Library · Biology & lab methods
What High-Throughput Assays & Screening got wrong, from 54 theses
Summary written by a model from the records below: High-throughput screening platforms across biological, chemical, and computational domains encounter frequent operational bottlenecks, analytical artifacts, and validation failures. Many screening methodologies struggle to translate initial candidate hits into reproducible findings or suffer from severe throughput constraints and assay interference. These records come from graduate theses, 2021 to 2026, each labeled with its degree where the repository states it, and each links to its thesis. They were extracted by language models reading the full text, so treat each as a lead to read, not a verdict.
Plus 9 problems the authors left open, listed at the end.
Failure modes, by theses reporting them
Select a mode to jump to its records.
Low-throughput analytical procedures and manual bottlenecks restrict screening scalability
Lengthy sample preparation times, slow analytical instrument runs, and manual triage bottlenecks severely restrict screening capacity and create operational backlogs. Several experimental techniques were abandoned or rejected because cumbersome assays, high cell loss during sorting, or low conjugation efficiencies prevented scaling to large mutant or compound libraries.
Considered and rejected
Considered and rejected: Rejected the HCS γH2AX assay as a high-throughput primary screening tool for food contact materials due to lengthy sample preparation and low throughput.
Lost to a baseline
High-throughput 96-well cellulose acetate filter conjugation had ~5-fold lower efficiency (4.7 x 10^-7 transconjugants/donor) than standard 50-mL analytical filter conjugation.
Synthetic biology approaches for engineering bacteria as living therapeutics · MIT · PhD
Considered and rejected
Considered and rejected: Single VH-primer amplification was used initially for rapid candidate screening, rejecting immediate dual-chain amplification across all single cells due to low throughput.
Isolation and characterization of the functional breadth of neutralizing antibodies that cross-react with diverse sarbecovirus strains · University of Washington · PhD
Considered and rejected
Considered and rejected: Rejected untargeted screening (HPLC-ICP-MS analysis of all individual isolates) due to excessive analytical instrument time and lack of throughput.
High-throughput isolation of anaerobic arsenic-transforming microorganisms · EPFL · PhD
Considered and rejected
Considered and rejected: Directed evolution random-mutagenesis screening on ssnBVMO was halted after Round 3 due to high NADPH costs, large-scale purification limits, and low plate-screening throughput, pivoting instead to rational engineering.
Investigation of Thermostable Enzymes Identified Through the Use of Sequence Similarity Networks · Queen's University · Doctorate
Considered and rejected
Considered and rejected: Rejected direct high-throughput screening on electrode arrays for whole-genome search because direct electrochemical testing across thousands of mutants was impractical.
ENGINEERING BIOLOGICAL SYSTEMS TO ADVANCE ELECTROMICROBIAL PRODUCTION · Cornell · PhD
Considered and rejected
Considered and rejected: Rejected standard PAGE/HPLC/MS assays as primary high-throughput screening tools due to being cumbersome, denaturing, and low-throughput, developing the fluorescent G-quadruplex sensor instead.
Investigating the Mechanism of Non-Enzymatic RNA Replication · Harvard · PhD
Tried and failed
radioactivity- or conductivity-based chromatography and TLC applied to high-throughput lipid quantitative relative profiling. Outcome: too slow. Reason: unsuited for high-throughput quantitative profiling compared to modified ELISA and mass spectrometry methods
A lipidomic approach to elucidating the effects of antifungal compounds on signalling in fungi · Imperial · Doctorate
Tried and failed
manual expert triage in high-throughput screening applied to large-scale disease screening programmes. Outcome: too slow. Reason: expert reader bottlenecks caused massive operational backlogs, leaving most collected images unanalyzed
Modelling active case-finding strategies for tuberculosis in urban India · Imperial · PhD
Tried and failed
Time-multiplexed switching between sensing and actuation electrodes applied to High-throughput flow-through single-cell processing. Outcome: too slow. Reason: Switching transients between high-voltage actuation and sensing electronics caused millisecond measurement settling delays limiting throughput
Single-Cell Impedance Cytometry for the Control of Single-Cell Electroporation in a Flow-Through Device · Georgia Tech · PhD
Considered and rejected
Considered and rejected: Smart-seq2 without UMIs for high-throughput single-cell experiments (suffered from low throughput of ~few hundred cells per plate, PCR amplification bias, and inefficient template switching for lowly expressed transcripts)
Considered and rejected
Considered and rejected: Rejected inkjet printing because it prints only a single reagent at a time and multi-step protocols limit high-throughput scalability
Developing the Next Generation Rapid Diagnostic Microfluidic Devices for Measuring the Protein Levels in Multiple Myeloma Patients for Early Detection of Disease Re-Appearance · Harvard · Master's
Considered and rejected
Considered and rejected: Rejected standard FACS isolation directly on low-yield MFD setups due to high cell-loss rates (~70% loss during sorting), necessitating redesign of high-capacity radial microfluidics or optical screening.
