Roby Bhattacharyya

@roby-b.bsky.social

9139 Followers 1402 Following

ID doc (MGH), PI (Broad Institute), antibiotic resistance resister, sepsis immune profiler, COVID doc, husband, dad. Coffee, tennis, kindness, science, & sleep enthusiast. Here to learn, as that other place devolves. Views mine. | bhattacharyyalab.org

manuscript submission & acceptance dates: "received 13 Nov 2023, accepted 9 Jun 2026, published 15 Jul 2026"
Screenshot of abstract of the original 1990 citation (Altschul et al, J Mol Biol 214(3):403, 1990) reporting BLAST (Basic Local Alignment Search Tool), still a core tool for sequence alignments of DNA and proteins: "A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straight-forward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity."
file named "*_nearFINAL.pdf"
incidence curves for COVID in household contacts of index cases when given ensitrelvir (blue) or placebo (gray), showing ~1/3 the number of cases in the ensitrelvir arm than the placebo arm
Calvin (of Calvin & Hobbes), pencil in mouth, staring at a blank page: "One... number one...... hmm.... nummmber one.... mm....."
Picture of a cheese tray, with brie labeled ‘cheddar’ and cheddar labeled ‘brie’
Screenshot of a spam email from a made-up address with subject line "Reg: We Want Your Brilliance"
screenshot of filename: "Paper_FinalV1_rpb_clean_figure_swap_caption_edit.docx"
Filename ending "Paper_FinalV1_rpb"
filename ending in "Paper_FinalV1.docx"
Fig 2 from the linked study (Mina et al, Science vol 366, p599-606, 1 Nov 2019)
Our new cat perched on a laptop, demanding attention. (We used to be a dog family, lost our 17.5 yo dog a few months ago, and just adopted a cat with a surprisingly dog-like personality)
Charles Darwin quote, excerpted from a letter to Thomas Huxley dated 10 Sep 1860: "I am very poorly today & very stupid & hate everybody & everything."
protest outside Boston city hall with a sign reading "no faux king way"
Cover of ‘Captain underpants and the tyrannical retaliation of the turbo toilet 2000’ book
A text box from a graduate school letter of recommendation asking "What would you describe as the applicant's most outstanding quality?" Asterisk indicates required question...
Trays of food labeled ‘infectious bacon and cheese’ and ‘infectious egg and cheese’ from Infectious Disease case conference
view of the phylogenetic Tree of Life showing remarkable diversity of bacteria occupying half the tree, with a tiny wedge representing all animals and fungi. Source linked in post
Faint green night skies over Boston - the Northern Lights!
Screenshot of text from the Guardian's live-match blog of the Alcaraz-Fritz round-robin match at the ATP finals: "*Alcaraz (2)6-7 7-5 5-2 Fritz Fritz, you have to think, knows. It took him a while but Alcaraz is now playing like himself and we’re back to what we said earlier: the way he makes the impossible inevitable is so ludicrous it feels fixed. He holds to 30 and is a game away; I feel vomitous on Fritz’s behalf because he’s given this the world, but elated at how Alcaraz has come back because he is the world."
Identical white blood cell counts, hemoglobins, platelets, blood urea nitrogens, creatinines, sodiums, cholesterols (including total, LDL, HDL, and triglycerides), and coagulation times for patients 101, 202, and 303; for patients 1, 102, 203, and 304; for patients 2, 103, 204, and 305; and so on...
screenshot from an email header saying that a manuscript "has been accepted for publication"
From graphical abstract of the linked paper: a plot of an interrupted time series analysis showing an abrupt increase in genomic antibiotic resistance elements (among cultured bacteria, which will often be from clinical samples) starting the year that the given antibiotic was introduced into clinical practice.
Picture of a tin of food labeled ‘Infection D | egg and cheese’ (from a meeting of the infectious diseases division)
Fig 2 in linked paper: the birthdate cutoff for shingles vaccine eligibility correlated with a reduction in shingles diagnoses
Fig 5 from the linked paper. Women (top), not men (bottom), exhibit a major discontinuity (stepwise reduction) in dementia diagnoses upon becoming eligible for the shingles vaccine.
Fig 1 in the linked paper, showing a vast difference in vaccine uptake by birthdate, but not in other relevant health traits, including prior shingles diagnoses, prior dementia, past flu shots, statin use, etc
Fig 3 from the linked paper, showing a discontinuity in the rates of dementia diagnoses corresponding to the precise date of eligibility for the shingles vaccine.
quote from Carl Sagan's book "The Demon-Haunted World: Science as a Candle in the Dark", pulled from goodreads (https://www.goodreads.com/quotes/11020760-i-have-a-foreboding-of-america-in-my-children-s-or). Full text of quote at that link, or in the thread I quoted in the post above this.
