Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders.

Code ↔ Paper

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Paper

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The authors' code

Rust · 38 lines · 1.5 KB · BSD-3-Clause

//! Replicate a BAM N times into a larger BAM for align-mode timing benchmarks.
//! Each copy's records stay contiguous, so per-fragment name grouping (by
//! adjacency) is preserved — copies are simply counted as additional fragments.
//!
//! Usage: replicate_bam <in.bam> <out.bam> <n>
use noodles_bam as bam;
use noodles_sam::alignment::io::Write as _;
fn main() -> anyhow::Result<()> {
let mut args = std::env::args().skip(1);
let input = args.next().expect("in.bam");
let output = args.next().expect("out.bam");
let n: usize = args.next().expect("n").parse()?;
// Read the whole input into memory: this is a benchmarking aid run on small
// BAMs, so simplicity beats streaming.
let mut reader = bam::io::Reader::new(std::fs::File::open(&input)?);
let header = reader.read_header()?;
let recs: Vec<_> = reader
.record_bufs(&header)
.collect::<std::io::Result<Vec<_>>>()?;
eprintln!("read {} records; writing {} copies", recs.len(), n);
let mut writer = bam::io::Writer::new(std::io::BufWriter::new(std::fs::File::create(&output)?));
writer.write_header(&header)?;
// Emit the records N times *in blocks*, not interleaved. Alignment mode
// groups a fragment's records by adjacency, so each block's copies read as
// additional fragments rather than corrupting the grouping.
for _ in 0..n {
for r in &recs {
writer.write_alignment_record(&header, r)?;
}
}
writer.finish(&header)?;
eprintln!("wrote {} records total", recs.len() * n);
Ok(())
}

replicate_bam.rs at commit ed926b8, under BSD-3-Clause · at the source

OverviewAuthors: Vukasin M. Jovanovic1, Narisu Narisu2, Lori L. Bonnycastle2, David Castellano1, Seungmi Ryu1, Ravi Tharakan1, Kendall T. Mesch1, Qiang Chen1, Fahrünisa Meryem Betül Erol3, Hannah J. Glover3, Tingfen Yan2, Neelam Sinha2, Chaitali Sen1, Shu Yang1, Dvir Blivis1, Daniel F. Bennett4, Giovanni Rosales-Soto4, Jason Inman1, Pinar Ormanoglu1, Christopher A. LeClair1and 10 other authorsNatalie D. Shaw5, Menghang Xia1, Martin Schneider4, Erick O. Hernandez-Ochoa4, Michael R. Erdos2, Anton Simeonov1, Shuibing Chen6, Francis S. Collins2, Claudia A. Doege3, Carlos A. Tristan1
ORCID iDs: Vukasin M. Jovanovic, Ravi Tharakan, Kendall T. Mesch, Shu Yang, Claudia A. Doege
National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation Rockville, Rockville, MD 20850, USA
Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
Department of Surgery, Center for Genomic Health, Weill Cornell Medicine, New York, NY 10065, USA
Institutions: National Center for Advancing Translational Sciences (United States); National Institutes of Health (United States); National Human Genome Research Institute (United States); Columbia University Irving Medical Center (United States); University of Maryland, Baltimore (United States); National Institute of Environmental Health Sciences (United States); Weill Cornell Medicine (United States)
Journal: Stem cell reports, volume 21, issue 7, article 102958
Dates: received 3 April 2025; accepted 13 May 2026; published online 11 June 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.stemcr.2026.102958 · PMID 42276059 · PMCID PMC13385436 · OpenAlex W7164397265
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, fMRI & imaging
Keywords: pluripotent stem cells, iPSC, human hypothalamus, POMC neurons, GnRH neurons, automated biomanufacturing, metabolic disease modeling, obesity, type 2 diabetes, GLP1R agonist, insulin
MeSH: Cell Differentiation*, Hypothalamus*, Metabolic Diseases*, Models, Biological*, Neurons*, Pluripotent Stem Cells*, Glucose, Humans, Insulin, Pro-Opiomelanocortin (* major topic)
Journal subjects: Resource
Topic: Pluripotent Stem Cells Research (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: RMP; NIH (HG000024); National Center for Advancing Translational Sciences (TR000244, TR000410); HHS; NHGRI; InterAccess (12003); U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS); Division of Translational Toxicology; Russell Berrie Foundation; New York Obesity Research Center (P30 DK026687-43, DK52431-25); School of Medicine; University of Maryland
Citations: not cited yet (Europe PMC); 145 references in the paper
Research resources: GAPDH RRID:AB_10167668, PAX6 RRID:AB_10715442, Donkey anti-mouse IgG 568 RRID:AB_11180865, FABP7 RRID:AB_11210770, ISL1 RRID:AB_1951287, GAD65/67 RRID:AB_2263114, Tyrosine hydroxylase (TH) RRID:AB_2313713, TUBB3 (TUJ1) RRID:AB_2313773, Donkey anti-rabbit IgG 488 RRID:AB_2535792, GABA RRID:AB_2549714, pCREB RRID:AB_2561044, PAX6 RRID:AB_2565003, IR-alpha RRID:AB_2799850, Anti-Mouse Secondary HRP Antibody RRID:AB_2860576, Anti-Rabbit Secondary HRP Antibody RRID:AB_2860577, POMC RRID:AB_2898516, IR-beta RRID:AB_2924796, CALB (d28k) RRID:AB_3542811, CREB RRID:AB_490881, Somatostatin (SST) RRID:AB_831726, NCRM5 RRID:CVCL_1E75, WA09 RRID:CVCL_9773, LiPSC-GR1.1 RRID:CVCL_RL65
AbstractThe abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above.