Primary screening hits fail to reproduce during secondary validation and replication assays
Top candidates identified in initial genetic, phenotypic, or biochemical screens repeatedly fail to demonstrate expected activity when subjected to secondary confirmation. False positives arise from assay artifacts, copurifying contaminants, or baseline culture variations that do not generalize across independent replicates or orthogonal experimental platforms.
Tried and failed
high-throughput phenotypic screening for candidate target selection applied to therapeutic target validation in cancer cells. Outcome: did not generalise. Reason: top-scoring screening candidate failed to reproduce apoptotic or anti-proliferative effects in secondary validation assays
Modulation of miR-361-3p alters apoptosis in endocrine-resistant and -responsive breast cancer · Imperial · PhD
Tried and failed
high-throughput directed evolution screening applied to engineered enzyme variants. Outcome: did not generalise. Reason: apparent screening hits were false positives caused by copurifying contaminants affecting initial normalization and readout
Tried and failed
genome-wide pooled screening with targeted validation applied to chemotherapy drug sensitisation targets. Outcome: did not generalise. Reason: hit depletion scores failed to reproduce during targeted follow-up screens
CRISPRi screens to identify combination therapies for the improved treatment of ovarian cancer · MIT · PhD
Tried and failed
mass spectrometry screening followed by western blot validation applied to identifying viral-host protein degradation targets. Outcome: no signal. Reason: candidate targets identified by proteomics failed to show differential expression on orthogonal validation
ZER1 CONTRIBUTES TO THE GROWTH OF HPV-POSITIVE CANCERS · Penn · PhD
Tried and failed
Forward genetic mutagenesis screening applied to identifying pathogen-resistant mutant lines. Outcome: did not generalise. Reason: Primary screen candidates failed to demonstrate statistically significant survival increases upon secondary validation assays
Characterisation of paired C-type lectins as receptors for Myzocytiopsis humicola and Haptoglossa zoospora recognition in Caenorhabditis elegans · Imperial · Doctorate
Tried and failed
High-throughput phenotyping screen using automated behavioral tracking applied to Metagenomic bacterial library bioactivity screening. Outcome: did not generalise. Reason: Variations in bacterial food lawn density produced non-reproducible behavioral artifacts across confirmation screens.
Integrating genomic methods with C. elegans phenotypic screening to identify bioactive natural products · Imperial · PhD
Tried and failed
linear model peak calling across sliding windows applied to cross-assay enhancer activity detection. Outcome: did not generalise. Reason: peak calls showed poor consistency across different high-throughput reporter assay protocols
Functional characterization of the human genome · Cornell · PhD
Tried and failed
arrayed CRISPR knockout genetic screening applied to identifying viral host dependency factors. Outcome: did not generalise. Reason: CRISPR screen hits failed to replicate results from a prior genome-wide siRNA screen
Utilization of High Throughput CRISPR Knockout Technologies to Identify Cellular Genes Involved in Human Papillomavirus Degradation of p53 · Harvard · Master's
Tried and failed
pooled CRISPR loss-of-function screening across independent knockdown conditions applied to synthetic lethality target identification in cancer. Outcome: did not generalise. Reason: Enrichment detected in only one shRNA condition arm failed to replicate across independent knockdown replicates.
