Neural cues differentially modulate colorectal cancer cell behavior depending on patients' genomic background.

Code ↔ Paper

1 match between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

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[1] § STAR★Methods › Method details › Genetic and transcriptomic profiling of cell lines ↔ pRSEM/Param.py, lines 19–97 · score 0.56 · RNA seq, RSEM, quantification, libraries, filtered, Transcript

Paper

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The authors' code

Python · 178 lines · 7.3 KB · GPL-3.0 · 1 match

__doc__="""
pliu 20150511
python module for all parameters, input arguments
"""
class Param:
IDR_THRESHOLD = 0.05
N_PEAK = 300000
PEAK_TYPE = '-savr'
EXCLUSION_ZONE = '-500:85' ## Anshul recommend -500:85
TRAINING_GENE_MIN_LEN = 1003
TRAINING_MIN_MAPPABILITY = 0.8
FLANKING_WIDTH = 500 ## in nt, flanking region around TSS and TES
INFORMATIVE_DATA_MAX_P_VALUE = 0.01 ## external data set is informative if
## p-value is not more than this value
def __init__(self):
self.argdict = None
## has to be in the same naming convention as prsem-calculate-expression
self.num_threads = None
self.chipseq_target_read_files = None
self.chipseq_control_read_files = None
self.chipseq_read_files_multi_targets = None
self.chipseq_bed_files_multi_targets = None
self.cap_stacked_chipseq_reads = None
self.n_max_stacked_chipseq_reads = None
self.bowtie_path = None
self.chipseq_peak_file = None
self.mappability_bigwig_file = None
self.partition_model = None
self.gibbs_burnin = None
self.gibbs_number_of_samples = None
self.gibbs_sampling_gap = None
self.quiet = False
## arguments
self.ref_fasta = None
self.ref_name = None
self.sample_name = None
self.stat_name = None
self.imd_name = None
## path and pRSEM scripts
self.temp_dir = None ## dir to save RSEM/pRSEM intermediate files
self.prsem_scr_dir = None ## pRSEM scripts dir
self.prsem_rlib_dir = None ## place to install pRSEM required R libraries
## genome reference: training set isoforms
self.fall_exon_crd = None
self.fall_tr_crd = None ## tr info + mappability
self.ftraining_tr_crd = None ## training set tr
## ChIP-seq
self.chipseqexperiment_target = None ## reference to ChIP-seq experiment
self.chipseqexperiment_control = None ## reference to ChIP-seq experiment
self.chipseq_rscript = None ## full name of process-chipseq.R
self.filterSam2Bed = None ## full name of filterSam2Bed binary
self.spp_tgz = None
self.spp_script = None
self.idr_scr_dir = None
self.idr_script = None
self.fgenome_table = None
self.fidr_chipseq_peaks = None
self.fall_chipseq_peaks = None
self.fchipseq_peaks = None ## full name of user supplied ChIP-seq peak
## file, otherwise is fidr_chipseq_peaks
self.chipseq_target_fraglen = None ## spp-estimated fragment length
self.fsppout_target = None ## full name of SPP output
## this implementation needs to be refined since
## the var is define in both Param and ChIPSeqExp
self.fchipseq_target_signals = None
self.fchipseq_control_signals = None
## transcripts and RNA-seq
self.transcripts = None ## reference to all transcripts to be quantified
self.genes = None ## reference to all genes to be quantified
self.rnaseq_rscript = None ## fullname of R script for dealing RNA-seq
self.fti = None ## RSEM's reference .ti file
self.bigwigsummary_bin = None ## bigWigSummary binary
self.fall_tr_features = None ## file for all isoforms' features
self.fall_tr_prior = None ## file for all isoforms' priors
self.fisoforms_results = None ## file for RSEM .isoforms.results
self.fpvalLL = None ## file for p-value on if informative
## and for log-likelihood
self.fall_pvalLL = None ## file to store all the p-val and log-likelihood
## for multiple external data sets
self.targetid2fchipseq_alignment = {}
self.finfo_multi_targets = None
self.flgt_model_multi_targets = None
## for testing procedure
self.targetids = []
def __str__(self):
ss = [ "%-33s %s\n" % (key, val) for (key, val) in self.argdict.items()] + \
[ "%-33s %s\n" % ('RSEM_temp_dir', self.temp_dir ) ] + \
[ "%-33s %s\n" % ('pRSEM_scr_dir', self.prsem_scr_dir) ]
return ''.join(ss)
@classmethod
def initFromCommandLineArguments(cls, argdict):
import os
prm = cls()
prm.argdict = argdict
for (key, val) in argdict.items():
setattr(prm, key, val)
if prm.imd_name is not None:
prm.temp_dir = os.path.split(prm.imd_name)[0] + '/'
prm.prsem_scr_dir = os.path.dirname(os.path.realpath(__file__)) + '/'
prm.prsem_rlib_dir = prm.prsem_scr_dir + 'RLib/'
if not os.path.exists(prm.prsem_rlib_dir):
os.mkdir(prm.prsem_rlib_dir)
## genome reference: pRSEM training set isoforms
prm.fall_exon_crd = prm.ref_name + '_prsem.all_exon_crd'
prm.fall_tr_crd = prm.ref_name + '_prsem.all_tr_crd'
prm.ftraining_tr_crd = prm.ref_name + '_prsem.training_tr_crd'
## ChIP-seq
prm.chipseq_rscript = prm.prsem_scr_dir + 'process-chipseq.R'
prm.filterSam2Bed = prm.prsem_scr_dir + 'filterSam2Bed'
prm.spp_tgz = prm.prsem_scr_dir + 'phantompeakqualtools/spp_1.10.1.tar.gz'
prm.spp_script = prm.prsem_scr_dir + 'phantompeakqualtools/run_spp.R'
prm.idr_scr_dir = prm.prsem_scr_dir + 'idrCode/'
prm.idr_script = prm.idr_scr_dir + 'batch-consistency-analysis.r'
prm.fgenome_table = prm.ref_name + '.chrlist'
if prm.temp_dir is not None:
prm.fsppout_target = prm.temp_dir + 'target_phantom.tab'
prm.fchipseq_target_signals = prm.temp_dir + 'target.tagAlign.gz'
prm.fchipseq_control_signals = prm.temp_dir + 'control.tagAlign.gz'
prm.fidr_chipseq_peaks = "%s/%s" % (prm.temp_dir,
'idr_target_vs_control.regionPeak.gz')
## have to name it this way due to run_spp.R's wired naming convention
## this names depens on the next two names
prm.fall_chipseq_peaks = "%s/%s" % (prm.temp_dir,
'target.tagAlign_VS_control.tagAlign.regionPeak.gz')
if prm.chipseq_peak_file is not None:
prm.fchipseq_peaks = prm.chipseq_peak_file
else:
prm.fchipseq_peaks = prm.fidr_chipseq_peaks
## transcripts and RNA-seq
prm.rnaseq_rscript = prm.prsem_scr_dir + 'process-rnaseq.R'
prm.fti = prm.ref_name + '.ti'
prm.ffasta = prm.ref_name + '.transcripts.fa'
prm.bigwigsummary_bin = prm.prsem_scr_dir + 'bigWigSummary'
#prm.fall_exon_crd = prm.imd_name + '_prsem.all_exon_crd'
#prm.fall_tr_crd = prm.imd_name + '_prsem.all_tr_crd'
#prm.ftraining_tr_crd = prm.imd_name + '_prsem.training_tr_crd'
if prm.sample_name is not None: ## for calc-expr
prm.fall_tr_gc = prm.imd_name + '_prsem.all_tr_gc'
prm.fall_tr_features = prm.stat_name + '_prsem.all_tr_features'
prm.fall_tr_prior = prm.stat_name + '_prsem.all_tr_prior'
prm.fpvalLL = prm.stat_name + '_prsem.pval_LL'
prm.fisoforms_results = prm.sample_name + '.isoforms.results'
prm.fall_pvalLL = prm.sample_name + '.all.pval_LL'
## for multiple external data sets
prm.finfo_multi_targets = prm.temp_dir + 'multi_targets.info'
prm.flgt_model_multi_targets = prm.stat_name + '_prsem.lgt_mdl.RData'
return prm
def initFromCommandLineArguments(argdict):
return Param.initFromCommandLineArguments(argdict)

