Aaron Zweig, Zaikang Lin, Elham Azizi, David Knowles. Towards Identifiability of Interventional Stochastic Differential Equations. axriv 2026 Jul 10.

Aaron Zweig, Mingxuan Zhang, David A. Knowles, Elham Azizi. Learning Lineage-guided Geodesics with Finsler Geometry. axriv 2026 Jul 10.

Wen-Wei Liang, Simon Müller, Sydney Hart, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Akash Sookdeo, Olivia Choi, Christina Caragine, Alba Corman, Lu Lu, Olena Kolumba, Breanna Williams, Neville Sanjana. Essential lncRNAs in the human transcriptome. Cell 2026 Jul 8.

Omar Y. Ahmed, Neha Saravanan, Anne B. Rovsing, Danny Simpson, Archit Devarajan, Sophia Gunn, Tarjinder Singh, Tuuli Lappalainen, Neville E. Sanjana. Current challenges in GWAS integration and fine-mapping for variant interpretation. bioRxiv 2026 Jul 8.

Masashi Nomura, Ramya Raviram, Joshua S. Schiffman, Lillian Bussema, Vivian Lu, Noelle Wheeler, John J. Y. Lee, Yilin Fan, Mian Hua Zheng, Florian Ruiz, Husain Danish, Sorcha Kellett, Labeeba Nusrat, Ronan Chaligne, Jason T. Huse, W. K. Alfred Yung, Shota Tanaka, Nobuhito Saito, Sunit Das, Catherine Potenski, Dan A. Landau, Mario L. Suvà . Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation. Nat Genet 2026 Jun 22.

Wei-Yu Chi, Sang-Ho Yoon, Evrim Goksel, Levan Mekerishvili, Joe Pelt, Yiyun Lin, Tamara Prieto, John Zinno, Saravanan Ganesan, Catherine Potenski, Franco Izzo, Dan A. Landau, Ivan Raimondi. Single-cell mapping of regulatory DNA:Protein interactions. Cell 2026 Jun 11.

Boshi Fu, Robert Tan, Zhenkun Cao, Xiuzhen Bai, Dongsheng Bai, Jinghui Song, Chenxu Zhu. The molecular asynchrony of single cells. bioRxiv 2026 Jun 5.

Rachel Martini, Abdulfatai Tijjani, Kyriaki Founta, Daniel Cha, Alexandria Awai, Sebastian Maurice, Jason A. White, Christopher E. Mason, Isidro Cortes-Ciriano, Nicolas Robine, Onyinye Balogun, Nyasha Chambwe, Melissa B. Davis. African Pan Genome Contigs Expose Biologically Relevant Sequence Still Hidden from Human Reference Frameworks. bioRxiv 2026 May 6.

Maithê Rocha Monteiro de Barros, Katharina Bosch, Salima Soualhi, Shirin Issa Bhaloo, Thomas Chu, Tanya Hemrajani, Jin Cho, Kurtay Ozuner, Rui Fu, Heather Geiger, Nicolas Robine, Jade E.B. Carter, Silas Maniatis, Sandra Ryeom, Simon Tavaré, Karol Nowicki-Osuch. Single-nucleus multiome sequencing identifies candidate regulators of mouse gastric epithelial homeostasis. bioRxiv 2026 Apr 27.

Dennis J. Yuan, John Zinno, Theo Botella, Dalia Dhingra, Shu Wang, Allegra G. Hawkins, Ariel Swett, Jesus Sotelo, Ramya Raviram, Clayton Hughes, Catherine Potenski, Katharine D. Godfrey, Kara M. Ainsworth, Shuzhen Xu, Jianwen Que, Julian A. Abrams, Akira Yokoyama, Nobuyuki Kakiuchi, Seishi Ogawa, Dan A. Landau. Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts. Cancer Discovery 2026 Apr 1.

