, none of the authors contacted me. It's MIT licenced, so that's OK, but is it really hard to drop a line to the original authors? What's their plan for maintenance? Are they going to port any future changes?
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Alexey Sergushichev @asergushichev.bsky.social · 23/07/2026
I released new 0.4 version of mascarade package with a much improved automatic label placement algorithm. It's a pretty neat algorithm, but it took a while to get there. 1/8 github.com/alserglab/ma... 🧬🖥️
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Alexey Sergushichev @asergushichev.bsky.social · 17/07/2026
New preprint from my lab with a methodological follow up on our work on fast GSEA algorithm: Hash-augmented adaptive multilevel splitting Monte Carlo algorithm for accurate estimation of two-sample permutation test p-values 1/7
Preprint abstract:

Nonparametric permutation tests are widely used for statistical analysis. However, exact computation of test p-values can be algorithmically challenging, particularly for custom tests with complex test statistics. In contrast, Monte Carlo sampling can be easily applied to any test statistic, but it suffers from poor relative accuracy when estimating small p-values, interfering with multiple hypothesis testing correction and leading to other issues. In this work, we present a hash-augmented adaptive multilevel splitting Monte Carlo algorithm that enables accurate estimation of arbitrarily small p-values in two-sample permutation tests. Using the Kolmogorov-Smirnov and the Mann-Whitney U tests as examples, we highlight potential pitfalls related to the discreteness of the test statistic distribution and show how to address them. By comparing with an exact algorithm, we demonstrate the accuracy of the p-value estimates provided by the proposed algorithm and the validity of the associated confidence intervals. We provide a reference implementation of the proposed algorithm in the Python package hamstest, which allows p-value estimation for a user-defined statistic.
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Reposted by Alexey Sergushichev
Sergey Nurk @sergeynurk.bsky.social · 07/07/2026
Senior Bioinformatics Software Developer opening in my team in ONT's Applications department! Hybrid with a few days a week in our Oxford headquarters. We can sponsor visas! www.linkedin.com/jobs/view/44...
linkedin.com
Oxford Nanopore Technologies hiring Senior Bioinformatics Software Engineer, Applications in Oxfordshire, England, United Kingdom | LinkedIn
Posted 3:04:10 PM. Job DescriptionOur goal is to bring the widest benefits to society through enabling the analysis of…See this and similar jobs on LinkedIn.
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Reposted by Alexey Sergushichev
Ryan Moulton @moultano.bsky.social · 19/06/2026
I spent the last month obsessed with finding colors that can't be displayed on a conventional screen. This is what I found. moultano.wordpress.com/2026/06/19/w...
moultano.wordpress.com
Where to Find the Colors Your Screen Can’t Show You
An atlas of the vibrance of the real world
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Reposted by Alexey Sergushichev
hex @hex.kolektiva.social.ap.brid.gy · 07/06/2026
But if *I* hijack *their* devices it's a "felony." blog.includesecurity.com/2026/06/th…
blog.includesecurity.com
The Smart TV in Your LivingRoom Is a Node in the AIScraping Economy
The work at Include Security has us working with AI day in and day out (hacking it, using it, training it, etc). We’re all aware of the community-level opposition happening against datacenters, aimed at improving AI capabilities, being built recently. What you might not be aware of are the distributed efforts to train AI that could be using the devices inside your home. In this post, we’re going to explore how the company Bright Data facilitates modern AI models scraping training data from the Internet using its residential proxy network. Bright Data is a data-collection company that sells access to what it markets as the world’s largest residential proxy network of 400M+ home IP addresses that its customers route web-scraping traffic through. The supply behind that network comes from an SDK: a piece of software embedded in consumer apps that, with the user’s consent, turns their phone or smart TV into one of those exit nodes. We’ll document what you, the average user, should know about what this company’s SDK does on your systems such as your mobile phone and your smart TV. We’re going to explore how their