Param.py at commit 800234e, under GPL-3.0 · at the source

Overview

Authors: Meike S. Thijssen^1,2, Rosaria Chilà³, Giovanni Crisafulli³, Kim M. Smits¹, Alberto Bardelli^3,4, Werend Boesmans^1,2, Veerle Melotte¹

ORCID iDs: Meike S. Thijssen, Rosaria Chilà, Giovanni Crisafulli, Veerle Melotte

Institutions: Maastricht University Medical Centre (Netherlands); Maastricht University (Netherlands); Hasselt University (Belgium); IFOM (Italy); University of Turin (Italy)

Journal: iScience, volume 29, issue 6, article 116153

Dates: received 19 November 2025; accepted 13 May 2026; published online 28 May 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1016/j.isci.2026.116153 · PMID 42256296 · PMCID PMC13233565 · OpenAlex W7162638011

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: human (organism), other condition (population), clinical / translational (subfield)

Methods: Statistics

Keywords: oncology, microenvironment, neuroscience

Topic: Cancer, Stress, Anesthesia, and Immune Response (Psychiatry and Mental health, Medicine), according to OpenAlex

Funding: Hasselt University; Maastricht University Medical Centre+; Kankeronderzoeksfonds Limburg (KOFL); Het Fonds voor Wetenschappelijk Onderzoek – Vlaanderen (FWO) (V472323N); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (09150172110100)