Valentina Grether, Zoe R. Goldstein, Jennifer M. Shelton, Timothy R. Chu, William F. Hooper, Heather Geiger, André Corvelo, Rachel Martini, Melissa B. Davis, Nicolas Robine, Will Liao. An explainable boosting machine model for identifying artifacts caused by formalin-fixed paraffin embedding. bioRxiv 2026 Mar 16.

Alexandre Pellan Cheng, Itai Rusinek, Aaron Sossin, Adam J. Widman, Eti Meiri, Gat Krieger, Ori Hirschberg, Doron Shem Tov, Shlomit Gilad, Ariel Jaimovich, Omer Barad, Sammantha Avaylon, Srinivas Rajagopalan, Catherine Potenski, Tamara Prieto, Dennis J. Yuan, Rob Furatero, Alexi Runnels, Benjamin M. Costa, Jonathan E. Shoag, Majd Al Assaad, Michael Sigouros, Jyothi Manohar, Abigail King, David Wilkes, John Otilano, Murtaza S. Malbari, Olivier Elemento, Juan Miguel Mosquera, Nasser K. Altorki, Ashish Saxena, Margaret K. Callahan, Nicolas Robine, Soren Germer, Gilad D. Evrony, Bishoy M. Faltas, Dan-Avi Landau. Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules. bioRxiv 2026 Mar 11.

Wells H. Burrell, Simon J. Mueller, Zharko Daniloski, P. Duffy Doyle Jr., Anne B. Rovsing, Christopher James, Max Drabkin, Chien-Yu Chou, Hei Yu Annika So, Lyla Katgara, Akash Sookdeo, Lu Lu, Georges-Ibrahim Cisse, Rachel E. Yan, Neville E. Sanjana. Rational design of synthetic proteins using a genome-scale CRISPR screen. bioRxiv 2026 Feb 20.

Alexandra Bradu, John D. Blair, Isabella N. Grabski, Isabella Mascio, Junsuk Lee, Cecilia McCormick, Rahul Satija. Genome-wide single-cell perturbation screens with VIPerturb-seq. bioRxiv 2026 Feb 14.

Benjamin K. Wesley, Frank Wos, Soren Germer, Jade E.B. Carter, Silas Maniatis, Khanh Dinh, James S. Roche, Timothy R. Chu, Nicolas Robine, Rebecca Fitzgerald, John Lizhe Zhuang, Simon Tavaŕe, Karol Nowicki-Osuch. Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling. bioRxiv 2025 Dec 22.

Dongsheng Bai, Zhenkun Cao, Chenxu Zhu. The ‘vulnerability code’: Is cell identity the architect of its own decay? Clin Transl Med 2025 Dec 15.

Simon Müller, Nathanael Andrews, Rachel E. Yan, Akash Sookdeo, Wells H. Burrell, Xiaoguang Dai, Priyesh Rughani, Zharko Daniloski, Sissel Juul, Neville E. Sanjana. Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq. bioRxiv 2025 Nov 25.

Maroš Pleška, Sanja Vickovic. From slices to deep dishes: spatial transcriptomics and translatomics of thick tissue blocks. Nat Methods 2025 Nov 24.

Alex Tokolyi, Saikat Banerjee, David A Knowles. Uncovering splicing-mediated disease associations in the UK Biobank and All of Us using a TWAS with Bayesian joint fine-mapping. medRxiv 2025 Nov 22.

Aaron Zweig, Mingxuan Zhang, Elham Azizi, David Knowles. Energy Guided Geometric Flow Matching. axriv 2025 Nov 17.

Brielin C. Brown, Alex Tokolyi, John A. Morris, Tuuli Lappalainen, David A. Knowles. Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells. Nat Commun 2025 Oct 31.

Aidan C. Daly, Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Sara Fernandez, Olena Kuksenko, Matthew Smith-Erb, Daniel Domovic, Nicholas Van Wittenberghe, Eugene Drokhlyansky, Gabriel K. Griffin, Hemali Phatnani, Richard Bonneau, Aviv Regev, Sanja Vickovic. Tissue and cellular spatiotemporal dynamics in colon aging. Nat Biotechnol 2025 Oct 22.