SDK works, which platforms have shipped it, and why your Internet-connected TV is the ultimate proxy for AI models looking to train on data scraped from the Internet. ### **Why This Matters Now** AI companies depend on web-scraped content: for pre-training, for retrieval, for agent grounding, for search. But the modern web isn’t scrapeable from a datacenter. Cloudflare, DataDome, HUMAN, among others throttle or block requests from known cloud IPs. The workaround is residential proxies. A scraping job routed through a Comcast or T-Mobile subscriber’s connection arrives at the target site from an IP that belongs to a paying residential customer. Krebs reported in October 2025 that _“a glut of proxies from Aisuru and other sources is fueling large-scale data harvesting efforts tied to various AI projects.”_ Academic measurement going back to 2019 shows these networks are overwhelmingly misused. The FBI issued a formal advisory earlier this year. Most of the existing press has focused on the **illegal** residential-proxy supply: botnets (Aisuru, Kimwolf), trojanized apps (HUMAN Security’s PROXYLIB disclosure), pre-infected IoT hardware (Google/Mandiant’s IPIDEA takedown). These are the bad actors. On the other hand, the legal supply side has received far less scrutiny. Today Bright Data is the largest residential proxy network in the world by its own marketing, advertising “150M+ IPs” sourced via a consent SDK embedded in partner apps. This research documents how that SDK works, which platforms have shipped it, and why the connected-TV is the ultimate residential proxy. ### **Why Connected TV (CTV) is the Ideal Proxy** Connected TV, a.k.a Smart TV, is a near-perfect residential proxy. Compared to a mobile phone: **Factor**| **Mobile phone**| **Smart TV / CTV** ---|---|--- Power| Battery most of the day| Always plugged in Network| WiFi + cellular| Always WiFi, high-speed Uptime| Intermittent| 24/7 in standby Bandwidth ceiling| Low (cellular caps)| Effectively unlimited User attention| Actively used| Often unattended Consent UI| Text on a phone screen| Text navigated via TV remote arrow keys Corporate/family oversight| Higher (MDM, mobile EDR)| Virtually none A TV never hits 1% battery, jumps between WiFi networks or gets locked when the user is asleep. Some partner publishers do disclose the Bright Data relationship in their privacy policies PlayWorks is one example. But privacy-policy disclosure is the wrong control surface for a TV. It is hard to scroll through a legal document navigated by arrow keys on a remote, and the in-app consent dialog, doesn’t convey that a paying Bright Data customer is about to route their scraping traffic through the user’s home internet. Petflix, a Roku app documented by The Verge, is a representative case. Its opt-in screen reads: _“To enjoy Petflix for free with fewer ads, you are allowing Bright Data to occasionally use your device’s free resources and IP address to download public web data from the internet. Bright Data will only use your IP address for approved business-related use cases. None of your personal information is accessed or collected except your IP address. Period.”_ The Petflix dialog says “occasionally.” The SDK’s publicly queryable config sets `max_bw_monthly_wifi: 200,000,000,000` bytes — a 200 GB default monthly WiFi budget. **Who Bright Data Names as Partners** Bright Data exposes a partner manifest endpoint. The endpoint is unauthenticated and anyone can fetch it. Names in the manifest that I was able to identify with high confidence from public sources: **Partner ID (from config)**| **Entity**| **Scale** ---|---|--- playworks_digital| **PlayWorks Digital Ltd**| 400+ CTV game titles; reach ~250M TV homes via Comcast, Sky, Cox, LG, Samsung, Vizio, Roku cloudtv| **CloudTV**| Integrated across 125+ TV brands and 15+ OEMs longvision_media_hong_kong_co_limited| **Longvision Media HK (LongTV)**| 5M OTT users across HK and Malaysia viber_media_s_r_l| **Viber Media S.à r.l. (Rakuten)**| 250M–820M monthly users of the Viber messenger supercent_inc| **Supercent** (Korea)| #1 Korean mobile publisher by downloads in 2023 moonfrog_labs_private_limited| **Moonfrog Labs** (Stillfront subsidiary)| ~10M MAU on Teen Patti Gold alone; acquired for $90M hola_networks| **Hola Networks**| Bright Data’s lineage parent; user base reported in the tens to ~100M+ range at peak per Hola’s own historical marketing Others (`desoline, free_time, ott_studio, global_microtrading, m_m_media, easystaff_lp`) are present but less identifiable from public sources. `bright_screensavers, bright_videos`, and `brightdata `are Bright Data’s own apps. A note on what the partner list proves: Being listed in Bright Data’s config means an integration might have existed at some point. It does _not_ by itself prove that a specific publisher’s currently-shipping app(s) includes the SDK in production. For any named publisher, per-app verification is required. What the partner list _does_ directly prove: 1. Bright Data ships this roster in an **unauthenticated public endpoint**. 