Citations: not cited yet (Europe PMC); 72 references in the paper

Abstract

While neurons are mostly described as pro-tumorigenic and linked with a poor prognosis, differing outcomes have been reported for colorectal cancer (CRC) due to the lack of control for neural and patient subtype diversity. In this study, we investigated the effect of neural cues on patient-derived CRC cell lines selected based on genomic status, e.g., microsatellite instability (MSI) and KRAS and BRAF mutations. Although most neural signals increased clonogenicity, the adrenergic neurotransmitter epinephrine had the opposite effect. Epinephrine also decreased CRC cell viability, independent of the genomic status. Vasoactive intestinal peptide decreased cell viability only in BRAF wild-type cells. Interestingly, all neural signals induced migration in microsatellite stable (MSS) cells, with no effect in cells with MSI. Epinephrine or glial cell line-derived neurotrophic factor also stimulated migration specifically in BRAF-mutated cells. These results emphasize the importance of targeting specific neural signaling pathways and highlight that patient stratification is essential for cancer neuroscience studies.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

alexdobin/STAR

License: MIT

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: b1edc1208d91a53bf40ebae8669f71d50b994851, 25 January 2024

Languages: C++ (160), C/C++ (133), C (34), Shell (1), MATLAB (1)

Size: 389 files, 329 scripts

Software Heritage: not archived

Found in: the text, “Key resources table”

Holds: README, license file, environment (extras/docker/Dockerfile), continuous integration, documentation

Not found: CITATION.cff, tests

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

27 September 2026: the link answers

331 files

extras/scripts/extractSJfromGTF.sh, Shell, 10 lines
extras/scripts/sjMotif.m, MATLAB, 45 lines
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source/htslib/hts.c, C, 1,326 lines
source/htslib/htslib/bgzf.h, C/C++, 313 lines
source/htslib/htslib/faidx.h, C/C++, 112 lines
source/htslib/htslib/hfile.h, C/C++, 204 lines
source/htslib/htslib/hts.h, C/C++, 305 lines
source/htslib/htslib/hts_defs.h, C/C++, 47 lines
source/htslib/htslib/kfunc.h, C/C++, 49 lines
source/htslib/htslib/khash.h, C/C++, 617 lines
source/htslib/htslib/khash_str2int.h, C/C++, 98 lines
source/htslib/htslib/klist.h, C/C++, 121 lines
source/htslib/htslib/knetfile.h, C/C++, 75 lines
source/htslib/htslib/kseq.h, C/C++, 253 lines
source/htslib/htslib/ksort.h, C/C++, 285 lines
source/htslib/htslib/kstdint.h, C/C++, 64 lines
source/htslib/htslib/kstring.h, C/C++, 270 lines
source/htslib/htslib/sam.h, C/C++, 401 lines
source/htslib/htslib/synced_bcf_reader.h, C/C++, 255 lines
source/htslib/htslib/tbx.h, C/C++, 52 lines
source/htslib/htslib/vcf.h, C/C++, 824 lines
source/htslib/htslib/vcf_sweep.h, C/C++, 15 lines
source/htslib/htslib/vcfutils.h, C/C++, 94 lines
source/htslib/kfunc.c, C, 254 lines
source/htslib/knetfile.c, C, 622 lines
source/htslib/kstring.c, C, 229 lines
source/htslib/sam.c, C, 1,797 lines
source/htslib/synced_bcf_reader.c, C, 1,183 lines
source/htslib/tabix.c, C, 374 lines
source/htslib/tbx.c, C, 290 lines
source/htslib/vcf.c, C, 2,967 lines
source/htslib/vcf_sweep.c, C, 158 lines
source/htslib/vcfutils.c, C, 642 lines
source/insertSeqSA.cpp, C++, 319 lines
source/insertSeqSA.h, C/C++, 11 lines
source/mapThreadsSpawn.cpp, C++, 33 lines
source/mapThreadsSpawn.h, C/C++, 7 lines
source/opal/opal.cpp, C++, 1,568 lines
source/opal/opal.h, C/C++, 171 lines
source/opal/simde_avx2.h, C/C++, 5,590 lines
source/outputSJ.cpp, C++, 163 lines
source/outputSJ.h, C/C++, 4 lines
source/readBarcodeLoad.h, C/C++, 9 lines
source/readLoad.cpp, C++, 100 lines
source/readLoad.h, C/C++, 12 lines
source/samHeaders.cpp, C++, 108 lines
source/samHeaders.h, C/C++, 10 lines
source/serviceFuns.cpp, C++, 351 lines
source/signalFromBAM.cpp, C++, 209 lines
source/signalFromBAM.h, C/C++, 13 lines
source/sjAlignSplit.cpp, C++, 15 lines
source/sjAlignSplit.h, C/C++, 9 lines
source/sjdbBuildIndex.cpp, C++, 333 lines
source/sjdbBuildIndex.h, C/C++, 10 lines
source/sjdbInsertJunctions.cpp, C++, 102 lines
source/sjdbInsertJunctions.h, C/C++, 10 lines
source/sjdbLoadFromFiles.cpp, C++, 27 lines
source/sjdbLoadFromFiles.h, C/C++, 10 lines
source/sjdbLoadFromStream.cpp, C++, 29 lines
source/sjdbLoadFromStream.h, C/C++, 8 lines
source/sjdbPrepare.cpp, C++, 225 lines
source/sjdbPrepare.h, C/C++, 10 lines
source/soloInputFeatureUMI.cpp, C++, 44 lines
source/soloInputFeatureUMI.h, C/C++, 13 lines
source/sortSuffixesBucket.h, C/C++, 3 lines
source/stitchAlignToTranscript.cpp, C++, 415 lines
source/stitchAlignToTranscript.h, C/C++, 7 lines
source/stitchGapIndel.cpp, C++, 59 lines
source/stitchWindowAligns.cpp, C++, 355 lines
source/stitchWindowAligns.h, C/C++, 12 lines
source/streamFuns.cpp, C++, 149 lines
source/streamFuns.h, C/C++, 17 lines
source/stringSubstituteAll.cpp, C++, 10 lines
source/stringSubstituteAll.h, C/C++, 8 lines
source/sysRemoveDir.cpp, C++, 28 lines
source/sysRemoveDir.h, C/C++, 8 lines
source/systemFunctions.cpp, C++, 27 lines
source/systemFunctions.h, C/C++, 6 lines
source/twoPassRunPass1.cpp, C++, 97 lines
source/twoPassRunPass1.h, C/C++, 11 lines
LICENSE, License, 21 lines
README.md, Text, 115 lines