Tamara Prieto, Dennis J. Yuan, John Zinno, Clayton Hughes, Nicholas Midler, Sheng Kao, Jani Huuhtanen, Ramya Raviram, Foteini Fotopoulou, Neil Ruthen, Srinivas Rajagopalan, Joshua S. Schiffman, Andrew R. D’Avino, Sang-Ho Yoon, Jesus Sotelo, Nathaniel D. Omans, Noelle Wheeler, Alejandro Garces, Barun Pradhan, Alexandre Pellan Cheng, Nicolas Robine, Catherine Potenski, Katharine Godfrey, Nobuyuki Kakiuchi, Akira Yokoyama, Seishi Ogawa, Julian Abrams, Ivan Raimondi, Dan A. Landau. Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus. bioRxiv 2025 Oct 13.

Isabella N. Grabski, Junsuk Lee, John Blair, Carol Dalgarno, Isabella Mascio, Alexandra Bradu, David A. Knowles, Rahul Satija. Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting. bioRxiv 2025 Sep 20.

Rashid Al-Abri, Gamze Gürsoy. Estimating the size of long tandem repeat expansions from short reads with ScatTR. Genome Research 2025 Aug 21.

Pascal Belleau, Astrid Deschênes, David A. Tuveson, Alexander Krasnitz. Inference of Genetic Ancestry from Cancer-Derived Molecular Data with RAIDS. Cancer Bioinformatics 2025 Aug 9.

Megan D. Schertzer, Andrew Stirn, Keren Isaev, Laura Pereira, Anjali Das, Claire Harbison, Stella H. Park, Hans-Hermann Wessels, Neville E. Sanjana, David A. Knowles. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. Nat Commun 2025 Jul 29.

Megan D Schertzer, Stella H Park, Jiayu Su, Gloria M Sheynkman, David A Knowles. Perplexity as a Metric for Isoform Diversity in the Human Transcriptome. bioRxiv 2025 Jul 2.

Lukas Arnroth, Sanja Vickovic. INLAomics for Scalable and Interpretable Spatial Multiomic Data Integration. bioRxiv 2025 May 8.

J. Carlos Angel, Narjis El Amraoui, and Gamze Gursoy. pC-SAC: Method for High-Resolution 3D Genome Reconstruction from Low-Resolution Hi-C Data. Nucleic Acids Research 2025 Apr 14.

Alexandre Pellan Cheng, Adam J. Widman, Anushri Arora, Itai Rusinek, Aaron Sossin, Srinivas Rajagopalan, Nicholas Midler, William F. Hooper, Rebecca M. Murray, Daniel Halmos, Theophile Langanay, Hoyin Chu, Giorgio Inghirami, Catherine Potenski, Soren Germer, Melissa Marton, Dina Manaa, Adrienne Helland, Rob Furatero, Jaime McClintock, Lara Winterkorn, Zoe Steinsnyder, Yohyoh Wang, Asrar I. Alimohamed, Murtaza S. Malbari, Ashish Saxena, Margaret K. Callahan, Dennie T. Frederick, Lavinia Spain, Michael Sigouros, Jyothi Manohar, Abigail King, David Wilkes, John Otilano, Olivier Elemento, Juan Miguel Mosquera, Ariel Jaimovich, Doron Lipson, Samra Turajlic, Michael C. Zody, Nasser K. Altorki, Jedd D. Wolchok, Michael A. Postow, Nicolas Robine, Bishoy M. Faltas, Genevieve Boland, Dan A. Landau. Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling. Nat Methods 2025 Apr 11.

Dongsheng Bai, Zhenkun Cao, Nivedita Attada, Jinghui Song, Chenxu Zhu. Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability. Nat Methods 2025 Mar 25.

Andrew A. Stirn, David A. Knowles. The VampPrior Mixture Model. axriv 2025 Mar 11.