2. At least three CTV-focused entities (PlayWorks, CloudTV, Longvision) monetized their user’s devices as residential proxy exit nodes. PlayWorks in particular reports CTV distribution across major TV platforms and ISPs, with reach figures in the hundreds of millions of households per its own marketing materials. ### **How does the Bright Data SDK turn a user’s device into a residential proxy exit node?** The Bright Data SDK is a publicly documented commercial product, offered to publishers via Bright Data’s SDK integration docs (with a JavaScript variant for web). What follows builds on that public surface with findings from reverse-engineering the shipping iOS framework and instrumenting 30 days of its runtime traffic. The SDK ships as an iOS framework (brdsdk.framework) inside partner apps. I reverse-engineered the binary and captured 30 days of traffic from a research fleet running the SDK inside a consent-installed partner app. #### **The Unauthenticated Config** On every launch the SDK calls: `GET <https://clientsdk.bright-sdk.com/sdk_config_ios.json>?appid=<bundle>&ver=<sdk-version>&uuid=sdk-ios-<32hex>` The endpoint is unauthenticated in any meaningful sense. The server gates only on two query parameters `appid `(an app bundle ID, which can be found in the App Store listing of the partner app) and `ver `(the SDK version string). Supply those and any randomly generated UUID, and the server returns the same response a real device gets: feature flags, idle-detection thresholds (battery %, CPU/memory ceilings, WiFi-vs-cellular rules), per-country bandwidth tiers, and the partner manifest I showcased above. Each of these branches is worth examining on its own: the idle rules that decide when your device is eligible to relay, a flag that routes peer traffic around your VPN, a map that stitches your installs across platforms into one identity, and the per-country bandwidth caps. #### **The Peer Tunnel** After config fetch, the SDK opens a persistent WebSocket to: `wss://proxyjs.brdtnet.com:443` This hostname resolves to AWS Global Accelerator IPs (3.33.193.183, 15.197.193.114 as of this writing). The TLS certificate is `CN=*.luminatinet.com` — the domain for Luminati Networks, Bright Data’s pre-2018 corporate name. The rebrand was publicly announced in 2018. Active SDK infrastructure still runs on the legacy cert, which is a useful detection pivot: the current customer-facing proxy service lives on brightdata.com-branded domains, so any luminatinet.com / brdtnet.com traffic on your network is specifically the peer-tunnel plane, not customer-side Bright Data usage. The server identifies itself as `uWebSockets: 20`. The peer endpoint requires no authentication to upgrade. The server accepts any TLS-valid WebSocket upgrade and immediately pushes the connecting client an application-layer frame with the client’s public IP echoed back. From there, a handshake unfolds: 1. **Server → client: tunnel_init** establishes the session, returns the client’s public IP. 2. **Server → client: cid_set** the server assigns the client a session-tracking identifier in the format `<IP>-<token>/ls<N>c<M>p443_<IP>_<counter>`. We confirmed this format matches the cid field present in the SDK’s captured telemetry traffic from real devices. 3. **Server → client: status_get** the server polls the device for its idle state, battery, network type, and available bandwidth. The device responds with a continuous telemetry feed: `idle, wifi_connected, mobile_connected, mobile_type` (LTE/5G), `roaming, battery_level, using_battery, screen_on, on_call, cpu_usage, mem_usage, raw_bw, bw, ipv6_supported, appid` (the host app), `sdk_version, platform`, and the assigned `cid`. This is a continuous feed of physical-device state to a third party, delivered via a consent dialog whose text is chosen by the host app publisher. 4. **Handshake complete.