At the source: github.com/alexdobin/STAR

deweylab/RSEM

License: GPL-3.0

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 800234e0d25d16bf7042804604c4371f12b96d9e, 3 August 2026

Languages: C/C++ (180), C (111), C++ (48), Perl (16), Python (11), R (11), Shell (7), Java (1)

Size: 3,057 files, 385 scripts

Software Heritage: not archived

Found in: the text, “Key resources table”

Holds: README, license file, environment (tests/environment.yml, pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/DESCRIPTION, pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/DESCRIPTION), tests, continuous integration, documentation

Not found: CITATION.cff

Tools: data.table (2 files), STAR (1 file)

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

27 September 2026: the link answers

387 files

AlignerRefSeqPolicy.h, C/C++, 19 lines
BamConverter.h, C/C++, 305 lines
BamWriter.h, C/C++, 148 lines
Buffer.h, C/C++, 83 lines
EBSeq/calcClusteringInfo.cpp, C++, 144 lines
EM.cpp, C++, 675 lines
GTFItem.h, C/C++, 184 lines
Gibbs.cpp, C++, 530 lines
GroupInfo.h, C/C++, 55 lines
HitContainer.h, C/C++, 118 lines
HitWrapper.h, C/C++, 35 lines
LenDist.h, C/C++, 298 lines
Model.h, C/C++, 7 lines
ModelParams.h, C/C++, 39 lines
NoiseProfile.h, C/C++, 159 lines
NoiseQProfile.h, C/C++, 181 lines
Orientation.h, C/C++, 42 lines
PairedEndHit.h, C/C++, 36 lines
PairedEndModel.h, C/C++, 461 lines
PairedEndQModel.h, C/C++, 481 lines
PairedEndRead.h, C/C++, 67 lines
PairedEndReadQ.h, C/C++, 67 lines
PolyARules.h, C/C++, 61 lines
Profile.h, C/C++, 220 lines
QProfile.h, C/C++, 208 lines
QualDist.h, C/C++, 151 lines
RSPD.h, C/C++, 206 lines
Read.h, C/C++, 23 lines
ReadIndex.h, C/C++, 59 lines
ReadReader.h, C/C++, 118 lines
RefSeq.h, C/C++, 140 lines
RefSeqPolicy.h, C/C++, 22 lines
Refs.h, C/C++, 159 lines
SamHeader.cpp, C++, 111 lines
SamParser.h, C/C++, 268 lines
SingleHit.h, C/C++, 56 lines
SingleModel.h, C/C++, 526 lines
SingleQModel.h, C/C++, 546 lines
SingleRead.h, C/C++, 92 lines
SingleReadQ.h, C/C++, 97 lines
Transcript.h, C/C++, 169 lines
Transcripts.h, C/C++, 145 lines
WriteResults.h, C/C++, 637 lines
bam2readdepth.cpp, C++, 27 lines
bam2wig.cpp, C++, 27 lines
bc_aux.h, C/C++, 120 lines
boost/predef/architecture.h, C/C++, 30 lines
boost/predef/architecture/alpha.h, C/C++, 60 lines
boost/predef/architecture/arm.h, C/C++, 58 lines
boost/predef/architecture/blackfin.h, C/C++, 47 lines
boost/predef/architecture/convex.h, C/C++, 67 lines
boost/predef/architecture/ia64.h, C/C++, 49 lines
boost/predef/architecture/m68k.h, C/C++, 83 lines
boost/predef/architecture/mips.h, C/C++, 74 lines
boost/predef/architecture/parisc.h, C/C++, 65 lines
boost/predef/architecture/ppc.h, C/C++, 73 lines
boost/predef/architecture/pyramid.h, C/C++, 43 lines
boost/predef/architecture/rs6k.h, C/C++, 56 lines
boost/predef/architecture/sparc.h, C/C++, 55 lines
boost/predef/architecture/superh.h, C/C++, 68 lines
boost/predef/architecture/sys370.h, C/C++, 44 lines
boost/predef/architecture/sys390.h, C/C++, 44 lines
boost/predef/architecture/x86.h, C/C++, 38 lines
boost/predef/architecture/x86/32.h, C/C++, 87 lines
boost/predef/architecture/x86/64.h, C/C++, 50 lines
boost/predef/architecture/z.h, C/C++, 43 lines
boost/predef/detail/_cassert.h, C/C++, 17 lines
boost/predef/detail/endian_compat.h, C/C++, 26 lines
boost/predef/detail/os_detected.h, C/C++, 10 lines
boost/predef/detail/test.h, C/C++, 17 lines
boost/predef/library/c/_prefix.h, C/C++, 13 lines
boost/predef/library/c/gnu.h, C/C++, 62 lines
boost/predef/make.h, C/C++, 87 lines
boost/predef/os/bsd.h, C/C++, 95 lines
boost/predef/os/bsd/bsdi.h, C/C++, 48 lines
boost/predef/os/bsd/dragonfly.h, C/C++, 50 lines
boost/predef/os/bsd/free.h, C/C++, 60 lines
boost/predef/os/bsd/net.h, C/C++, 84 lines
boost/predef/os/bsd/open.h, C/C++, 171 lines
boost/predef/os/macos.h, C/C++, 58 lines
boost/predef/os/windows.h, C/C++, 51 lines
boost/predef/other/endian.h, C/C++, 205 lines
boost/predef/version_number.h, C/C++, 54 lines
boost_compat.h, C/C++, 69 lines
buildReadIndex.cpp, C++, 86 lines
calcCI.cpp, C++, 581 lines
extractRef.cpp, C++, 376 lines
getUnique.cpp, C++, 83 lines
my_assert.h, C/C++, 107 lines
pRSEM/ChIPSeqExperiment.py, Python, 257 lines
pRSEM/ChIPSeqReplicate.py, Python, 43 lines
pRSEM/File.py, Python, 47 lines
pRSEM/Gene.py, Python, 143 lines
pRSEM/Param.py, Python, 178 lines, 1 match