combine-lab/salmon

License: BSD-3-Clause

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: ed926b8f6120c592ba13e696fe24732004ee0132, 25 September 2026

Languages: Rust (88), Shell (4), TypeScript (1)

Size: 176 files, 93 scripts

Software Heritage: not archived

Found in: the text, “Key resources table”

Holds: README, license file, environment (Dockerfile), tests, continuous integration, documentation

Not found: CITATION.cff

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

95 files

crates/salmon-align/examples/replicate_bam.rs, Rust, 38 lines
crates/salmon-align/src/bam_rad.rs, Rust, 900 lines
crates/salmon-align/src/error_model.rs, Rust, 654 lines
crates/salmon-align/src/genome_project.rs, Rust, 751 lines
crates/salmon-align/src/lib.rs, Rust, 3,526 lines
crates/salmon-align/src/rad.rs, Rust, 2,660 lines
crates/salmon-align/tests/alignment_bias.rs, Rust, 80 lines
crates/salmon-align/tests/bootstrap_output.rs, Rust, 133 lines
crates/salmon-align/tests/deterministic_bam.rs, Rust, 577 lines
crates/salmon-align/tests/output_contract.rs, Rust, 199 lines
crates/salmon-align/tests/rad_input.rs, Rust, 1,278 lines
crates/salmon-align/tests/rad_lib_format_counts.rs, Rust, 293 lines
crates/salmon-align/tests/stranded_num_mapped.rs, Rust, 297 lines
crates/salmon-cli/examples/cache_bench.rs, Rust, 51 lines
crates/salmon-cli/src/global_alloc.rs, Rust, 31 lines
crates/salmon-cli/src/main.rs, Rust, 3,757 lines
crates/salmon-cli/tests/decoy_bias.rs, Rust, 144 lines
crates/salmon-cli/tests/deterministic_default.rs, Rust, 152 lines
crates/salmon-cli/tests/deterministic_skip_quant.rs, Rust, 196 lines
crates/salmon-cli/tests/dump_eq_deterministic.rs, Rust, 224 lines
crates/salmon-cli/tests/flag_matrix.rs, Rust, 241 lines
crates/salmon-cli/tests/input_validation.rs, Rust, 683 lines
crates/salmon-cli/tests/metadata_truth.rs, Rust, 408 lines
crates/salmon-cli/tests/mode_applicability.rs, Rust, 332 lines
crates/salmon-cli/tests/output_contract.rs, Rust, 166 lines
crates/salmon-cli/tests/readiness_blockers.rs, Rust, 226 lines
crates/salmon-core/src/atomic.rs, Rust, 89 lines
crates/salmon-core/src/compress.rs, Rust, 200 lines
crates/salmon-core/src/diagnostics.rs, Rust, 260 lines
crates/salmon-core/src/error.rs, Rust, 42 lines
crates/salmon-core/src/genemap.rs, Rust, 762 lines
crates/salmon-core/src/lib.rs, Rust, 224 lines
crates/salmon-core/src/libtype.rs, Rust, 833 lines
crates/salmon-core/src/mate.rs, Rust, 47 lines
crates/salmon-core/src/math.rs, Rust, 151 lines
crates/salmon-core/src/progress.rs, Rust, 25 lines
crates/salmon-core/src/quantmerge.rs, Rust, 207 lines
crates/salmon-core/src/refprovider.rs, Rust, 36 lines
crates/salmon-core/src/timing.rs, Rust, 57 lines
crates/salmon-eqclass/src/lib.rs, Rust, 894 lines
crates/salmon-index/src/lib.rs, Rust, 1,661 lines
crates/salmon-infer/benches/em_step.rs, Rust, 207 lines