** Once the device reports favorable status, the server’s job-matching layer is free to push `cmd_tun` frames: individual scraping-job instructions that the SDK executes as HTTP requests against third-party sites, using the user’s residential IP as the source. Every frame on the WebSocket is plain JSON with a fixed envelope: `{"type": "ipc_call"|"ipc_post"|"ipc_result"|"ipc_error", "cmd": <command>, "cookie": <correlation-id>, "err_code": 0, "msg": { ...payload... }}` The full command vocabulary extracted from the binary and verified on the wire: **Direction**| **cmd**| **Purpose** ---|---|--- Server → Client| tunnel_init| Open session, echo public IP Server → Client| cid_set| Assign session identifier Server → Client| status_get| Poll device idle/battery/bandwidth Server → Client| cmd_tun / tun| Dispatch a scraping job Server → Client| dns| Request DNS resolution of a target Server → Client| consent| Request consent state Client → Server| status_send| Periodic heartbeat with device state Client → Server| tun_report / tun_ack / tun_fin| Relay-job lifecycle responses Client → Server| tunnel_init_decline| Decline a session Client → Server| logs| Ship diagnostic logs to server There’s no message signing, HMAC, client certificate or device attestation. Only the TLS layer and the server’s IP-reputation filter gating which peers actually receive jobs. For readers familiar with commercial malware protocol design: this is substantially less secure than typical C2. #### **When the SDK considers you “idle”** The config ships an explicit rulebook for when the device is eligible to relay someone else’s traffic: `"idle_metrics": { "ignore_screen_on": true, // relay even with the screen on "ignore_on_call": true, // relay while the user is on a phone call "max_bw_ratio": 1, "min_battery": 0.2, "wifi_on_battery": true, "min_battery_wifi": 0.2, "max_cpu_usage": 70, "max_mem_usage": 90, "mem_screen_off": true, "idle_timeout": 30, "not_idle_timeout": 10 }` The ignore_screen_on and ignore_on_call flags are notable: “idle” does not mean the user is away from the device. It means the device’s CPU, memory, and battery are within the SDK’s thresholds. A user on a phone call, actively reading the screen, is considered idle for relay purposes. #### **Cross-Platform Identity Linkage** The config also ships a dual_pairing map: ``**"dual_pairing":** { "ios_com.brd.earnapp": ["win_earnapp.com", "mac_com.earnapp"] }`` That’s a server-side map tying a user’s iOS, Windows, and macOS installations of the same brand into one entity. It’s cross-platform identity stitching documented inside a public config file.One more forward-looking field: http3_enabled: true. The SDK is already shipping the flag for QUIC-based peer transport. A future version may move the peer tunnel from TCP/443 to UDP/443, which would break any defender relying on TCP connection tracking to detect the WebSocket. #### **The Inspection Bypass** The SDK’s config ships a flag “use_netifs”: true. That flag triggers code in the SDK binary that constructs its NWConnection with a specific required interface: `en0 `(WiFi) or `pdp_ip0 `(cellular), rather than using the system default route. **On iOS, this bypasses any configured VPN’s tun0 interface entirely.** The peer tunnel does not cross a user-configured VPN, even when the rest of the app’s HTTPS traffic does. We observed this empirically. My research setup includes transparent TLS interception. It captured every HTTPS call the SDK made, except the peer tunnel to proxyjs.brdtnet.com:443, even though port 443 is explicitly redirected to the inspector. The bypass uses Apple’s documented NWParameters.requiredInterface API. It’s worth emphasizing that the SDK uses **two independent inspection bypasses** , one per plane: * **Control plane** (config fetch, telemetry pings): built on CFNetwork’s CFHTTPMessage primitives rather than URLSession/NSURLConnection. This defeats URLSessionlevel instrumentation (swizzling, network extensions, URLProtocol subclasses) commonly used in mobile app-sec tooling, while still respecting the system proxy and so remaining visible to TLS-intercepting researchers. * **Data plane** (peer tunnel): built on NWConnection with requiredInterface set to the physical interface. This is what defeats VPNs and ensures the scraping is executed from a residential IP. Both choices are legitimate Apple APIs. The combination is the interesting artifact: the data plane is invisible to VPN-based inspection _and_ the control plane is invisible to URLSession-based hooks. Researchers who rely on either single technique see only half the SDK’s behavior. For enterprise security teams running MDM, corporate-VPN-based traffic inspection, or home-router parental controls: the most sensitive channel