SMARCB1 Maintains Lineage Fidelity in Clear Cell Renal Cell Carcinoma · Cambridge · PhD
Tried and failed
bioassay screening of microbial isolates applied to antimicrobial and toxicity hit identification. Outcome: did not generalise. Reason: initial phenotypic bioactivity hits failed to reproduce during subsequent follow-up testing
An exploration of chemical cues as mediators of marine predator-prey interactions · Georgia Tech · PhD
Tried and failed
yeast surface display kinase activity screening applied to drug-resistant kinase mutant identification. Outcome: did not generalise. Reason: enrichment in yeast display screen did not replicate in orthogonal biochemical and cellular validation assays
High-throughput screen reveals novel resistance mechanisms of Bruton’s Tyrosine Kinase to targeted therapeutics · UT Austin · PhD
Tried and failed
nanoliter-scale combinatorial library synthesis and screening applied to protein-protein interaction inhibitor discovery. Outcome: no signal. Reason: Screening crude reaction mixtures yielded no reproducible hits; initial signals were assay artifacts.
Generating macrocyclic inhibitors of protein-protein interactions · EPFL · PhD
Tried and failed
fixed cell microarray screening for protein interactions applied to validating viral glycoprotein host receptors. Outcome: no signal. Reason: Microarray binding hits failed to reproduce when assayed on live cells via flow cytometry.
Structural basis of antibody-mediated immunity against Crimean-Congo hemorrhagic fever virus glycoproteins · UT Austin · PhD
Tried and failed
phenotypic drug screening with morphological linear models applied to 3D organoid size perturbations. Outcome: did not generalise. Reason: Screening hits predicting size increases failed to replicate in 3D validation experiments
Uncovering Constraints On Organoid Morphologies · Penn · PhD
Rigid statistical thresholds and high computational complexity undermine screening pipelines
Premature filtering using strict p-value cutoffs or conservative multiple testing corrections discards genuine biological hits before downstream evaluation. High-fidelity quantum mechanical simulations and non-linear optimization frameworks become computationally intractable when scaled across large candidate libraries, forcing reliance on alternative workflows.
Tried and failed
sample splitting with hard p-value threshold screening applied to multiple testing outcome selection. Outcome: worse than baseline. Reason: premature filtering of true signals due to low sample size or weak treatment effect thresholds
MODERN ADVANCES IN ACCOUNTING FOR UNMEASURED CONFOUNDING VIA SENSITIVITY ANALYSIS · Penn · PhD
Lost to a baseline
Naive hypothesis screening performs worse than full-sample Bonferroni correction in small samples, fewer candidate hypotheses, or low Gamma_con due to premature filtering of signals.
MODERN ADVANCES IN ACCOUNTING FOR UNMEASURED CONFOUNDING VIA SENSITIVITY ANALYSIS · Penn · PhD
Considered and rejected
Considered and rejected: Rejected FWER-controlling multiple-testing corrections due to overly conservative true-positive penalties in high-throughput data.
Tried and failed
quality-based sample screening prior to testing applied to high-dimensional hypothesis testing without reference data. Outcome: no signal. Reason: Screening does not improve test performance without an external reference database.
High-dimensional statistical models and hypothesis tests with a focus on forensic and genetic applications · Iowa State · PhD
Considered and rejected
Considered and rejected: Restricting high-throughput virtual screening exclusively to closed-shell/singlet reaction coordinates was rejected for open-shell transition metal catalysis because it misclassifies ground-state spin surfaces and misses distortion-tuning effects.
Considered and rejected
Considered and rejected: Rejected TD-DFT excited-state geometry relaxation/adiabatic energy calculations for virtual screening due to prohibitive computational expense
High-throughput virtual screening of molecules for photon conversion · Imperial · Master's
Considered and rejected
Considered and rejected: Rejected superstructure MINLP targeting methods for large-scale screening due to poor polynomial/exponential constraint scaling
Nonsmooth Methods for Process Integration · MIT · PhD
Considered and rejected
Considered and rejected: Rejected direct high-fidelity DFT redox calculation for large-scale screening due to prohibitive computational costs on uncharacterized candidate libraries.