pRSEM/Prsem.py, Python, 253 lines
pRSEM/Transcript.py, Python, 189 lines
pRSEM/Util.py, Python, 173 lines
pRSEM/filterSam2Bed.c, C, 52 lines
pRSEM/idrCode/batch-consistency-analysis.r, R, 164 lines
pRSEM/idrCode/batch-consistency-plot-merged2.r, R, 213 lines
pRSEM/idrCode/batch-consistency-plot.r, R, 67 lines
pRSEM/idrCode/functions-all-clayton-12-13.r, R, 3,182 lines
pRSEM/idrCode/idrOverlap2npk.sh, Shell, 37 lines
pRSEM/idrCode/submit.idrmerge.lsf.sh, Shell, 72 lines
pRSEM/idrCode/submit.idrpair.lsf.sh, Shell, 90 lines
pRSEM/installRLib.R, R, 71 lines
pRSEM/phantompeakqualtools/run_spp.R, R, 885 lines
pRSEM/phantompeakqualtools/run_spp_nodups.R, R, 886 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/R/zroutines.R, R, 2,501 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BGZF.cpp, C++, 398 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BGZF.h, C/C++, 322 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAlignment.cpp, C++, 696 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAlignment.h, C/C++, 203 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAux.h, C/C++, 227 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamIndex.cpp, C++, 230 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamIndex.h, C/C++, 145 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamMultiReader.cpp, C++, 450 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamMultiReader.h, C/C++, 136 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamReader.cpp, C++, 66 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamReader.h, C/C++, 130 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamReader_p.cpp, C++, 729 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamReader_p.h, C/C++, 137 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamStandardIndex_p.cpp, C++, 910 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamStandardIndex_p.h, C/C++, 213 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamToolsIndex_p.cpp, C++, 577 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamToolsIndex_p.h, C/C++, 192 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamWriter.cpp, C++, 47 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamWriter.h, C/C++, 50 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamWriter_p.cpp, C++, 379 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamWriter_p.h, C/C++, 63 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/api_global.h, C/C++, 22 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/bamread.cpp, C++, 214 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/bamtools_global.h, C/C++, 32 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/bed2vector.cpp, C++, 2,492 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/cdensum.c, C, 144 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/const.h, C/C++, 18 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/maqmap.c, C, 164 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/maqmap.h, C/C++, 70 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/maqread.cpp, C++, 206 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/pc.h, C/C++, 7 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/peaks.cpp, C++, 803 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/wdl.cpp, C++, 656 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/R/zroutines.R, R, 2,501 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BGZF.cpp, C++, 398 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BGZF.h, C/C++, 322 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAlignment.cpp, C++, 696 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAlignment.h, C/C++, 203 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAux.h, C/C++, 227 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamIndex.cpp, C++, 230 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamIndex.h, C/C++, 145 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamMultiReader.cpp, C++, 450 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamMultiReader.h, C/C++, 136 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamReader.cpp, C++, 66 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamReader.h, C/C++, 130 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamReader_p.cpp, C++, 729 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamReader_p.h, C/C++, 137 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamStandardIndex_p.cpp, C++, 