this SDK operates is designed to go around your visibility layer. ### **The geography tiers** The config ships per-country bandwidth thresholds. Four countries get explicit non-default policies: **Country**| **Min battery to relay**| **Daily cap**| **Monthly cap** ---|---|---|--- **Uzbekistan**| **1%**| 1 GB| 30 GB **Oman**| **1%**| 1 GB| 30 GB Qatar| 20%| 40 MB| 250 MB UAE| 20%| 40 MB| 250 MB default (worldwide)| 20%| 50 MB| 500 MB Looking at the config, Uzbekistan and Oman devices are permitted to relay down to **1% battery** , with daily caps 20× the default and monthly caps 60× the default. Qatar and UAE devices are throttled _below_ default. We can only speculate as to why the tiers are drawn this way. One reading is deliberate market segmentation, relaxing limits where grid power is stable and throttling where mobile data is expensive. The default-worldwide allowance still permits **500 MB of someone else’s traffic per month** over the user’s home internet. ### **Testing Setup and Methodology** Three data sources: 1. **Thirty days of TLS-inspecting proxy captures** from iOS device running consent-installed partner apps (including XYO COIN, which embeds the Bright SDK). 2. **Static analysis of the SDK binary** (brdsdk.framework, version 1.532.120, iOS arm64). All specific Bright Data hostnames, cert fingerprints, and TLS infrastructure described are publicly observable by anyone making the same requests. No session-specific identifying data from either the research fleet or the research client appears in this document. ### **Timeline** * **May 11, 2026** – Email notice sent to privacy@brightdata.com notifying their team about the release of this blog post. No response to the notification has been received at the time of this article’s publishing. ### **Defense Approaches** The traffic leaves clear fingerprints at the network boundary, and the SDK leaves identifiable symbols in the app binary. The approaches below let you detect and block the peer tunnel — at the network level or on the device itself. Three approaches, ordered by ease of deployment: **Approach 1: DNS block** (trivial, effective for network-routed devices): proxyjs.brdtnet.com proxyjs.luminatinet.com proxyjs.bright-sdk.com clientsdk.bright-sdk.com clientsdk.brdtnet.com Blocking proxyjs.* kills the peer tunnel without affecting any customer who legitimately uses Bright Data’s customer-facing proxy service on a different domain. **Approach 2: TLS SNI filtering:** Drop or alert on TLS handshakes where server_name matches *.brdtnet.com, *.luminatinet.com, or *.luminati.io. Works at the network boundary without TLS inspection. **Approach 3: TLS certificate fingerprint:** * .brdtnet.com → SHA256 313ce4ec7d5a51e5… * .luminatinet.com → SHA256 5028612e625befea… Stable until Sectigo cert rotation (current certs valid through mid-2026). **The use_netifs caveat:** All three layers only work on traffic that crosses your network boundary. The SDK’s use_netifs binding means that on iOS, when the device is on cellular, peer traffic bypasses corporate WiFi entirely. For managed fleets, the complementary control is MDM-based app binary scanning: search installed apps for the Swift symbols BrdWebSocketFacade and BrdNetwork.DNSResolver, and prohibit apps containing them on corporate-issued devices. For household users concerned about a specific smart TV or mobile app: block the hostnames above at your router’s DNS settings (Pi-hole, NextDNS, Cloudflare Gateway, your ISP’s equivalent). — This blog post was written in partnership with our guest author and independent security researcher Buchodi. ### Share this: * Share on X (Opens in new window) X * Share on Facebook (Opens in new window) Facebook * ### Like this: Like Loading…
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Reposted by Alexey Sergushichev
c0nc0rdance @c0nc0rdance.bsky.social · 29/05/2026
Pigeon pathfinding may depend on IMMUNE CELLS in their LIVERS 😕. Macrophages in the liver break down old red blood cells & in the process accumulate iron compounds like 'ferritin', which is superparamagnetic. These liver immune cells are found in proximity to nerve clusters. Compass cells!
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Laurel Oldach @laureloldach.bsky.social · 28/05/2026
Thermo Fisher has responded to research integrity activists who spotted apparent manipulation in its antibody catalog: "In ... preparing antibody images for publication on our website, some images may have been adjusted to clarify for presentation purposes." More: cen.acs.org/research-int...