Christina M. Caragine, Victoria T. Le, Meer Mustafa, Bianca Jay Diaz, John A. Morris, Simon Müller, Alejandro Mendez-Mancilla, Evan Geller, Noa Liscovitch-Brauer, and Neville E. Sanjana. Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers. Nat Commun 2025 Feb 13.

Sydney K. Hart, Simon Müller, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Gediminas Drabavicius, Olivia Choi, Neville E. Sanjana. Precise RNA targeting with CRISPR–Cas13d. Nat Biotechnol 2025 Feb 11.

Zaikang Lin, Sei Chang, Aaron Zweig, Minseo Kang, Fabian J. Theis, Elham Azizi, David A. Knowles. Interpretable Neural ODEs for Gene Regulatory Network Discovery under Perturbations. axiriv 2025 Jan 5.

Sohrab Salehi, Achille Nazaret, Sohrab P. Shah, David M. Blei. Popular Priors for Matrix Factorization. Transactions on Machine Learning Research 2024 Dec 24.

Xinhe Xue, Zoran Z. Gajic, Christina M. Caragine, Mateusz Legut, Conor Walker, James Y.S. Kim, Xiao Wang, Rachel E. Yan, Hans-Hermann Wessels, Congyi Lu, Neil Bapodra, Gamze Gürsoy, Neville E. Sanjana. Paired CRISPR screens to map gene regulation in cis and trans. bioRxiv 2024 Nov 27.

Rachel E. Yan, Alba Corman, Lyla Katgara, Xiao Wang, Xinhe Xue, Zoran Z. Gajic, Richard Sam, Michael Farid, Samuel M. Friedman, Jungwook Choo, Ivan Raimondi, Shridar Ganesan, Eugene Katsevich, Jeffrey P. Greenfield, Nadia Dahmane and Neville E. Sanjana. Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling. Nat Biotechnol 2024 Nov 21.

Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Satyen Gohil, Shuqiang Li, Teddy Huang, David A. Knowles, Catherine J. Wu, Elham Azizi. A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. Genome Research 2024 Oct 11.

Ganesan S, Murray RM, Sotelo J, Eton EO, Takashima K, Botella T, Beattie K, Indart AC, Chraiki N, Croizier C, Izzo F, Potenski C, Marro S, Wu Z, Gao S, Young NS, Blair JD, Satija R, Terrier B, Heiblig M, Papapetrou EP, Sujobert P, Kosmider O, Beck DB, Landau DA. Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome. bioRxiv 2024 Oct. 1.

Joshua S. Schiffman, Andrew R. D’Avino, Tamara Prieto, Yakun Pang, Yilin Fan, Srinivas Rajagopalan, Catherine Potenski, Toshiro Hara, Mario L. Suvà, Charles Gawad, Dan A. Landau. Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution. Nat Genet 2024 Sep 24.

Adam J. Widman, Minita Shah, Amanda Frydendahl, Daniel Halmos, Cole C. Khamnei, Nadia Øgaard, Srinivas Rajagopalan, Anushri Arora, Aditya Deshpande, William F. Hooper, Jean Quentin, Jake Bass, Mingxuan Zhang, Theophile Langanay, Laura Andersen, Zoe Steinsnyder, Will Liao, Mads Heilskov Rasmussen, Tenna Vesterman Henriksen, Sarah Østrup Jensen, Jesper Nors, Christina Therkildsen, Jesus Sotelo, Ryan Brand, Joshua S. Schiffman, Ronak H. Shah, Alexandre Pellan Cheng, Colleen Maher, Lavinia Spain, Kate Krause, Dennie T. Frederick, Wendie den Brok, Caroline Lohrisch, Tamara Shenkier, Christine Simmons, Diego Villa, Andrew J. Mungall, Richard Moore, Elena Zaikova, Viviana Cerda, Esther Kong, Daniel Lai, Murtaza S. Malbari, Melissa Marton, Dina Manaa, Lara Winterkorn, Karen Gelmon, Margaret K. Callahan, Genevieve Boland, Catherine Potenski, Jedd D. Wolchok, Ashish Saxena, Samra Turajlic, Marcin Imielinski, Michael F. Berger, Sam Aparicio, Nasser K. Altorki, Michael A. Postow, Nicolas Robine, Claus Lindbjerg Andersen, Dan A. Landau. Ultrasensitive plasma-based monitoring of tumor burden using machine-learning- guided signal enrichment. Nat Med 2024 Jun 14.