FIG 2. Example heatmaps and squared projected distance (SPD) calculation from transcriptional response. The transcriptional profile is distilled into a measure of treatment response with SPD, a single-value summary of the transcriptional response across the genes of interest (see Materials and Methods). (A and B) Heatmaps of the log 2-fold change in the transcriptional response of each (A) E. coli or (B) K. pneumoniae isolate after exposure to ceftriaxone. Each row corresponds to a different gene of interest, while each column is a different blood culture sample. KPC and CTX-M-15 genotypes are shown above the heatmap, while sample numbers, SPD values, and MICs (μg/mL) are shown below.
Schematic figure depicting workflow for our assay: RNA sequencing defines antibiotic-responsive transcripts that best distinguish susceptible from resistant organisms (shown in MA plots, with many statistically significant differences in transcript abundance in a susceptible strain, but no differences in a resistant strain). This allows the selection of the 10 genes whose differential expression best distinguishes susceptible from resistant. These 10 transcripts are then measured (and normalized to a set of housekeeping genes) using a much simpler assay, NanoString; resulting data is shown as a heatmap, with 12 susceptible strains showing marked changes (in red = up-regulated, and blue = down-regulated) but 12 resistant strains showing no changes (white).
Crossover study showing evidence of waning: the original vaccine cohort had crossed over 5 months before Delta emerged, which means at the time Delta swept, there were two groups who had been effectively randomized to receive vaccine 5 mo ago, or 10 mo ago. The group whose vaccine was 10 mo old, had considerably more infections than the group whose vaccine was 5 mo old. Crossover was not blinded (ie each group knew who was who), but short of that, this was near-perfect RCT-style evidence that waning mattered for Delta immunity.
Slide from a talk I gave in May 2021, asking if SARS-CoV-2 will be more like measles, or more like flu. I thought it would come down to if it could mutate enough to evade our immune response while still preserving its ability to bind receptors required for cell entry. It obviously could.
Sad screenshot of 30+ open tabs of partially-skimmed papers I will get to someday...
Children’s book asking them ‘Who is the funniest person you know?’ - my 6 yo wrote in ‘Roby’ 💙
email header from Amazon Kids (subject: "Your child's book request requires your approval")
Step one: from Word menu, select "Preferences"
Graph of cervical cancer rates among those unvaccinated, vaccinated at age 17-30 (incidence rate ratio 0.37, 95% CI 0.21-0.57), or vaccinated prior to age 17 (incidence rate ration 0.12, 95% CI 0.00 - 0.34)
Panel of Winnie-the-Pooh and Piglet walking through a field. Dialogue: "But how will we know if our pandemic guidelines work?" asked Piglet "The world will think we overreacted," said Pooh. "So even when we're right, everyone thinks we're wrong?" "Welcome to Public Health," said Pooh. And Piglet understood.
David Roach giving his pitch at IDWeek’s IDea ‘shark tank’
Cartoon showing "population" on the left: a group of horses, rhinos, and swans; and "population average" on the right: a unicorn (horn of a rhino, body of a horse, wings of a swan)
Dotplots of gene expression (scRNAseq) & cell surface protein expression (CITE-Seq) for each major immune cell substate, generated by standard Ficoll vs new Cryo-PRO sample prep method
UMAPs generated from the standard Ficoll method vs the new Cryo-PRO method of on-site clinical sample prep for 32 patients with sepsis, showing similar cell type & substate distributions. Data from each method was generated & analyzed (clustered) entirely separately, then projected onto a shared set of axes for visual comparison.
Fig 2c-d from preprint, showing very similar scRNAseq QC metrics between the standard Ficoll method & the new Cryo-PRO method for on-site sample prep.
Schematic of a on-site CRYOpreservation method followed by Pbmc Recovery Offsite (Cryo-PRO), compared with the standard Ficoll method, for preparing clinical blood samples for scRNAseq
screenshot looking for the right "pin" emoji on a Mac running the Chrome browser, with no options for the correct one
tray of brie labeled "cheddar" in front of a tray of cheddar slices labeled "brie"
colorful sunset over the Charles River
Screenshot from lab website: "News & notes from the Bhattacharyya lab (2024 Mar): After a long hiatus, Roby finally finds the bandwidth to update the lab website, haha."
A word cloud created from Roby Bhattacharyya's google scholar page
Meme image of "heartbreaking: the worst person you know made a great point" from the Onion
Smashing Pumpkins, Siamese Dream album cover