crates/salmon-infer/src/daarem.rs, Rust, 874 lines
crates/salmon-infer/src/lib.rs, Rust, 1,329 lines
crates/salmon-infer/src/online.rs, Rust, 242 lines
crates/salmon-infer/src/packed.rs, Rust, 1,262 lines
crates/salmon-infer/src/uncertainty.rs, Rust, 583 lines
crates/salmon-map/benches/align.rs, Rust, 110 lines
crates/salmon-map/examples/dump_txome.rs, Rust, 33 lines
crates/salmon-map/examples/trace_pair.rs, Rust, 83 lines
crates/salmon-map/examples/trace_reads.rs, Rust, 190 lines
crates/salmon-map/src/align.rs, Rust, 1,144 lines
crates/salmon-map/src/chain.rs, Rust, 567 lines
crates/salmon-map/src/collect.rs, Rust, 397 lines
crates/salmon-map/src/extend.rs, Rust, 628 lines
crates/salmon-map/src/lib.rs, Rust, 82 lines
crates/salmon-map/src/mapper.rs, Rust, 782 lines
crates/salmon-map/src/mem.rs, Rust, 138 lines
crates/salmon-map/src/pair.rs, Rust, 772 lines
crates/salmon-map/src/score.rs, Rust, 720 lines
crates/salmon-map/src/sketch.rs, Rust, 379 lines
crates/salmon-map/tests/collect_on_index.rs, Rust, 441 lines
crates/salmon-model/examples/conv_bench.rs, Rust, 123 lines
crates/salmon-model/src/bias.rs, Rust, 509 lines
crates/salmon-model/src/dumps.rs, Rust, 209 lines
crates/salmon-model/src/fld.rs, Rust, 830 lines
crates/salmon-model/src/gcbias.rs, Rust, 849 lines
crates/salmon-model/src/lib.rs, Rust, 78 lines
crates/salmon-model/src/libdetect.rs, Rust, 408 lines
crates/salmon-model/src/posbias.rs, Rust, 340 lines
crates/salmon-model/src/seqbias.rs, Rust, 1,168 lines
crates/salmon-model/src/spline.rs, Rust, 342 lines
crates/salmon-quant/src/bam.rs, Rust, 558 lines
crates/salmon-quant/src/decode.rs, Rust, 405 lines
crates/salmon-quant/src/lib.rs, Rust, 1,488 lines
crates/salmon-quant/src/mapping_record.rs, Rust, 451 lines
crates/salmon-quant/src/output.rs, Rust, 608 lines
crates/salmon-quant/src/processor.rs, Rust, 1,723 lines
crates/salmon-quant/src/sam.rs, Rust, 139 lines
crates/salmon-quant/tests/bgzf_worker_count.rs, Rust, 64 lines
crates/salmon-quant/tests/decoder_per_file.rs, Rust, 163 lines
crates/salmon-quant/tests/pool_resize_flush_safety.rs, Rust, 263 lines
crates/salmon-quant/tests/quant_end_to_end.rs, Rust, 1,320 lines
crates/salmon-rad/src/lib.rs, Rust, 665 lines
crates/salmon-rad/src/record.rs, Rust, 198 lines
crates/salmon-rad/src/schema.rs, Rust, 201 lines
crates/salmon-rad/src/writer.rs, Rust, 414 lines
crates/salmon-rad/tests/roundtrip.rs, Rust, 527 lines
scripts/bench_em_rad.sh, Shell, 131 lines
scripts/bump_and_publish.sh, Shell, 212 lines
scripts/decode_crossover.sh, Shell, 159 lines
scripts/profile.sh, Shell, 106 lines
website/src/content.config.ts, TypeScript, 7 lines
LICENSE, License, 28 lines
README.md, Text, 99 lines

At the source: github.com/COMBINE-lab/salmon/releases

The paper's code and data availability statement is in the Data section.