Atomistic Modeling and Machine Learning for the Rational Design of Organic Energy Storage Materials · Georgia Tech · PhD
Considered and rejected
Considered and rejected: Single-target docking virtual screening models rejected in favor of proteome-scale multitarget interaction signatures to account for polypharmacology and evade mutation-driven resistance.
Rigorous Evaluation of Comparability and Fidelity of Drug Repurposing Technologies · University at Buffalo · PhD
Off-target effects, non-specific cytotoxicity, and detection artifacts generate deceptive readouts
Candidate molecules frequently induce severe cellular toxicity or seed-mediated off-target impacts that confound primary phenotypic and viability readouts. Luminescent reagents and line blot platforms also suffer from assay interference, plate artifacts, and high false-positive rates that mask true biological mechanisms.
Considered and rejected
Considered and rejected: Discarded exclusive reliance on single-protein commercial line blots due to high false-positivity rates compared to tissue indirect immunofluorescence assay screening.
Characterising Autoimmune Neurologic Disorders: Biomarker Identification and Clinical Phenotyping · University College Dublin · PhD
Tried and failed
ATP-based luminescence assay for cell viability applied to drug-perturbed high-throughput cell screening. Reason: Severe plate artifacts and poor correlation with cell counts due to drug-altered ATP generation and morphology
A Framework for The Study of Compound Interactions in L1000 · Harvard · Master's
Considered and rejected
Considered and rejected: Rejected using pour-plating for colony PCR screening due to agar contamination inhibiting PCR and causing false positives.
Establishment of tools for genetic modification of the thermophilic methanogenic archaeon Methanothermobacter thermautotrophicus deltaH · Tübingen · PhD
Tried and failed
host-directed small molecule phenotypic screening applied to blood-stage antiparasitic drug discovery. Reason: host-targeted candidate compounds induced severe host cell toxicity and eryptosis, precluding translational utility
Integrative Antiparasitic & Erythrotoxic Characterization of a Red Blood Cell Host-Biased Compound Library · Harvard · PhD
Tried and failed
polymer-lipid hybrid nanoparticle formulation applied to in vivo mRNA delivery screening. Reason: formulations caused severe in vivo systemic toxicity requiring exclusion
Considered and rejected
Considered and rejected: Omitted 114 out of 1056 compounds (10.8%) from the survival screen after a pre-screen determined they were toxic to zebrafish embryos at the screening concentration.
Elucidating kynurenine pathway control of systemic bacterial infection in macrophages · Harvard · PhD
Simplified in vitro screening models fail to replicate complex in vivo physiological activity
Enrichment signals and enzyme performance observed in heterologous hosts or cell-free formats fail to translate to native in vivo cellular systems. Standard ex vivo culture environments and simplified reporter sensors lack the physiological context needed to produce consistent differential responses or maintain native structural phases.
Tried and failed
in vitro high-throughput motif enrichment screening applied to identifying in vivo protein-RNA binding motifs. Outcome: did not generalise. Reason: weakly enriched in vitro motifs failed to show corresponding binding peaks in in vivo crosslinking validation
Tried and failed
in vitro high-throughput secondary motif identification applied to in vivo RNA-protein binding enrichment. Outcome: did not generalise. Reason: secondary low-affinity binding motifs detected in vitro lacked robust enrichment in in vivo crosslinking-immunoprecipitation peaks
Considered and rejected
Considered and rejected: Decided against whole-cell screening in deep-well plates due to poor correlation with cell-free extract activity.
Biocatalytic synthesis of chiral amine building blocks · Nottingham · PhD
Considered and rejected
Considered and rejected: RNA-based and FRET-based biosensors were rejected for high-throughput screening due to narrow ligand classes, poor in vivo translation, and low signal-to-noise ratios.
Measuring chemicals with biology : engineering genetic biosensors for chemical analysis · UT Austin · PhD
Tried and failed
organoid drug screening across culture conditions applied to tumor cell state-specific drug sensitivity. Outcome: no signal. Reason: standard ex vivo culture conditions failed to produce consistent, discernable differential sensitivities across isogenic states
Cell states and therapeutic targets in pancreatic cancer · Harvard · PhD
Considered and rejected
Considered and rejected: Rejected thin film sputtering method for high-throughput combinatorial alloy screening because non-equilibrium synthesis produces phases inconsistent with bulk phase diagrams and hinders mass-production scaling.