Alvin Wei Tian Ng, Dylan Peter McClurg, Ben Wesley, Shahriar A. Zamani, Emily Black, Ahmad Miremadi, Olivier Giger, Rogier ten Hoopen, Ginny Devonshire, Aisling M. Redmond, Nicola Grehan, Sriganesh Jammula, Adrienn Blasko, Xiaodun Li, Samuel Aparicio, Simon Tavaré, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Karol Nowicki-Osuch & Rebecca C. Fitzgerald. Disentangling oncogenic amplicons in esophageal adenocarcinoma. Nat Commun 2024 May 14.

Franco Izzo, Robert M. Myers, Saravanan Ganesan, Levan Mekerishvili, Sanjay Kottapalli, Tamara Prieto, Elliot O. Eton, Theo Botella, Andrew J. Dunbar, Robert L. Bowman, Jesus Sotelo, Catherine Potenski, Eleni P. Mimitou, Maximilian Stahl, Sebastian El Ghaity-Beckley, JoAnn Arandela, Ramya Raviram, Daniel C. Choi, Ronald Hoffman, Ronan Chaligné, Omar Abdel-Wahab, Peter Smibert, Irene M. Ghobrial, Joseph M. Scandura, Bridget Marcellino, Ross L. Levine & Dan A. Landau. Mapping genotypes to chromatin accessibility profiles in single cells. Nature 2024 May 8.

Morris JA, Sun JS, Sanjana NE. Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis. Trends in Genetics 2024 Feb 11.

Andrew J. Dunbar, Robert L. Bowman, Young C. Park, Kavi O'Connor, Franco Izzo, Robert M. Myers, Abdul Karzai, Zachary Zaroogian, Won Jun Kim, Inés Fernández-Maestre, Michael R. Waarts, Abbas Nazir, Wenbin Xiao, Tamara Codilupi, Max Brodsky, Mirko Farina, Louise Cai, Sheng F. Cai, Benjamin Wang, Wenbin An, Julie L. Yang, Shoron Mowla, Shira E. Eisman, Amritha Varshini Hanasoge Somasundara, Jacob L. Glass, Tanmay Mishra, Remie Houston, Emily Guzzardi, Anthony R. Martinez Benitez, Aaron D. Viny, Richard P. Koche, Sara C. Meyer, Dan A. Landau, Ross L. Levine. Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms. Cancer Discov 2024 Jan 10.

Congyi Lu, Görkem Garipler, Chao Dai, Timothy Roush, Jose Salome-Correa, Alex Martin, Noa Liscovitch-Brauer, Esteban O. Mazzoni & Neville E. Sanjana. Essential transcription factors for induced neuron differentiation. Nat Commun 2023 Dec 15.

Hanzhi Luo, Mariela Cortés-López, Cyrus L. Tam, Michael Xiao, Isaac Wakiro, Karen L. Chu, Aspen Pierson, Mandy Chan, Kathryn Chang, Xuejing Yang, Daniel Fecko, Grace Han, Eun-Young Erin Ahn, Quaid D. Morris, Dan A. Landau, Michael G. Kharas. SON is an essential m6A target for hematopoietic stem cell fate. Cell Stem Cell 2023 Dec 7.

John A. Morris, Christina Caragine, Zharko Daniloski, Júlia Domingo, Timothy Barry, Lu Lu, Kyrie Davis, Marcello Ziosi, Dafni A. Glinos, Stephanie Hao, Eleni P. Mimitou, Peter Smibert, Kathryn Roeder , Eugene Katsevich, Tuuli Lappalainen, And Neville E. Sanjana. Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens. Science 2023 May 4.