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93 scripts, each with its path and the digest of its content;
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Data

Datasets cited

bioproject:PRJNA1085406, at NCBI BioProject; found in “Data and code availability”

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

it points to a dataset: NCBI BioProject PRJNA1085406

Read it in the paper: doi.org/10.1016/j.stemcr.2026.102958.

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 30 authors, 11 keywords, 10 MeSH terms, 12 funders, 145 references, 23 RRIDs.

Cite

This paper

Jovanovic, V. M., Narisu, N., Bonnycastle, L. L., Castellano, D., Ryu, S., Tharakan, R., Mesch, K. T., Chen, Q., Betül Erol, F. M., Glover, H. J., Yan, T., Sinha, N., Sen, C., Yang, S., Blivis, D., Bennett, D. F., Rosales-Soto, G., Inman, J., Ormanoglu, P., . . . Tristan, C. A. (2026). Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders. Stem cell reports, 21(7), 102958. https://doi.org/10.1016/j.stemcr.2026.102958

BibTeX

@article{jovanovic2026scalable, author = {Jovanovic, Vukasin M. and Narisu, Narisu and Bonnycastle, Lori L. and Castellano, David and Ryu, Seungmi and Tharakan, Ravi and Mesch, Kendall T. and Chen, Qiang and Betül Erol, Fahrünisa Meryem and Glover, Hannah J. and Yan, Tingfen and Sinha, Neelam and Sen, Chaitali and Yang, Shu and Blivis, Dvir and Bennett, Daniel F. and Rosales-Soto, Giovanni and Inman, Jason and Ormanoglu, Pinar and LeClair, Christopher A. and Shaw, Natalie D. and Xia, Menghang and Schneider, Martin and Hernandez-Ochoa, Erick O. and Erdos, Michael R. and Simeonov, Anton and Chen, Shuibing and Collins, Francis S. and Doege, Claudia A. and Tristan, Carlos A.}, title = {{Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders}}, journal = {Stem cell reports}, year = {2026}, month = jun, volume = {21}, number = {7}, pages = {102958}, publisher = {Elsevier}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2026.102958}, url = {https://doi.org/10.1016/j.stemcr.2026.102958}, pmid = {42276059}, pmcid = {PMC13385436} }

RIS

TY - JOUR AU - Jovanovic, Vukasin M. AU - Narisu, Narisu AU - Bonnycastle, Lori L. AU - Castellano, David AU - Ryu, Seungmi AU - Tharakan, Ravi AU - Mesch, Kendall T. AU - Chen, Qiang AU - Betül Erol, Fahrünisa Meryem AU - Glover, Hannah J. AU - Yan, Tingfen AU - Sinha, Neelam AU - Sen, Chaitali AU - Yang, Shu AU - Blivis, Dvir AU - Bennett, Daniel F. AU - Rosales-Soto, Giovanni AU - Inman, Jason AU - Ormanoglu, Pinar AU - LeClair, Christopher A. AU - Shaw, Natalie D. AU - Xia, Menghang AU - Schneider, Martin AU - Hernandez-Ochoa, Erick O. AU - Erdos, Michael R. AU - Simeonov, Anton AU - Chen, Shuibing AU - Collins, Francis S. AU - Doege, Claudia A. AU - Tristan, Carlos A. TI - Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders T2 - Stem cell reports J2 - Stem Cell Reports PY - 2026 DA - 2026/06/11 VL - 21 IS - 7 SP - 102958 SN - 2213-6711 PB - Elsevier DO - 10.1016/j.stemcr.2026.102958 UR - https://doi.org/10.1016/j.stemcr.2026.102958 LA - en ER -

CSL-JSON

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