Investigation on Electrodeposition of Metals and Alloys with Advanced Characterizations · Georgia Tech · PhD
Virtual screening candidates frequently suffer from poor solubility, high molecular weight, and cytotoxicity
In silico docking and pharmacophore linking often identify compounds that exhibit severe molecular liabilities including high lipophilicity and mammalian cytotoxicity. Downstream crystallographic soaking and cellular rescue tests fail because computational hits lack physical solubility or fail to stabilize target proteins in biological validation assays.
Tried and failed
structure-based virtual screening for pharmacological chaperones applied to destabilized mutant protein rescue. Outcome: no signal. Reason: most computationally docked candidates failed to rescue protein levels in cellular validation assays
Disease Mechanisms and Therapeutic Strategies in Munc18-1 Encephalopathies · Cornell · PhD
Tried and failed
pharmacophore linking virtual screening applied to enzyme active site ligand discovery. Outcome: no signal. Reason: Screened compounds lacked binding affinity in crystallographic soaking and thermal shift assays due to poor solubility.
Characterization and targeting of the 2-methylcitrate cycle in Pseudomonas aeruginosa · Cambridge · PhD
Tried and failed
similarity-based virtual screening of monomers applied to thermoset polymer synthesis. Outcome: unstable. Reason: Screened comonomer candidate failed to yield a stable crosslinked network during experimental synthesis
Designing Macromolecules using Machine Learning and Simulations · MIT · PhD
Flawed selection pressures and perturbation kinetics prevent effective candidate enrichment
Short exposure durations and low perturbation doses fail to provide sufficient selection pressure to separate active clones from inactive background populations. Selection platforms can also inadvertently favor intracellular retention over product secretion or suffer from signal dilution when unperturbed cells are co-encapsulated in overloaded screening droplets.
Tried and failed
high-throughput screening with primary immune cells applied to co-culture functional genomics screens. Outcome: unstable. Reason: post-expansion cellular impurity and high donor-to-donor variability compromised assay reproducibility
Loss of Bromodomain-Containing Protein 9 (BRD9) Reprograms Tumor Response to Natural Killer (NK) Cell-Mediated Killing · Cornell · PhD
Tried and failed
metabolic detoxifier coexpression in growth selection applied to enzyme directed evolution library screening. Outcome: no signal. Reason: alleviating intermediate toxicity sped growth but failed to alter evolutionary selection pressure away from low-activity variants
Engineering of human enzymes for amino acid depletion therapy in cancer · UT Austin · PhD
Tried and failed
short-duration low-dose perturbation in functional screening applied to CRISPR interference fitness screens. Outcome: no signal. Reason: Dose and exposure time were insufficient to drive differential guide RNA selection
Investigating the Role of RNA-Binding Proteins in Tumor Response to DNA Damage-Inducing Chemotherapy · MIT · PhD
Tried and failed
single-cell FACS screening for secreted small molecules applied to strain engineering for metabolite overproduction. Outcome: worse than baseline. Reason: biases selection toward intracellular retention rather than secretion, lowering total yield
Enhancing secreted production from yeast species with high throughput microdroplet screening methods · UT Austin · PhD
Tried and failed
cell-pooling in single-cell droplet screening applied to single-cell knockout perturbation screens. Outcome: worse than baseline. Reason: signal dilution across unperturbed cells within overloaded droplets reduced out-of-sample accuracy
Investigating human disease mechanisms through population genetics and experimental genetic screens · Harvard · PhD
Left open by the authors
Problems the authors named and did not get to.