910 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamStandardIndex_p.h, C/C++, 213 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamToolsIndex_p.cpp, C++, 577 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamToolsIndex_p.h, C/C++, 192 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamWriter.cpp, C++, 47 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamWriter.h, C/C++, 50 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamWriter_p.cpp, C++, 379 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamWriter_p.h, C/C++, 63 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/api_global.h, C/C++, 22 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/bamread.cpp, C++, 215 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/bamtools_global.h, C/C++, 32 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/bed2vector.cpp, C++, 2,494 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/cdensum.c, C, 144 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/const.h, C/C++, 18 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/maqmap.c, C, 164 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/maqmap.h, C/C++, 70 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/maqread.cpp, C++, 208 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/pc.h, C/C++, 7 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/peaks.cpp, C++, 807 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/string_utils.h, C/C++, 32 lines
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/wdl.cpp, C++, 659 lines
pRSEM/process-chipseq.R, R, 61 lines
pRSEM/process-rnaseq.R, R, 982 lines
parseIt.cpp, C++, 230 lines
preRef.cpp, C++, 90 lines
samValidator.cpp, C++, 193 lines
sam_utils.h, C/C++, 210 lines
sampling.h, C/C++, 92 lines
samtools-1.3/bam.c, C, 235 lines
samtools-1.3/bam.h, C/C++, 577 lines
samtools-1.3/bam2bcf.c, C, 841 lines
samtools-1.3/bam2bcf.h, C/C++, 139 lines
samtools-1.3/bam2bcf_indel.c, C, 531 lines
samtools-1.3/bam2depth.c, C, 301 lines
samtools-1.3/bam_addrprg.c, C, 476 lines
samtools-1.3/bam_aux.c, C, 79 lines
samtools-1.3/bam_cat.c, C, 558 lines
samtools-1.3/bam_color.c, C, 169 lines
samtools-1.3/bam_endian.h, C/C++, 66 lines
samtools-1.3/bam_flags.c, C, 68 lines
samtools-1.3/bam_import.c, C, 63 lines
samtools-1.3/bam_index.c, C, 121 lines
samtools-1.3/bam_lpileup.c, C, 223 lines
samtools-1.3/bam_lpileup.h, C/C++, 57 lines
samtools-1.3/bam_mate.c, C, 362 lines
samtools-1.3/bam_md.c, C, 441 lines
samtools-1.3/bam_plbuf.c, C, 66 lines
samtools-1.3/bam_plbuf.h, C/C++, 55 lines
samtools-1.3/bam_plcmd.c, C, 1,028 lines
samtools-1.3/bam_quickcheck.c, C, 134 lines
samtools-1.3/bam_reheader.c, C, 482 lines
samtools-1.3/bam_rmdup.c, C, 261 lines
samtools-1.3/bam_rmdupse.c, C, 187 lines
samtools-1.3/bam_sort.c, C, 1,839 lines
samtools-1.3/bam_split.c, C, 567 lines
samtools-1.3/bam_stat.c, C, 177 lines
samtools-1.3/bam_tview.c, C, 439 lines
samtools-1.3/bam_tview.h, C/C++, 105 lines
samtools-1.3/bam_tview_curses.c, C, 352 lines
samtools-1.3/bam_tview_html.c, C, 375 lines
samtools-1.3/bamshuf.c, C, 213 lines
samtools-1.3/bamtk.c, C, 227 lines
samtools-1.3/bedcov.c, C, 177 lines
samtools-1.3/bedidx.c, C, 258 lines
samtools-1.3/cut_target.c, C, 242 lines
samtools-1.3/dict.c, C, 151 lines
samtools-1.3/errmod.c, C, 192 lines
samtools-1.3/errmod.h, C/C++, 49 lines
samtools-1.3/faidx.c, C, 95 lines
samtools-1.3/htslib-1.3/bgzf.c, C, 1,125 lines
samtools-1.3/htslib-1.3/bgzip.c, C, 297 lines
samtools-1.3/htslib-1.3/cram/cram.h, C/C++, 61 lines
samtools-1.3/htslib-1.3/cram/cram_codecs.c, C, 1,949 lines
samtools-1.3/htslib-1.3/cram/cram_codecs.h, C/C++, 194 lines
samtools-1.3/htslib-1.3/cram/cram_decode.c, C, 3,143 lines
samtools-1.3/htslib-1.3/cram/cram_decode.h, C/C++, 112 lines
samtools-1.3/htslib-1.3/cram/cram_encode.c, C, 3,094 lines
samtools-1.3/htslib-1.3/cram/cram_encode.h, C/C++, 105 lines
samtools-1.3/htslib-1.3/cram/cram_external.c, C, 377 lines
samtools-1.3/htslib-1.3/cram/cram_index.c, C, 582 lines
samtools-1.3/htslib-1.3/cram/cram_index.h, C/C++, 99 lines
samtools-1.3/htslib-1.3/cram/cram_io.c, C, 4,555 lines
samtools-1.3/htslib-1.3/cram/cram_io.h, C/C++, 669 lines
samtools-1.3/htslib-1.3/cram/cram_samtools.c, C, 149 lines
samtools-1.3/htslib-1.3/cram/cram_samtools.h, C/C++, 105 lines
samtools-1.3/htslib-1.3/cram/cram_stats.c, C, 448 lines
