Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment

Widman AJ, Shah M, Frydendahl A, Halmos D, Khamnei CC, Øgaard N, Rajagopalan S, Arora A, Deshpande A, Hooper WF, Quentin J, Bass J, Zhang M, Langanay T, Andersen L,  Steinsnyder Z, Liao W, Rasmussen MH, Henriksen TV, Jensen SO, Nors J, Therkildsen C, Sotelo J, Brand R, Schiffman JS, Shah RH, Cheng AP, Maher C, Spain L, Krause K, Frederick DT, den Brok W, Lohrisch C, Shenkier T, Simmons C, Villa D, Mungall AJ, Moore R, Zaikova E, Cerda V, Kong E, Lai D, Malbari MS, Marton M, Manaa D, Winterkorn L, Gelmon K, Callahan MK, Boland G, Potenski C, Wolchok JD, Saxena A, Turajlic S, Imielinski M, Berger MF, Aparicio S, Altorki NK, Postow MA, Robine N, Andersen CL, Landau DA. Nature Medicine, 2024.

Preprint: Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts

Yuan DJ, Zinno J, Botella T, Dhingra D, Wang S, Hawkins A, Swett A, Sotelo J, Raviram R,  Hughes C, Potenski C, Yokoyama A, Kakiuchi N, Ogawa S, Landau DA. bioRxiv (2024) doi.org/10.1101/2024.05.22.595241

Defining ancestry, plasticity and transition dynamics of cellular phenotypes in somatic evolution.

Schiffman JS, D’Avino AR, Prieto T, Pang Y, Fan Y, Rajagopalan S, Potenski C, Hara T, Suvà ML, Gawad C, Landau DA. Nature Genetics, 2024.

Preprint: Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome

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. bioRxiv (2024)  doi.org/10.1101/2024.05.19.594376

Mapping genotypes to chromatin accessibility profiles in single cells

Izzo F, Myers RM, Ganesan S, Mekerishvili L, Kottapalli K, Prieto T, Eton EO, Botella T, Dunbar AJ, Bowman RL, Sotelo J, Potenski C, Mimitou EP, Stahl M, El Ghaity-Beckley S, Arandela J, Raviram R, Choi DC, Hoffman R, Chaligné R, Abdel-Wahab O, Smibert P, Ghobrial IM, Scandura JM, Marcellino B, Levine RL, Landau DA. Nature, 2024.

Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms

Dunbar AJ, Bowman RL, Park YC, O'Connor K, Izzo F, Myers RM, Karzai A, Zaroogian Z, Kim WJ, Fernandez-Maestre I, Waarts MR, Nazir A, Xiao W, Codilupi T, Brodsky M, Farina M, Cai L, Cai SF, Wang B, An W, Yang JL, Mowla S, Eisman SE, Hanasoge Somasundara AV, Glass JL, Mishra T, Houston R, Guzzardi E, Martinez Benitez AR, Viny AD, Koche RP, Meyer SC, Landau DA, Levine RL. Cancer Discovery, 2024.

Cancer Evolution: A Multifaceted Affair

Ciriello G, Magnani L, Aitken SJ, Akkari L, Behjati S, Hanahan D, Landau DA, Lopez-Bigas N, Lupiáñez DG, Marine JC, Martin-Villalba A, Natoli G, Obenauf AC, Oricchio E, Scaffidi P, Sottoriva A, Swarbrick A, Tonon G, Vanharanta S, Zuber J. Cancer Discovery, 2024.

SON is an essential m6A target for hematopoietic stem cell fate

Luo H, Cortés-López M, Tam CL, Xiao M, Wakiro I, Chu KL, Pierson A, Chan M, Chang K, Yang X, Fecko D, Han G, Ahn EE, Morris QD, Landau DA, Kharas MG. Cell Stem Cell, 2023.

Preprint: Breast cancer macrophage heterogeneity and self-renewal are determined by spatial location. 