Headline "Sleuths say Thermo Fisher doctored data to sell antibodies," subhead "Apparent manipulation of validation images in reagent catalog concern researchers," byline Laurel Oldach, image of a pipette loading an SDS-PAGE gel for a western blot
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Reese Richardson @reeserichardson.bsky.social · 21/05/2026
@johanduchene.bsky.social @sholtodavid.bsky.social Spent the last hour looking, found ten more apparently manipulated Western blots in Thermo Fisher's antibody verification data (across eight different catalogued products). Thread below. www.thermofisher.com/antibody/pro...
Apparent manipulation in the antibody verification data in Thermo Fisher's online catalog
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Alexey Sergushichev @asergushichev.bsky.social · 22/05/2026
What a great news to read, while still waiting for more than a year to get my adjustment of status approved.
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Sholto David @sholtodavid.bsky.social · 22/05/2026
Earlier this week I posted an example of a fake western blot provided by ThermoFisher to demonstrate the validity of a p53 antibody. I considered it an amusing curiosity. In fact Thermo Fisher Scientific has systematically manipulated antibody validation data!
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William DeWitt @wsdewitt.github.io · 29/04/2026
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. Preprint (w/ Gian Marco Visani and Aayush Verma): www.biorxiv.org/content/10.6... Blog: dewitt-lab.github.io/posts/2026-0...
dewitt-lab.github.io
Additivity is all you need?
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.
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Bioconductor @bioconductor.bsky.social · 30/04/2026
🚀 We’re excited to share the release of Bioconductor 3.23, featuring: ✅2418 software packages (94 new) ✅437 experiment data packages (5 new) ✅928 annotation packages ✅8 books (2 new) ✅28 workflows 🔗 Please see the full release announcement here: bioconductor.org/news/bioc_3_...
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Ed Zitron @edzitron.com · 21/04/2026
News: Anthropic seems to have removed access to Claude Code for its $20-a-month Pro Plans in another cost-cutting move. Some users still report having access, but documents reflect only Max users having access to Claude Code with their subscription. www.wheresyoured.at/news-anthrop...
NEWS
News: Anthropic Removes Claude Code From $20-A-Month "Pro" Subscription Plan
For New Users (Developing)
ED ZITRON / APR 21, 2026 / 2 MIN READ
Executive Summary:
• Anthropic appears to have removed access to Claude Code for its $20-a-month "Pro" Plans.
• Current Pro users appear to still have access via the Claude web app.
• Claude Code support documents exclusively refer to accessing Claude Code
via "your Max Plan," after previously saying you could access "with your Pro or Max Plan."
In developing news, Anthropic appears to have removed access to Al coding tool Claude Code from its $20-a-month "Pro" accounts. This is likely another cost-cutting move that follows a recent change (per The Information) that forced enterprise users to pay on a per-million-token based rate rather than having rate limits that were, based on researchers' findings, often much higher than the cost of the subscription.
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Alexey Sergushichev @asergushichev.bsky.social · 20/04/2026
After trying to explain to my less computationally inclined colleagues how to use markdown in SciENcv I made this web-site: alserglab.wustl.edu/sciencv-conv... You paste formatted text from Word/GDocs/... and get a formatted text to copy to the forms. Data doesn't leave you computer!
Screenshot of a web-site with styled text on the left (with leveled headers, bold, italic, underscores, unordered and ordered lists, subscripts and superscripts) and markdown-formatted text on the right
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Arjun Krishnan @compbiologist.bsky.social · 07/04/2026
Sean Davis & I are hiring a postdoc to work on turning massive public biological data collections into reusable engines for discovery. #ML / #AI + large-scale omics + open software Details + apply: cu.taleo.net/careersectio... seandavi.github.io | thekrishnanlab.org @cubiomedinfo.bsky.social
cu.taleo.net
Post-Doctoral Fellow
Click the link provided to see the complete job description.