Left open
Experimentally evaluate synthesized factorizable mAb libraries via high-throughput screening panning against targets. Blocker: Requires a wet lab and physical reagents for high-throughput screening of mAb libraries
Safe and Ethical Implementation of Intelligent Systems · MIT · PhD
Left open
Identify and validate targets for the category 1 and category 3 screening hits from the ΔugtP pathway-directed screen. Blocker: Requires wet-lab experimental biology and biochemistry facilities to validate molecular targets of small molecule hits
Discovery of highly selective inhibitors to probe the physiology of the bacterial cell envelope · Harvard · PhD
Left open
Construct in vivo RiPP combinatorial libraries for high-throughput activity-based screening against therapeutic protein-protein interaction targets. Blocker: Requires wet lab facilities, biological reagents, and experimental screening infrastructure
Design of Post-Translationally Modified Peptides by Combining Enzymes from Diverse Pathways · MIT · PhD
Left open
Perform high-throughput proteomics screening and train a deep learning model on surface electronics data to predict protein surface azidation. Blocker: Requires wet-lab high-throughput proteomics screening experiments to generate training data.
Azide-Containing Hypervalent Iodine Reagents for Biomolecules Functionalization · EPFL · PhD
Left open
Perform high-throughput knockout screens and apply machine learning models to identify proteins involved in cholesterol trafficking. Blocker: Requires wet-lab biological facilities to execute high-throughput knockout screens
EXPLORATION AND DEVELOPMENT OF XYLOPYRINDE FLUORESCENT TOOLS FOR SPATIOTEMPORAL IMAGING · Penn · PhD
Left open
Perform library-based screening across thousands of targets and train machine learning models to predict the optimal PE6 variant for given target sites. Blocker: Requires a wet lab to perform library-based high-throughput screening across thousands of target sites to generate training data.
Enhancing precision genome editing agents through directed evolution and protein engineering · Harvard · PhD
Left open
Perform large-scale screens to establish guide design and target site selection rules for RADARS sensors targeting lowly expressed transcripts. Blocker: Requires a wet lab to perform large-scale experimental screening and molecular assays in biological cells.
Base Editing–Enabled Technologies and Multiplex Genome Editing · Harvard · PhD
Left open
Apply neural networks and high-throughput screening to discover next-generation photothermal materials and simulate solar desalination architectures. Blocker: Lack of specific target properties, dataset specifications, or concrete simulation model details
Design Architectures and Analysis of Solar Driven Evaporative Technology for Desalination · University at Buffalo · PhD
Left open
Formally validate multi-targeted screening hits as bona fide pan-DUB inhibitors using biochemical assays. Blocker: Requires physical screening hit compounds and wet-lab biochemical validation assays
Discovery and Development of Novel Deubiquitinase Inhibitors via Parallel High-Throughput Screening · Harvard · PhD
Who has worked on this
Authors of the public theses cited on this page, most-cited first.
- Abhinandan Dalal · Penn · PhD · 2026
MODERN ADVANCES IN ACCOUNTING FOR UNMEASURED CONFOUNDING VIA SENSITIVITY ANALYSIS - Bridget E. Begg · MIT · PhD · 2022
Concentration-dependent Splicing through Suboptimal Motifs Enables Waves of Gene Regulation in Neuronal Development - Michael Gilligan · University College Dublin · PhD · 2026
Characterising Autoimmune Neurologic Disorders: Biomarker Identification and Clinical Phenotyping - Verena Volf · Harvard · PhD · 2025
Base Editing–Enabled Technologies and Multiplex Genome Editing - Josiah Rudge · Georgia Tech · PhD · 2025
Single-Cell Impedance Cytometry for the Control of Single-Cell Electroporation in a Flow-Through Device - Ka Chun Liu · Imperial · Doctorate · 2025
Characterisation of paired C-type lectins as receptors for Myzocytiopsis humicola and Haptoglossa zoospora recognition in Caenorhabditis elegans - Bonnie Evans · Imperial · PhD · 2025
Integrating genomic methods with C. elegans phenotypic screening to identify bioactive natural products - Hugo Sallet · EPFL · PhD · 2025
High-throughput isolation of anaerobic arsenic-transforming microorganisms - Amir Bunyat-zada · Queen's University · Doctorate · 2025
Investigation of Thermostable Enzymes Identified Through the Use of Sequence Similarity Networks - Emily Rose Goering · Harvard · PhD · 2024
Elucidating kynurenine pathway control of systemic bacterial infection in macrophages - Zheng Dai · MIT · PhD · 2024
Safe and Ethical Implementation of Intelligent Systems - Junke Zhang · Cornell · PhD · 2024
Functional characterization of the human genome
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