Ben-Chetrit N, Nui X, Sotelo J, Swett AD, Rajasekhar VK, Jiao MS, Stewart CM, Bhardwaj P, Kottapalli S, Ganesan S, Loyher P-L, Potenski C, Hannuna A, Brown KA, Iyengar NM, Giri DD, Lowe SW, Healey JH, Geissmann F, Sagi I, Joyce JA, Landau DA. bioRxiv (2023)  doi:10.1101/2023.10.24.563749

Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gait, F, Landau DA. Cell Stem Cell, 2023.

See article in the Cornell Daily Sun.

Integration of whole transcriptome spatial profiling with protein markers

Ben-Chetrit N, Niu X, Swett AD, Sotelo J, Jiao MS, Stewart CM, Potenski C, Mielinis P, Roelli P, Stoeckius M, Landau DA. Nature Biotechnology, 2022.

Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution 

Stuart T, Hao S, Zhang B, Mekerishvili L, Landau DA, Maniatis S, Satija R, Raimondi I. Nature Biotechnology, 2022.

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Nam, AS, Dusaj, N, Izzo, F, Murali R, Myers RM, Mouhieddine T, Sotelo J, Benbarche S, Waarts M, Gaiti F, Tahri S, Levine R, Abdel-Wahab O, Godley LA, Chaligne R, Ghobrial I, Landau DA.  Nature Genetics, 2022.

See News & Views piece in Nature Genetics

See Research Briefing in Nature Genetics

A heritable, non-genetic road to cancer evolution

Prieto T and Landau DA. Nature, 2021.

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states.​

Chaligne R, Gaiti F, Silverbush D, Schiffman JS, Weisman HR, Kluegel L, Gritsch S, Deochand S, Gonzalez castro N, Richman AR, Klughammer J, Biancalani T, Muus C, Sheridan C, Alonso A, Izzo F, Park J, Rozenblatt-Rosen O, Regev A, Suva M and Landau DA. Nature Genetics, 2021.

See News & Views piece in Nature Genetics

Discovery of candidate DNA methylation cancer driver genes

Pan H, Renaud L, Chaligne R, Bloehdorn J, Tausch E, Mertens D,  Fink AM, Fischer K, Zhang C, Betel D, Gnirke A, Imielinski M, Moreaux J, Hallek M, Meissner A, Stilgenbauer A, Wu CJ, Elemento O and Landau DA. Cancer Discovery, 2021.

See commentary in epigenie

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

Nam AS, Chaligne R, Landau DA. Nature Review Genetics, 2021.

Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

Zviran A, Schulman RC, Shah M, Hill STK, Deochand S, Khamnei CC, Maloney D, Patel K, Liao W, Widman AJ, Wong P, Callahan MK, Ha G, Reed S, Rotem D, Frederick D, Sharova T,  Miao B, Kim T, Gydush G, Rhoades J, Huang KY, Omans ND, Bolan P, Lipsky A, Ang C, Malbari M, Spinelli CF, Kazancioglu S, Runnels AM, Fennessey S, Stolte C, Gaiti F,  Inghirami GG, Adalsteinsson V, Houck-Loomis B, Ishii J, Wolchok JD, Boland G, Robine N,  Altorki NK, Landau DA. Nature Medicine, 2020.

Highlight in Nature, selected as top 10 Clinical Research Achievement by the Clinical Research Forum

DNA methylation disruption reshapes the hematopoietic differentiation landscape

Izzo F, Lee SC, Poran A, Chaligne R, Gaiti F, Gross B, Murali R, Deochand S, Ang C, Jones PW,  Nam AS, Kim KT, Kothen-Hill S, Schulman RC, Ki M, Lhoumaud P, Skok JA, Viny AD, Levine RL, Kenigsberg E, Abdel-Wahab O,  Landau DA. Nature Genetics, 2020.

See blogpost in Nature Cancer Community

EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation

Lhoumaud P, Sethia G, Izzo F, Sakellaropoulos T, Snetkova V, Vidal S, Badri S, Cornwell M, Giammartino D, Kim KT, Apostolou E, Stadfeld M, Landau DA, Skok J. Genome Biology, 2019. 