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Ed Zitron @edzitron.com · 31/03/2026
Free newsletter: The Subprime AI Crisis is here. I explore the disturbing parallels between the run-up to the global financial crisis and the heavily-subsidized AI bubble, and how Anthropic and OpenAI's rush to IPO accelerates the crisis further. www.wheresyoured.at/the-subprime-ai-crisis-is-here/
wheresyoured.at
The Subprime AI Crisis Is Here
Hi! If you like this piece and want to support my independent reporting and analysis, why not subscribe to my premium newsletter? It’s $70 a year, or $7 a month, and in return you get a weekly newslet...
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Alexey Sergushichev @asergushichev.bsky.social · 06/03/2026
To close the loop, an OpenClaw should have created the malformed issue to install itself on other machines. A couple of years of evolution after that and we'll get sentient AI.
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Stephen Turner @stephenturner.us · 04/03/2026
Torsional flexibility of the thoracic spine is superior to that of the lumbar spine in cats: Implications for the falling cat problem anatomypubs.onlinelibrary.wiley.com/doi/full/10....
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Brent Pedersen @brent-p.bsky.social · 22/02/2026
I had a similar, less principled way of doing this, but this does seem to work quite well after trying a couple of large changes with it: boristane.com/blog/how-i-u... (I use codex, but same idea)
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Arjun Krishnan @compbiologist.bsky.social · 18/02/2026
PhD programs worldwide face an urgent question: How should trainees use ChatGPT, Claude & similar tools? Now online: two resources on thoughtfully integrating generative AI into research training. 📄 Conceptual framework: zenodo.org/records/18649847 📋 Practical guide: zenodo.org/records/18452319 🧵
zenodo.org
Build expertise first: why PhD training must sequence AI use after foundational skill development
Generative AI tools have arrived in PhD training environments faster than principled frameworks for their use. The debate has polarized between enthusiasts who argue trainees must adopt AI immediately...
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Rob Patro @robp.bsky.social · 15/02/2026
I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...
combine-lab.github.io
COMBINE-lab - The skeptic’s guide to generative AI assisted coding
An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.
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Valentina Boeva @valboeva.bsky.social · 20/01/2026
Boeva Lab is #hiring postdocs and senior scientists in AI/ML for Cancer Biology! Check the offer and apply at: jobs.ethz.ch/job/view/JOP...
jobs.ethz.ch
Postdoctoral Researcher or Senior Scientist (AI × Biology)
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Kevin Bonham @kevinbonham.com · 17/01/2026
Been hearing some horrifying chatter about dealing with the new #NIH common form and #ScienCV system, so I put together a short video with some tricks for mitigating some of those pain points. Hope it helps? 🧪 open.substack.com/pub/emptymod...
open.substack.com
Dealing with ScienCV formatting
Some tips for composing and making your new NIH biosketch not look like garbage
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Alexey Sergushichev @asergushichev.bsky.social · 20/01/2026
Somehow I got a lot of duplicate publications in ScieENcv. Does anyone know what's best way to fix it? Does it matter at all?
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Alexey Sergushichev @asergushichev.bsky.social · 16/01/2026
mascarade R package for generating borders on UMAP/t-SNE plots is out on CRAN! 🧬🖥️ 1/3
Shows PBMC3k single cell RNA-seq dataset with borders and labels around cell clusters
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Steven Salzberg @stevensalzberg.bsky.social · 07/01/2026
if you're interested, note that the time is UK time. In the US, that will be 9:00am.
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Jonathan Pritchard @jkpritch.bsky.social · 05/01/2026
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology. Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
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Alexey Sergushichev @asergushichev.bsky.social · 02/01/2026
Am I the only #rstats package developer annoyed that I can't easily run devtools::check() on the current version of the git tree (+staged)? Hate that options are either pushing it to CI/CD, or running a custom script. Anyone to support the corresponding devtools issue github.com/r-lib/devtoo...?
github.com
Option to build/check package from the git tree · Issue #2579 · r-lib/devtools
I find it useful to build/check package using only the changes in the git tree (committed and/or staged). Current build/check functions use all of the files in the package directory. These leads to...