samtools-1.3/htslib-1.3/cram/cram_stats.h, C/C++, 59 lines
samtools-1.3/htslib-1.3/cram/cram_structs.h, C/C++, 816 lines
samtools-1.3/htslib-1.3/cram/files.c, C, 74 lines
samtools-1.3/htslib-1.3/cram/mFILE.c, C, 694 lines
samtools-1.3/htslib-1.3/cram/mFILE.h, C/C++, 89 lines
samtools-1.3/htslib-1.3/cram/misc.h, C/C++, 110 lines
samtools-1.3/htslib-1.3/cram/open_trace_file.c, C, 414 lines
samtools-1.3/htslib-1.3/cram/open_trace_file.h, C/C++, 125 lines
samtools-1.3/htslib-1.3/cram/os.h, C/C++, 308 lines
samtools-1.3/htslib-1.3/cram/pooled_alloc.c, C, 188 lines
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samtools-1.3/htslib-1.3/cram/rANS_byte.h, C/C++, 336 lines
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samtools-1.3/htslib-1.3/cram/zfio.c, C, 183 lines
samtools-1.3/htslib-1.3/cram/zfio.h, C/C++, 62 lines
samtools-1.3/htslib-1.3/faidx.c, C, 484 lines
samtools-1.3/htslib-1.3/hfile.c, C, 744 lines
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samtools-1.3/htslib-1.3/hfile_irods.c, C, 259 lines
samtools-1.3/htslib-1.3/hfile_libcurl.c, C, 919 lines
samtools-1.3/htslib-1.3/hfile_net.c, C, 112 lines
samtools-1.3/htslib-1.3/hts.c, C, 2,055 lines
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samtools-1.3/htslib-1.3/htsfile.c, C, 234 lines
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samtools-1.3/htslib-1.3/htslib/hfile.h, C/C++, 215 lines
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samtools-1.3/htslib-1.3/htslib/ksort.h, C/C++, 285 lines
samtools-1.3/htslib-1.3/htslib/kstring.h, C/C++, 277 lines
samtools-1.3/htslib-1.3/htslib/regidx.h, C/C++, 154 lines
samtools-1.3/htslib-1.3/htslib/sam.h, C/C++, 454 lines
samtools-1.3/htslib-1.3/htslib/synced_bcf_reader.h, C/C++, 302 lines
samtools-1.3/htslib-1.3/htslib/tbx.h, C/C++, 79 lines
samtools-1.3/htslib-1.3/htslib/vcf.h, C/C++, 907 lines
samtools-1.3/htslib-1.3/htslib/vcf_sweep.h, C/C++, 47 lines
samtools-1.3/htslib-1.3/htslib/vcfutils.h, C/C++, 134 lines
samtools-1.3/htslib-1.3/kfunc.c, C, 280 lines
samtools-1.3/htslib-1.3/knetfile.c, C, 632 lines
samtools-1.3/htslib-1.3/kstring.c, C, 274 lines
samtools-1.3/htslib-1.3/md5.c, C, 386 lines
samtools-1.3/htslib-1.3/plugin.c, C, 171 lines
samtools-1.3/htslib-1.3/regidx.c, C, 340 lines
samtools-1.3/htslib-1.3/sam.c, C, 2,059 lines
samtools-1.3/htslib-1.3/synced_bcf_reader.c, C, 1,284 lines
samtools-1.3/htslib-1.3/tabix.c, C, 538 lines
samtools-1.3/htslib-1.3/tbx.c, C, 333 lines
samtools-1.3/htslib-1.3/test/compare_sam.pl, Perl, 194 lines
samtools-1.3/htslib-1.3/test/cross_validate.sh, Shell, 126 lines
samtools-1.3/htslib-1.3/test/fieldarith.c, C, 72 lines
samtools-1.3/htslib-1.3/test/hfile.c, C, 204 lines
samtools-1.3/htslib-1.3/test/sam.c, C, 208 lines
samtools-1.3/htslib-1.3/test/test-regidx.c, C, 116 lines
samtools-1.3/htslib-1.3/test/test-vcf-api.c, C, 282 lines
samtools-1.3/htslib-1.3/test/test-vcf-sweep.c, C, 112 lines
samtools-1.3/htslib-1.3/test/test.pl, Perl, 227 lines
samtools-1.3/htslib-1.3/test/test_view.c, C, 194 lines
samtools-1.3/htslib-1.3/test/test_view.pl, Perl, 93 lines
samtools-1.3/htslib-1.3/vcf.c, C, 3,389 lines
samtools-1.3/htslib-1.3/vcf_sweep.c, C, 183 lines
samtools-1.3/htslib-1.3/vcfutils.c, C, 691 lines
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samtools-1.3/misc/ace2sam.c, C, 249 lines
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samtools-1.3/misc/md5fa.c, C, 89 lines
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samtools-1.3/test/merge/test_bam_translate.c, C, 596 lines
samtools-1.3/test/merge/test_rtrans_build.c, C, 118 lines
samtools-1.3/test/merge/test_trans_tbl_init.c, C, 574 lines
samtools-1.3/test/mpileup/regression.sh, Shell, 158 lines
samtools-1.3/test/split/test_count_rg.c, C, 123 lines
samtools-1.3/test/split/test_expand_format_string.c, C, 123 lines
samtools-1.3/test/split/test_filter_header_rg.c, C, 192 lines
samtools-1.3/test/split/test_parse_args.c, C, 215 lines
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samtools-1.3/test/tview/test_get_rg_sample.c, C, 81 lines
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simulation.cpp, C++, 225 lines
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tests/assert_path_flag_honored.sh, Shell, 27 lines
tests/check_option_coverage.py, Python, 114 lines
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COPYING, License, 674 lines
README.md, Text, 703 lines