Genotype-Fitness Maps of EGFR-Mutant Lung Adenocarcinoma Chart the Evolutionary Landscape of Resistance for Combination Therapy Optimization

Bolan PO, Zviran A, Brenan L, Schiffman JS, Duasj N, Goodale A,  Piccioni F, Johannessen CM, Landau DA. Cell Systems, 2019.

m6A RNA Methylation Maintains Hematopoietic Stem Cell Identity and Symmetric Commitment.

Cheng Y, Luo H, Izzo F, Pickering BF, Nguyen D, Myers R,  Schurer A, Gourkanti S, Bruning JC, Vu LP, Jaffrey S, Landau DA, Kharas MG. Cell Reports, 2019.

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

Nam AS, Kim KT, Chaligne R, Izzo F, Ang C, Taylor J, Myers RM, Abu-Zeinah G, Brand R, Omans ND, Alonso A, Sheridan C, Mariani M, Dai X, Harrington E, Pastore A, Cubillo-Ruiz JR, Tam W, Hoffman R, Rabadan R, Scandura JM, Abdel-Wahab O, Smibert P and Landau DA. Nature, 2019.

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

Gaiti F, Chaligne R, Gu H, Brand RM, Kothen-Hill S, Schulman RC, Grigorev K, Risso D, Kim KT, Huang KY, Pastore A, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Feldenfeld J, Bhavsar E, Aryee MJ, Allan JN, Furman RR, Gnirke A, Wu CJ, Meissner A and Landau DA. Nature, 2019.

Highlight in Nature Reviews Genetics

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL

Pastore A, Gaiti F, Lu SX, Brand RM, Kulm S, Chaligne R, Gu H, Huang KY, Stamenova EK, Béguelin W, Jiang Y, Schulman RC, Kim KT, Alonso A, Allan JN, Furman RR, Gnirke A, Wu CJ, Melnick AM, Meissner A, Bernstein BE, Abdel-Wahab O and Landau DA. Nature Communications, 2019.

Highlight in Nature Reviews Genetics

TARGET-seq Takes Aim at Cancer Evolution through Multi-omics Single-Cell Genotyping and Transcriptomics

Chaligne R, Nam AS, Landau DA. Molecular Cell, 2019.

Discovery of a periosteal stem cell mediating intramembranous bone formation

Debnath S, Yallowitz AR, McCormick J, Lalani S, Zhang T, Xu R, Li N, Liu Y, Yang YS, Eiseman M, Shim JH,  Hameed M, Healey JH, Bostrom MP, Landau DA, Greenblatt MB. Nature, 2018.

DeTiN: overcoming tumor-in-normal contamination

Taylor-Weiner A, Stewart C, Giordano T, Miller M, Rosenberg M, Macbeth A, Lennon N, Rheinbay E, Landau DA, Wu CJ, Getz G. Nature Methods, 2018.

The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy

Landau DA, Sun C, Rosebock D, Herman SEM, Fein J, Sivina M, Underbayev C, Liu D, Hoellenriegel J, Farooqui MZH, Zhang W, Cibulskis C, Zviran A, Neuberg DS, Livitz D, Bozic I, Leshchiner I, Getz G, Burger JA, Wiestner A & Wu CJ. Nature Communications, 2017.

Cancer Evolution: No Room for Negative Selection

Bakhoum SF, Landau DA. Cell, 2017.

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Sade-Feldman M, Jiao YJ, Chen JH, Rooney MS, Barzily-Rokni M, Eliane JP, Bjorgaard SL, Hammond MR, Vitzthum H, Blackmon SM, Frederick DT, Hazar-Rethinam M, Nadres BA,  Van Seventer EE, Shukla AS, Yizhak K, Ray JP, Rosebrock D, Livitz D, Adalsteinsson V, Getz G, Duncan LM, Li B, Corcoran RB, Lawrence DP, Rachamimov A, Boland GM, Landau DA, Flaherty KT, Sullivan RJ & Hacohen N. Nature Communications, 2017.

Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution

Bakhoum SF, Landau DA. Cold Spring Harb Perspect Med, 2017.

Clonal evolution in patients with chronic lymphocytic leukemia developing resistance to BTK inhibition

Burger J*, Landau DA*, Taylor-Weiner A*, Bozic I*, Zhang H*, Sarosiek K, Wang L, Stewart C, Fan J, Hoellenriegel J, Sivina M, Dubuc A, Fraser C, Han Y, Li S, Livak KJ, Zou L,  Wan Y, Konoplev S, Cibulskis C, Brown J, Abruzzo LV, Carter S, Keating M, Davids M,  Wierda WG, Cibulskis K, Zenz T, Werner L, Dal Cin P, Kharchenko P, Neuberg D, Kantarjian H, Lander ES, Gabriel S, O'Brien S, Letai A, Weitz D, Nowak M, Getz G, and Wu CJ. Nature Communications, 2016.

Genetic and Epigenetic Determinants of B-cell Lymphoma Evolution

Izzo F, Landau DA. Current Opinion in Hematology, 2016.

Frequent evolution of copy number alterations in CLL following first-line treatment with FC(R) is enriched with TP53 alterations: results from the CLL8 trial

Edelmann J, Tausch E, Landau DA, Robrecht S, Bahlo J, Fischer K, Fink AM, Bloehdorn J, Holzmann K, Böttcher S, Werner L, Kneba M, Gribben JG, Neuberg DS, Wu CJ, Hallek M, Döhner H, Stilgenbauer S. Leukemia, 2017.

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia

Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca D, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Cancer Cell, 2016.

Genomic complexity in Multiple Myeloma and its clinical implication

Manier S, Salem K, Park J, Landau DA, Getz G, Ghobrial I. Nature Reviews Clinical Oncology, 2016.

Mutations driving CLL and their evolution in progression and relapse

Landau DA*, Tausch E*, Taylor-Weiner AN*, Stewart C, Reiter JG, Bahlo J, Kluth S, Bozic I, Lawrence M, Bottcher S, Cibulskis K, Mertens D, Sougnez C, Rosenberg M, Hess JM, Carter SL, Edelmann J, Kless S, Fink A, Fischer K, Gabriel S, Lander ES, Nowak MA, Dohner H, Hallek M, Neuberg D, Getz G*, Stilgenbauer S*, Wu CJ*. Nature, 2015. 

Locally disordered methylation forms the basis of intra-tumor methylome variation in chronic lymphocytic leukemia

Landau DA*, Clement K*, Ziller MZ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Zhang W, Ghandi M, Garraway G, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G*, Meissner A*, Wu CJ*. Cancer Cell, 2014.

See comment in Cancer Cell. 

Clonal evolution in hematologic malignancies and therapeutic implications

Landau DA, Carter SL, Getz G, Wu CJ. Leukemia, 2014.

Proceedings from the National Cancer Institute¹s Second International Workshop on the Biology, Prevention, and Treatment of Relapse After Hematopoietic Stem Cell Transplantation: Biology of Relapse after Transplantation

Gress RA, Miller JS, Battiwalla M, Bishop MR, Giralt SA, Hardy NM, Kroger N, Wayne AS, Landau DA, Wu CJ. BBMT, 2013.

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Nature, 2013.

Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics

Landau DA, Wu CJ. Genome Medicine, 2013.

Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.

Landau DA*, Carter SL*, Stojanov P*, McKenna A, Stevenson K, Lawrence MS, Sougnez C, Stewart C, Sivachenko A, Wang L, Wan Y, Zhang W, Shukla SA, Vartanov A, Fernandes SM, Saksena G, Cibulskis K, Tesar B, Gabriel S, Hacohen N, Meyerson M, Lander ES, Neuberg D, Brown JR, Getz G*, Wu CJ*. Cell, 2013.

See comment in: Nature Genetics, Nature Reviews Cancer, Nature Medicine: Notable advances 2013.

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