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Jonathan Pritchard @jkpritch.bsky.social · 11/12/2025
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:
nature.com
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
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Michael Baym @baym.lol · 01/12/2025
Bioinformatics is in shambles at the Denver airport’s acronym game
CATS: Canine Airport Therapy Squad
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Greifflab @victorgreiff.bsky.social · 22/10/2025
📢 We are announcing the Adaptive Immune Profiling Challenge 2025! Can you predict immune state labels from adaptive immune receptor repertoires? 💰 $10,000 prize pool! 🗓️ Launches Nov 5 on @kaggle.com More Info: uio-bmi.github.io/adaptive_imm...
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Alexey Sergushichev @asergushichev.bsky.social · 19/10/2025
Does anyone have a high-res version of NCBI GEO logo (www.ncbi.nlm.nih.gov/geo/img/geo_...)? I hate putting their low-res version in the slides/figures. I've tried to use AI tools for upscaling, but the results aren't perfect (colors are off). Anyone want to take a shot at it? Here is my best take:
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Jeff Mold @jeffmold.bsky.social · 08/10/2025
ohhhhhhhh wow www.nature.com/articles/s41...
nature.com
Somatic mutation and selection at population scale - Nature
A new version of nanorate DNA&nbsp;sequencing, with an&nbsp;error rate&nbsp;lower than five errors&nbsp;per billion base pairs&nbsp;and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection&nbsp;and&nbsp;the generation of high-resolution&nbsp;selection&nbsp;maps across coding and non-coding sites for many genes.
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Rob Patro @robp.bsky.social · 08/10/2025
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon: docs.google.com/document/d/1...
docs.google.com
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
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Waggoner Lab @labwaggoner.bsky.social · 02/10/2025
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution @cellcellpress.bsky.social @sstevenwang.bsky.social @yalepress.bsky.social www.cell.com/cell/fulltex...
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Craig Kaplan @triggerloop.bsky.social · 30/09/2025
Redid this thanks to @james-gagnon.bsky.social reminding me about NIH Databook. R01 applications numbers are dropping greatly at NIGMS but success rates (after being flat) dropped greatly last year. Suspect this will be even more drastic in 2025
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Pascal Mamassian @mamassian.bsky.social · 24/09/2025
A nice shift in perceived colour between central and peripheral vision. The fixated disc looks purple while the others look blue. The effect presumably comes from the absence of S-cones in the fovea. From Hinnerk Schulz-Hildebrandt: arxiv.org/pdf/2509.115...
An array of 9 purple discs on a blue background. Figure from Hinnerk Schulz-Hildebrandt.
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Adam Phillippy @aphillippy.bsky.social · 22/09/2025
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
biorxiv.org
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
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Sofya Garushyants @garushyants.bsky.social · 15/09/2025
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
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James Bonfield @jbonfield.bsky.social · 15/09/2025
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned
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Bastian Greshake Tzovaras @gedankenstuecke.scholar.social.ap.brid.gy · 05/09/2025
Oh, fun: Someone did some personal science to evaluate if _they personally_ benefit from "AI", and this is what they found: «Yes, it’s a limited sample and could be chance, but also so far AI appears to slow me down by a median of 21%, exactly in line with the METR study. I can say definitively […]
scholar.social
Original post on scholar.social
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Anshul Kundaje @anshulkundaje.bsky.social · 12/08/2025
Job Alert: A stealth startup focused on non-cancer diagnostics is keen to hire a deep learning for genomics/bio engineer. I am an advisor for the startup & closely involved. Please see the job description below and get in touch if interested. Plz forward.
Stealth genomics startup focused on non-cancer diagnostic applications

Senior Deep Learning Engineer
•	Ph.D. in relevant field with 3+ years practical experience in deep learning for biology
•	Demonstrated proficiency in building DL architectures using Pytorch or TensorFlow+Keras.
•	Substantial expertise in training lightweight deep learning models and tuning large foundation models.
•	Substantial expertise with developing efficient data loaders for large datasets and optimizing training workflows.
•	Deep expertise training and deploying models in Cloud-based compute environments and local hardware.
•	Sufficient knowledge of the genomics of gene regulation to ask the right questions for the specific information to be gained.
•	Expertise in developing models of gene regulation and sequence-to-function models is a plus.
•	Interactive team player in highly collaborative small setting. Experience collaborating and communicating with biologists.

Interested candidates can send their CV to anshul @ kundaje . net
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