At the source: github.com/deweylab/RSEM

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Version 2, 28 September 2026

Authors: added Veerle Melotte (0000-0002-9459-123X); removed Veerle Melotte

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 3 keywords, 5 funders, 71 references.

Cite

This paper

Thijssen, M. S., Chilà, R., Crisafulli, G., Smits, K. M., Bardelli, A., Boesmans, W., & Melotte, V. (2026). Neural cues differentially modulate colorectal cancer cell behavior depending on patients' genomic background. iScience, 29(6), 116153. https://doi.org/10.1016/j.isci.2026.116153

BibTeX

@article{thijssen2026neural, author = {Thijssen, Meike S. and Chilà, Rosaria and Crisafulli, Giovanni and Smits, Kim M. and Bardelli, Alberto and Boesmans, Werend and Melotte, Veerle}, title = {{Neural cues differentially modulate colorectal cancer cell behavior depending on patients' genomic background}}, journal = {iScience}, year = {2026}, month = may, volume = {29}, number = {6}, pages = {116153}, publisher = {Elsevier}, issn = {2589-0042}, doi = {10.1016/j.isci.2026.116153}, url = {https://doi.org/10.1016/j.isci.2026.116153}, pmid = {42256296}, pmcid = {PMC13233565} }

RIS

TY - JOUR AU - Thijssen, Meike S. AU - Chilà, Rosaria AU - Crisafulli, Giovanni AU - Smits, Kim M. AU - Bardelli, Alberto AU - Boesmans, Werend AU - Melotte, Veerle TI - Neural cues differentially modulate colorectal cancer cell behavior depending on patients' genomic background T2 - iScience J2 - iScience PY - 2026 DA - 2026/05/28 VL - 29 IS - 6 SP - 116153 SN - 2589-0042 PB - Elsevier DO - 10.1016/j.isci.2026.116153 UR - https://doi.org/10.1016/j.isci.2026.116153 LA - en ER -

CSL-JSON

{ "id": "10.1016/j.isci.2026.116153", "type": "article-journal", "title": "Neural cues differentially modulate colorectal cancer cell behavior depending on patients' genomic background", "container-title": "iScience", "author": [ { "family": "Thijssen", "given": "Meike S." }, { "family": "Chilà", "given": "Rosaria" }, { "family": "Crisafulli", "given": "Giovanni" }, { "family": "Smits", "given": "Kim M." }, { "family": "Bardelli", "given": "Alberto" }, { "family": "Boesmans", "given": "Werend" }, { "family": "Melotte", "given": "Veerle" } ], "container-title-short": "iScience", "volume": "29", "issue": "6", "page": "116153", "DOI": "10.1016/j.isci.2026.116153", "PMID": "42256296", "PMCID": "PMC13233565", "ISSN": "2589-0042", "publisher": "Elsevier", "URL": "https://doi.org/10.1016/j.isci.2026.116153", "language": "en", "issued": { "date-parts": [ [ 2026, 5, 28 ] ] } }

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